Datasets:

clinicalnlplab

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PubmedSumm_train

like 0

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: a 38 - year - old man was injured in a car accident while driving , sustaining a left acetabular posterior wall fracture ( fig .1 ) . we explain to patient that it can be treated with non - weight bearing for 4 to 6 weeks , but he denied conservative treatment because he must return to his job . so , we decided to perform arthroscopic reduction and screw fixation after three days from trauma . under spinal anesthesia , the patient was positioned supine on a fracture table with the affected limb in traction and the opposite limb . we made three portal ( anterolateral , anterior , and posterolateral portals ) , the fracture fragment of the acetabular posterior wall was visualized after hematoma evacuation ( fig . the fracture fragment was reduced into the intact acetabular side using a flexible guide wire through posterolateral portal . after anatomical reduction in the fracture site was confirmed by arthroscopy , we used a 4.0 - mm - diameter cannulated screws to fixate the fragment under direct arthroscopic visualization ( fig .3 ) . postoperative radiographs and computed tomography ( ct ) was performed , the fragment was satisfactory reduced and compressed ( fig . , the patient discharged after care for postoperative wound and went back to normal life with crutch . he did not complain pain or discomfort after six months from the surgery , began heavy sports activities . a 41 - year - old man was injured in a car accident while driving , sustaining a right acetabular posterior wall fracture ( fig .5 c ) . skeletal traction was initially attempted , we decided to perform closed reduction and intramedullary nail fixation for femur shaft fracture . in same time , we decide to perform arthroscopic reduction and internal fixation with screws for acetabular fracture , because of early rehabilitation . under general anesthesia , femoral shaft fracture was treated by intramedullary nail system first . and , along the same way as case 1 , the fracture fragment of the acetabular posterior wall was visualized after hematoma evacuation ( fig . the fracture fragment was reduced into the intact acetabular side using a flexible guide wire . after anatomical reduction in the fracture site was confirmed by arthroscopy , we used a 4.0 - mm - diameter cannulated screws to fixate the fragment under direct arthroscopic visualization . after surgery , satisfactory reduction and compression were confirmed in postoperative radiographs and ct image ( fig . the patient was instructed to walk with partial weight - bearing with the aid of two crutches for four weeks after surgery . by three months post - operatively , he recovered full activities . after one year , femoral shaft fracture was united , we decided to removal intramedullary nail and to perform second look arthroscopy , we were able to confirm united acetabular fracture ( fig . the patient was treated in the supine position on a commercially available hip arthroscopy distraction . we used a conventional anterolateral viewing portal and an anterior and posterolateral working portal and examined the joint space with a 70 arthroscope . after a blood clot and the bloody joint fluid had been aspirated , we examined the joint space and found the fracture site . after capsulotomy was performed through the anterior to anterolateral site , joint debridement and loose body removal were perfomed . the fracture fragment was reduced into the intact acetabular side using a flexible guide wire . so , this technique is not available on severe comminuted fractures that are not compressed by screws . at this time , must keep three notices in mind . first , check the size and shape of obturator foramen in intraoperative c - arm image are not different from preoperative obturator foramen view ( fig .9 ) . if size and shape are not same , tilt table like taking obturator foramen viewin this way , it will help to find accurate insertion site of a flexible guide wire . second , we need a curved guide because of curved acetabular shape . if you use straight guide wire , guide wire can penetrate articular surface . for this reason , we decided to use curved guide of jugger knot ( 1.4 and 1.5 mm , curved reusable guide ; biomet inc . , it can help to access easily to posterior wall of acetabulum , to maintain reduction by gently compressive force while a flexible guide wire was fixated . so , you may make a choice among to produce long reamer , or to extend skin incision , in posterolateral portal , insert the shortest arthroscopic cannula deeply . after anatomical reduction in the fracture site was confirmed by arthroscopy , we used a 4.0 - mm - diameter cannulated screws to fixate the fragment under direct arthroscopic visualization . a 38 - year - old man was injured in a car accident while driving , sustaining a left acetabular posterior wall fracture ( fig .1 ) . we explain to patient that it can be treated with non - weight bearing for 4 to 6 weeks , but he denied conservative treatment because he must return to his job . so , we decided to perform arthroscopic reduction and screw fixation after three days from trauma . under spinal anesthesia , the patient was positioned supine on a fracture table with the affected limb in traction and the opposite limb . we made three portal ( anterolateral , anterior , and posterolateral portals ) , the fracture fragment of the acetabular posterior wall was visualized after hematoma evacuation ( fig . the fracture fragment was reduced into the intact acetabular side using a flexible guide wire through posterolateral portal . after anatomical reduction in the fracture site was confirmed by arthroscopy , we used a 4.0 - mm - diameter cannulated screws to fixate the fragment under direct arthroscopic visualization ( fig .3 ) . postoperative radiographs and computed tomography ( ct ) was performed , the fragment was satisfactory reduced and compressed ( fig . , the patient discharged after care for postoperative wound and went back to normal life with crutch . he did not complain pain or discomfort after six months from the surgery , began heavy sports activities . a 41 - year - old man was injured in a car accident while driving , sustaining a right acetabular posterior wall fracture ( fig . skeletal traction was initially attempted , we decided to perform closed reduction and intramedullary nail fixation for femur shaft fracture . in same time , we decide to perform arthroscopic reduction and internal fixation with screws for acetabular fracture , because of early rehabilitation . under general anesthesia , , along the same way as case 1 , the fracture fragment of the acetabular posterior wall was visualized after hematoma evacuation ( fig . the fracture fragment was reduced into the intact acetabular side using a flexible guide wire . after anatomical reduction in the fracture site was confirmed by arthroscopy , we used a 4.0 - mm - diameter cannulated screws to fixate the fragment under direct arthroscopic visualization . after surgery , satisfactory reduction and compression were confirmed in postoperative radiographs and ct image ( fig . the patient was instructed to walk with partial weight - bearing with the aid of two crutches for four weeks after surgery . by three months post - operatively , he recovered full activities . after one year , femoral shaft fracture was united , we decided to removal intramedullary nail and to perform second look arthroscopy , we were able to confirm united acetabular fracture ( fig . 8 ) . the patient was treated in the supine position on a commercially available hip arthroscopy distraction . we used a conventional anterolateral viewing portal and an anterior and posterolateral working portal and examined the joint space with a 70 arthroscope . after a blood clot and the bloody joint fluid had been aspirated , we examined the joint space and found the fracture site . after capsulotomy was performed through the anterior to anterolateral site , joint debridement and loose body removal were perfomed . the fracture fragment was reduced into the intact acetabular side using a flexible guide wire . so , this technique is not available on severe comminuted fractures that are not compressed by screws . at this time , must keep three notices in mind . first , check the size and shape of obturator foramen in intraoperative c - arm image are not different from preoperative obturator foramen view ( fig .9 ) . if size and shape are not same , tilt table like taking obturator foramen view . in this waysecond , we need a curved guide because of curved acetabular shape . if you use straight guide wire , guide wire can penetrate articular surface . for this reason , we decided to use curved guide of jugger knot ( 1.4 and 1.5 mm , curved reusable guide ; biomet inc . ,10 ) . it can help to access easily to posterior wall of acetabulum , to maintain reduction by gently compressive force while a flexible guide wire was fixated . so , you may make a choice among to produce long reamer , or to extend skin incision , in posterolateral portal , insert the shortest arthroscopic cannula deeply . after anatomical reduction in the fracture site was confirmed by arthroscopy , we used a 4.0 - mm - diameter cannulated screws to fixate the fragment under direct arthroscopic visualization . nonoperative treatment generally consists of bed rest and traction followed by bed - to - chair transfer . nonoperative treatment can be used in patients with simple , undisplaced , minimally displaced and those without free fragments in the joint . the prolonged bed rest necessary for conservative treatment , however , can lead to different complications in elderly patients , including potentially life - threatening bed sores , pneumonia , and urinary infections . elderly patients frequently have compromised strength , agility and balance , altered mental status , or neurological disorders . these patients are unlikely to comply with nonoperative management , and risk falling or involuntarily putting excessive weight on the injured limb , resulting in secondary fracture displacement4 ) . of course , surgery is not needed in simple acetabular fracture , but early internal fixation can help to avoid these complications in high - risk patients by simple and less - invasive surgery . arthroscopic techniques for fixation of intra - articular fractures offer the advantage of superior visualization and reduction of the articular surface , diagnosis and treatment5 ) . many author treated acetabular fracture with arthroscopic reduction and had a good result even in femoral head fracture and dislocation367 ) . the additional benefits of this method were joint lavage and debridement of the hip joint . joint debridement is known to be helpful in removing loose osteochondral fragments and might be helpful in reducing the risk of future osteoarthritis8 ) . furthermore , arthroscopic reduction techniques offer another benefit for intraarticular lesions . in case 2 , patient had a metallic artifact , it would be impossible to obtain magnetic resonance imaging . so , this technique is a useful method for diagnosing and treating intraarticular lesions after hip trauma . in case 2 , so we worried about destruction of interlocking screw and distraction of fracture site by traction during hip arthroscopy . there is no reference about these problems , but beutel et al. 9 ) reported that in the patients with prior lower - extremity arthroplasty , the use of traction during hip arthroscopy is safe in this population . we applied gentle traction , fracture site and interlocking screw were visualized with fluoroscopy to confirm that traction was free of complications . although hip arthroscopy is technically more demanding , it is less invasive and can be easy way to return to normal life . however , there are concerns in relation to fluid extravasation creating compartment syndrome - type complications in the acute setting10 ) . so , arthroscopic reduction technique will be good choice for acetabulum fracture , even in anterior or posterior column fracture , if only to overcome fluid extravasation . we observed closely intraoperative and postoperative monitoring of abdominal distention , core body temperature , and hemodynamic stability . high pump pressures may be risk factors , pump pressures were limited by 30 - 60 mmhg . and we tried to reduce operative time within 90 minutes . arthroscopic reduction and screw fixation technique is useful for reducing postoperative pain and achieving early return to activities for the patient . this technique will be tried in non - displaced and non - comminuted fractures , be the cornerstone to extend its indications with developments of techniques and equipments .\noutput:\n" }, { "from": "agent", "value": "acetabular fractures can be treated with variable method . in this study , acetabular posterior wall fracture was treated with arthroscopic reduction and fixation using cannulated screw . the patient recovered immediately and had a satisfactory outcome . in some case of acetabular fracture could be good indication with additional advantages of joint debridement and loose body removal . so , we report our case with technical note ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: obesity and associated comorbidities such as hypertension and diabetes result in significant changes in the cardiovascular system . currently , obesity is classified on the basis of body mass index ( bmi ) , and patients with bmi 30 kg / m are considered obese . a bmi 30 kg / m is associated with premature atherosclerosis , increased risk of myocardial infarction , heart failure , and decreased survival .1,2 although bmi is a useful predictor , other factors , including the adiposity distribution , degree of visceral or ectopic fat burden , and percentage of body fat , have an influence on clinical disease expression .3 recent studies have demonstrated that obesity is associated with cardiac dysfunction . in several echocardiographic studies , the presence of mild systolic and diastolic dysfunction in obese individuals has been reported .4,5 morbidity and mortality in patients with diastolic dysfunction are similar to values observed in patients with systolic heart failure .6 importantly , these alterations in cardiovascular structure and function have also been shown to be reversible with weight loss strategies such as bariatric surgery resulting in a decreased cardiovascular risk .710 we hypothesized that dysfunctional cardiac responses in obese subjects are reversible after substantial weight loss via a low - calorie diet program . thus , we studied the effect of weight reduction on left ventricular ( lv ) diastolic function as well as on cardiac structure using transthoracic echocardiography ( tte ) and tissue doppler imaging ( tdi ) . ethical approval for the study was obtained from the ethics committee of the state medical association ( approval number ff 112/2015 ) . all participants provided written informed consent . all patients were participants in the optifast - 52 diet program ( nestl health science , frankfurt , germany ) . the study design has previously been described in detail .11 briefly , the 52 - week program included a fasting phase of 12 weeks with food ingestion restricted to formula products with a high protein content ( total calorie intake approximately 800 kcal per day ) . a subsequent transitional phase and a final stabilization phase aimed to introduce the patients to a balanced diet . twenty - two patients withdrew from the study , discontinuing the diet plan prematurely for personal reasons ( figure 1 ) . inclusion criteria were as follows : 1 ) age 18 years and 65 years ; 2 ) bmi 30 kg / m ; 3 ) presence of secondary and concomitant conditions requiring treatment , such as hypertension , hypercholesterolemia , diabetes mellitus , and locomotor system disorders ; 4 ) medical certification of the necessity for participation in the program ; and 5 ) participants had to have made at least three previous unsuccessful attempts to reduce weight . exclusion criteria were cardiac arrhythmia , history of myocardial infarction , severe ( malign ) general illnesses , pregnancy and nursing , or a documented eating disorder . in addition , total body composition and fat content were measured using dual - energy x - ray absorptiometry ( dxa ) at week 1 and week 12 . echocardiography was performed using a commercially available ultrasound machine ( vivid 7 ; ge healthcare , little chalfont , uk ) and a 3.5 mhz ( 3s - rs ) transducer . patients were examined in a resting , left - lateral position and , for specific parts of the examination , in end - expiration by an experienced examiner . all images were obtained from standard parasternal and apical position using two - dimensional , m - mode , and doppler echocardiographic techniques . pulse doppler sample volume was placed at the mitral valve tips in the apical four - chamber view to record trans - mitral lv inflow velocity . diastolic lv filling normally consists of an early passive filling phase ( e ) and late active filling with atrial contraction phase ( a ) , where the e - wave is greater than the a - wave and the e / a ratio is positive . when the ventricle becomes noncompliant , the e - wave is reduced , and the a - wave increases resulting in a reversal of the e / a ratio . the pulsed - wave doppler volume was placed on the septal corner of the mitral annulus . care was taken to ensure that the ultrasound beam was parallel to the direction of the mitral annulus motion . filters and gains were set to exclude high - frequency signals and to obtain clear tissue signals . peak early ( e ) and late ( a ) diastolic mitral septum annular velocities were measured . indices derived from tdi , including e and a velocities of the mitral annulus , were reduced in heart failure patients .12 dxa is a common measurement of human body composition . it divides the body into total body mineral , fat - free soft mass and fat tissue mass . measurements were taken with the patient lying in the supine position on the scanning table . by means of the appropriate software , information on the body composition was obtained from the whole - body scan ( hologic densitometer qdr discovery wi ; hologic inc . , for the descriptive statistics , the arithmetic mean , minimum , and maximum were calculated . for the comparison of two measurements at different times , all patients were participants in the optifast - 52 diet program ( nestl health science , frankfurt , germany ) . the study design has previously been described in detail .11 briefly , the 52 - week program included a fasting phase of 12 weeks with food ingestion restricted to formula products with a high protein content ( total calorie intake approximately 800 kcal per day ) . a subsequent transitional phase and a final stabilization phase aimed to introduce the patients to a balanced diet . twenty - two patients withdrew from the study , discontinuing the diet plan prematurely for personal reasons ( figure 1 ) . inclusion criteria were as follows : 1 ) age 18 years and 65 years ; 2 ) bmi 30 kg / m ; 3 ) presence of secondary and concomitant conditions requiring treatment , such as hypertension , hypercholesterolemia , diabetes mellitus , and locomotor system disorders ; 4 ) medical certification of the necessity for participation in the program ; and 5 ) participants had to have made at least three previous unsuccessful attempts to reduce weight . exclusion criteria were cardiac arrhythmia , history of myocardial infarction , severe ( malign ) general illnesses , pregnancy and nursing , or a documented eating disorder . in addition , total body composition and fat content were measured using dual - energy x - ray absorptiometry ( dxa ) at week 1 and week 12 . echocardiography was performed using a commercially available ultrasound machine ( vivid 7 ; ge healthcare , little chalfont , uk ) and a 3.5 mhz ( 3s - rs ) transducer . patients were examined in a resting , left - lateral position and , for specific parts of the examination , in end - expiration by an experienced examiner . all images were obtained from standard parasternal and apical position using two - dimensional , m - mode , and doppler echocardiographic techniques . pulse doppler sample volume was placed at the mitral valve tips in the apical four - chamber view to record trans - mitral lv inflow velocity . diastolic lv filling normally consists of an early passive filling phase ( e ) and late active filling with atrial contraction phase ( a ) , where the e - wave is greater than the a - wave and the e / a ratio is positive . when the ventricle becomes noncompliant , the e - wave is reduced , and the a - wave increases resulting in a reversal of the e / a ratio . the pulsed - wave doppler volume was placed on the septal corner of the mitral annulus . care was taken to ensure that the ultrasound beam was parallel to the direction of the mitral annulus motion . filters and gains were set to exclude high - frequency signals and to obtain clear tissue signals . peak early ( e ) and late ( a ) diastolic mitral septum annular velocities were measured . indices derived from tdi , including e and a velocities of the mitral annulus , were reduced in heart failure patients .12 it divides the body into total body mineral , fat - free soft mass and fat tissue mass . measurements were taken with the patient lying in the supine position on the scanning table . by means of the appropriate software , information on the body composition was obtained from the whole - body scan ( hologic densitometer qdr discovery wi ; hologic inc . , the arithmetic mean , minimum , and maximum were calculated . for the comparison of two measurements at different times , after the 12 - week diet , body weight was significantly reduced from 124.727.3 kg to 102.524.4 kg ( p 0.01 ) . bmi was also significantly reduced , from 40.36.6 kg / m to 33.26.1 kg / m ( p 0.01 ) . sex and age did not have a significant impact on weight reduction . the number of patients with arterial hypertension , defined as blood pressure 140 mmhg systolic and 90 mmhg diastolic , decreased from 26 to nine . blood pressure medication was able to be reduced or even discontinued in some patients ( table 2 ) . total body fat mass decreased significantly by 19 % from 53.418.1 kg to 43.514.3 kg ( p 0.01 ) . changes in fat distribution resulting from the 12 - week fasting phase are reported in table 3 . grading of the image quality before weight loss was good in 10 , moderate in eight , and poor in 12 patients . after weight loss , image quality improved and was good in 12 , moderate in nine , and poor in nine patients . after weight loss , pulsed - wave doppler of the mitral inflow showed a significant reduction of the a - wave velocity , from 65.819.2 cm / s at week 1 to 57.016.8 cm / s ( p 0.01 ) at week 12 , and the e / a ratio increased significantly , from 1.20.4 to 1.40.5 ( p 0.01 ) ( figure 2 ) . tdi revealed a significant decrease of the a-wave , from 10.32.3 cm / s to 8.91.7 cm / s ( p 0.01 ) , and a significant increase of the e / a ratio , from 0.90.3 to 1.10.3 ( p 0.04 ) ( figure 3 ) . normal values for deceleration time and e-wave are age - dependent .13 in the present study , deceleration time before and after weight loss was prolonged , at 25060 ms and 24846 ms , respectively ( normal value in age group 4160 years : 18119 ms ) . the e-wave was decreased , at 8.42.2 cm / s and 9.11.8 cm / s , respectively ( normal value in age group 4160 years : 12.22.3 cm / s ) . the e / e ratio of 9.54.3 decreased slightly to 8.32.0 , but the difference was not significant . we found no changes in cardiac structures and dimensions occurring secondary to weight loss after 12 weeks ( table 4 ) . these findings suggest that diastolic lv function improved as a result of significant weight loss . after the 12 - week diet , body weight was significantly reduced from 124.727.3 kg to 102.524.4 kg ( p 0.01 ) . bmi was also significantly reduced , from 40.36.6 kg / m to 33.26.1 kg / m ( p 0.01 ) . sex and age did not have a significant impact on weight reduction . the number of patients with arterial hypertension , defined as blood pressure 140 mmhg systolic and 90 mmhg diastolic , decreased from 26 to nine . blood pressure medication was able to be reduced or even discontinued in some patients ( table 2 ) . total body fat mass decreased significantly by 19 % from 53.418.1 kg to 43.514.3 kg ( p 0.01 ) . changes in fat distribution resulting from the 12 - week fasting phase are reported in table 3 . grading of the image quality before weight loss was good in 10 , moderate in eight , and poor in 12 patients . after weight loss , image quality improved and was good in 12 , moderate in nine , and poor in nine patients . after weight loss , pulsed - wave doppler of the mitral inflow showed a significant reduction of the a - wave velocity , from 65.819.2 cm / s at week 1 to 57.016.8 cm / s ( p 0.01 ) at week 12 , and the e / a ratio increased significantly , from 1.20.4 to 1.40.5 ( p 0.01 ) ( figure 2 ) . tdi revealed a significant decrease of the a-wave , from 10.32.3 cm / s to 8.91.7 cm / s ( p 0.01 ) , and a significant increase of the e / a ratio , from 0.90.3 to 1.10.3 ( p 0.04 ) ( figure 3 ) . normal values for deceleration time and e-wave are age - dependent .13 in the present study , deceleration time before and after weight loss was prolonged , at 25060 ms and 24846 ms , respectively ( normal value in age group 4160 years : 18119 ms ) . the e-wave was decreased , at 8.42.2 cm / s and 9.11.8 cm / s , respectively ( normal value in age group 4160 years : 12.22.3 cm / s ) . the e / e ratio of 9.54.3 decreased slightly to 8.32.0 , but the difference was not significant . we found no changes in cardiac structures and dimensions occurring secondary to weight loss after 12 weeks ( table 4 ) . these findings suggest that diastolic lv function improved as a result of significant weight loss . obesity is associated with structural and functional abnormalities of the heart . in agreement with other studies , we observed doppler echocardiographic signs for diastolic dysfunction in patients with severe obesity . interestingly , we found evidence of improvement in diastolic function in patients who achieved successful weight reduction after following a 12 - week low - calorie diet . diastolic dysfunction can be measured by analyzing the trans - mitral flow pattern using conventional doppler echocardiography . diastolic dysfunction with impaired myocardial relaxation is characterized by a decreased early ( e - wave ) , but enhanced atrial lv filling ( a - wave ) . thus , atrial contraction basically compensates for the decrease in early passive filling and results in a lower e / a ratio .14 in a study by chakko et al , the e / a ratio was decreased in patients with obesity due to an increase in the a - wave velocity , while the e - wave velocity was constant .15 in our study , the trans - mitral e / a ratio increased significantly by 17.8 % after 12 weeks of the diet , mainly due to a significant decrease in the a - wave velocity . similar findings were reported after weight loss with a diet and an exercise program over 34 months .16,17 a study by valezi and machado showed a similar increase in the e / a ratio of 26.2 % after weight loss 1 year after gastric bypass surgery .18 the tdi index e / a correlates closely with lv stiffness .19 in our study , tdi revealed reduction of the e / a ratio at baseline with significant increase after 12 weeks due to a decrease of the a-wave . in contrast , yuksel et al reported no significant change of the a velocity after weight loss whereas the e velocity increased also resulting in a statistically significant increase of the e / a ratio .16 in line with our findings , fenk et al also found a significant improvement of the e / a ratio after a 1 - year weight reduction program comprising diet and lifestyle components .20 compared to normal values reported in the literature , in our study , the diastolic trans - mitral deceleration time was prolonged , and the e-wave velocity was decreased indicating impaired diastolic function at baseline and at the end of the fasting phase .13 a reduction of the e-wave velocity in people with obesity has also been reported in other studies .15,21 a parameter widely used to measure diastolic dysfunction is the e / e ratio , which can predict lv filling pressures . an e / e ratio ranging from 8 to 15 is considered a suggestive but nondiagnostic evidence of diastolic lv dysfunction .22 in our data , mean e / e values were only modestly elevated ( between 8 and 10 ) at baseline and reduced after weight loss , but the difference was not statistically significant . other studies showed a significant reduction of the e / e ratio after bariatric surgery or nonsurgical weight loss strategies .16,23 in moderate - to - severe cases of obesity , increased cardiac output due to the high metabolic activity of excessive fat may lead to left atrial and lv dilation , increased lv wall stress , and compensatory ( eccentric ) lv hypertrophy .24 in the present study , mean lv diameter and thickness of the lv wall were normal at week 1 and remained unchanged after 12 weeks on the diet . other studies reported a decrease in lv dilatation , hypertrophy , and mass after weight reduction interventions with longer follow - up periods .2527 lifestyle and diet therapies have demonstrated some cardiovascular benefits . data from a number of recent meta - analyses , however , suggest that bariatric operations result in greater improvement of cardiovascular risk parameters than other weight loss therapies .28 however , no randomized controlled trials currently exist comparing the effects of bariatric surgery with standardized nonsurgical treatments , specifically focusing on cardiovascular end points . in our study , the dxa measurement showed a significant reduction of total fat mass after weight loss , but overall , the regional body composition did not change . other authors have emphasized that remarkable individual differences exist in regional body fat accumulation and such variation in regional adiposity may determine the cardiovascular risk . therefore , bmi or total body fat and the magnitude of weight loss may not represent the most relevant therapeutic targets in the management of obesity .29 excess abdominal fat is known to be associated with increased risk of atherosclerosis and cardiovascular mortality .30,31 several intervention studies using a combination of physical activity and moderate caloric restriction have reported a preferential mobilization of visceral and ectopic fat beyond that which could be predicted due to weight loss .32,33 first , we were unable to demonstrate cardiac changes due to obesity such as lv hypertrophy and enlargement or atrial dilatation as described by other authors . however , patients in our group were relatively young ( mean age 45 years ) in terms of the risk of other causes of structural cardiac abnormalities . second , criteria measured by conventional doppler echocardiography in order to determine diastolic dysfunction are in part heart rate , preload , and afterload dependent and are subject to change within any given patient . third , echocardiographic measurements in people with obesity may be error - prone or imprecise . obesity is associated with diastolic dysfunction , which can be measured by conventional doppler and tissue doppler echocardiography . a 12 - week low - calorie diet with successful weight loss can reduce blood pressure and heart rate and partially normalize diastolic dysfunction .\noutput:\n" }, { "from": "agent", "value": "background / objectivesobesity is independently associated with left ventricular ( lv ) diastolic dysfunction and altered cardiac morphology . morbidity and mortality in patients with diastolic dysfunction are similar to values observed in patients with systolic heart failure . we hypothesized that dysfunctional cardiac responses in people with obesity are reversible after weight loss . thus , we studied the effect of dietary weight reduction on lv diastolic function as well as on cardiac structure using transthoracic echocardiography and tissue doppler imaging ( tdi ) . subjects / methodsthirty - two subjects with obesity underwent a 12 - week low - calorie fasting phase of a formula diet . echocardiographic tissue doppler indices of diastolic function and measurements of cardiac size were obtained prior to and after the fasting phase.resultsa 12 - week diet significantly reduced body mass index from 40.3 6.6 kg / m2 to 33.2 6.1 kg / m2 ( p < 0.01 ) . weight loss was associated with a significant reduction in blood pressure and heart rate . echocardiography revealed diastolic dysfunction in subjects with obesity , which was improved by dieting . after weight loss , trans - mitral doppler echocardiography showed a significant reduction in a - wave velocity , from 65.8 19.2 cm / s to 57.0 16.8 cm / s , and an increase in e / a ratio from 1.2 0.4 to 1.4 0.5 ( p < 0.01 ) . tdi displayed a significantly lower a-wave velocity ( 10.3 2.3 cm / s and 8.9 1.7 cm / s ; p < 0.01 ) . left atrial and lv dimensions were normal and remained unchanged after weight loss.conclusionobesity is associated with diastolic dysfunction . a 12 - week low - calorie diet with successful weight loss can reduce blood pressure and heart rate and partially normalize diastolic dysfunction ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: seventeen eyes underwent manual pccc ( group a ) and 33 eyes underwent vitrectorhexis ( group b ) . cases with fibrosed posterior capsule and traumatic cataracts with ruptured anterior or posterior capsule were excluded . eyes that had received a capsulotomy using other than a vitrectorhexis or manual capsulorhexis or without iol insertion were excluded from the study . the initial steps of surgery till cortical aspiration were same in both groups . while performing manual pccc , the anterior chamber was filled with methylcellulose , taking care that the surface of posterior capsule was more or less flat . after an initial nick in the center of the posterior capsule , high molecular weight ocular viscosurgical device like sodium hyaluronate 1 % was injected in the berger 's space between the posterior capsule and the anterior vitreous phase . this would prevent entanglement of the vitreous fibres in the capsular forceps if there was disturbance in anterior vitreous phase . the leading edge of the pccc would be gripped and re - gripped with an aim to achieve a pccc diameter of about 4 mm . after completing the pccc anterior vitrectomy was done with settings of 800 cuts per minute and aspiration of 150 mm hg . end point of vitrectomy would be when the posterior capsule remnant falls back with a smooth margin . after a good anterior vitrectomy , the iol would be inserted in the bag with the leading haptic being pushed in the bag , and the trailing haptic dialed into it . a single piece acrylic hydrophobic iol ( acrysof sn60at ) was used in most of the cases after manual pccc due to the ease of insertion and manipulation in the bag . in cases where vitrectorhexis was performed , multipiece acrylic hydrophobic iol ( sensar ar40e or acrysof mn60ac ) was implanted in all but 2 of the surgeries . in those two cases singleafter iol implantation , the main incision site was sutured using single 100 nylon suture . the iol was implanted before vitrectorhexis with presumption that the rhexis margin would be ragged , thereby risking posterior rhexis extension during iol implantation . then the vitrector was introduced behind the iol optic with port down and the irrigation cannula was kept in anterior chamber . the settings of vitrectomy were a cut rate of 800 per minute and aspiration of 100 - 150 mm hg . once the opening was made in the posterior capsule , the port was turned anterior so that the enlargement could be done under visualization . once an appropriate sized posterior capsulotomy was achieved , anterior vitrectomy was done by moving the vitrector in the center of the opening . then with the cutter off , the instrument was gently brought back in the anterior chamber and iol optic manipulated back in the bag . the instruments were withdrawn from the eye and side ports and main port hydrated till the eyeball was normotensive . this procedure of vitrectorhexis was preferred over pars plana vitrectomy with vitrectorhexis , as the surgeon was a trained anterior segment surgeon , not performing regular pars plana vitrectomy . moreover , this technique would avoid additional three incisions in the eye for similar result . as per the details in table 1 the average age of patients was 3.7 years ( range 3 months to 8 years ) . the average age of group a was 3.38 years and group b was 3.86 years . in group a , 10 cases were operated in right eye and 7 in left eye . in groupthere was extension of the pccc in 2 ( 11.76 % ) of the 17 cases ( 4 and 12 case ) in group a. and in 3 ( 9.09 % ) of the 33 ( 2 , 7 , and 16 ) cases in group b. of the three pccc extensions in group b , first two occurred with aspiration setting of 150 mm hg . after that aspiration was brought down to 100 mm hg and only 1 extension occurred in the remaining 26 cases . another significant aspect was that the surgeon had been practicing manual pccc for the last 7 years and the 33 cases of vitrectorhexis where his first 33 cases . the size of anterior rhexis was about 6 - 6.5 mm in both the methods ; it made insertion of the vitrector behind the lens optic easier . in two cases of vitrectorhexis , the anterior rhexis has to be enlarged after making in nick with vannas scissor , to facilitate easy insertion of vitrector behind the bag . in 17 of the manual pccc cases , three multipiece iol had to be placed in sulcus , two due to extension of the posterior rhexis and one due to large pccc . in the vitrectorhexis group , all iols were placed in the bag irrespective of the extension of the posterior rhexis . surgical time in the manual rhexis group averaged to 26 min , while that of the vitrectorhexis group was 17 min . in 2007 , wilson and colleagues , found out that vitrectorhexis is well suited for use in children less than 6 years of age due to their highly elastic anterior lens capsule . in 2009 , hazirolan and colleagues , concluded that both the techniques for anterior and posterior capsulorhexis are comparable in terms of corneal edema , anterior chamber reaction , and visual axis clarity . surprisingly , that was the only study published for vitrector being used for posterior capsulorhexis . andreo , trivedi and neuhann et al concluded that the manual ccc offered greater resistance to capsule tearing than the vitrectorhexis and also revealed a more smooth , regular edge . however , the vitrectorhexis displayed more than adequate resistance to unwanted anterior capsule tears when used for iol insertion through capsulotomy sizes currently used in clinical practice . in this studyit is evident that inspite of having good experience in manual pccc , the predictability and reproducibility of the procedure were average , where as in the vitrectorhexis group , in a small number of cases , both the factors increased significantly . initial two cases of posterior rhexis extension were probably due to higher aspiration setting of the cutter ( 150 mm hg ) , which improved once the aspiration was brought down to 100 mm hg . iol implantation in the bag is desirable in small children , which was achieved in 100 % of the cases in vitrectorhexis group , irrespective of the extension of the rhexis margin . also , the surgical time was significantly reduced from average 26 to 17 min . the obtained t value 9.68 is greater than p value ( 2.014 ) at 0.05 level . thus , there is a significant difference between the surgical time taken in group a and group b. in the three cases where the posterior vitrectorhexis extended , care was taken that the lens haptic was perpendicular to the area of extension . the wound was gently hydrated and the lens was found to be nicely centered in the postoperative visits . the limitations of the study were a small sample size , lack of randomization of the sample and unequal size of the samples . the group b was deliberately kept larger as the surgeon wanted to study the learning curve of a new procedure that he was trying . vitrectorhexis after iol implantation is an easy to learn alternative to manual pccc in pediatric cataract surgery . it is more predictable and reproducible , with a short learning curve and lesser surgical time .\noutput:\n" }, { "from": "agent", "value": "this study was done to compare the results of posterior continuous curvilinear capsulorhexis created using forceps with those created using vitrector in eyes suffering from congenital cataract . vitrectorhexis term was first used by wilson et al in 1999 . [ 1 ] fifty eyes with congenital and developmental cataract were included in this study . the posterior capsulorhexis was created using utrata forceps in 17 eyes or through a vitrector in 33 eyes . forceps capsulorhexis was performed before iol implantation , while vitrectorhexis was performed after iol implantation in the bag . the results of both the surgery were compared using the following criteria : incidence of extension of rhexis , ability to achieve posterior rhexis of appropriate size , ability to implant the iol in the bag , the surgical time , and learning curve . vitrectorhexis after iol implantation was an easy to learn alternative to manual posterior continuous curvilinear capsulorhexis in pediatric cataract surgery . it was more predictable and reproducible , with a short learning curve and lesser surgical time ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: haemophilus influenzae is a gram - negative , coccobacillary , facultatively anaerobic bacterium belonging to the pasteurellaceae family . haemophilus influenzae strains , which commonly reside as commensals within the human pharynx and may cause respiratory or invasive infections , are variable for the presence of a polysaccharide capsule ( 1 ) . isolates of h. influenzae can be subdivided into two major forms , encapsulated and non - encapsulated . encapsulated strains express one of six structurally and antigenically distinct capsular polysaccharides , referred to as serotypes a through f ( 2 ) . while the capsules are generally composed of a polysaccharide containing two hexose sugars as subunit carbohydrates , the type b polysaccharide capsule is the only capsular type which contains two pentose monosaccharides rather than the hexose sugars as subunit carbohydrates ( 3 , 4 ) . more importantly , haemophilus influenzae type b ( hib ) conjugate vaccines which consist of the capsular polysaccharide of hib , polyribosyl - ribitol - phosphate ( prp ) , conjugated to a carrier protein are safe and highly effective in preventing invasive hib disease ( 5 ) . in the pre - vaccination era , about 90 % of the invasive cases , such as meningitis and sepsis , were associated with type b strains ( 6 ) . since the introduction of the hib conjugate vaccine in europe and america in the 1990s , the incidence of invasive hib disease has dramatically decreased in most countries ( 5 ) . based on genetic analyses , two major phylogenetic divisions of encapsulated h. influenzae , divisions i and ii , have been already described ( 79 ) . division i consists of the great majority of serotype a and b strains and all of serotype c , d , and e strains . on the other hand , division ii includes all strains with serotype f and some with serotypes a and b ( 7 , 9 , 10 ) . it should be noted that most isolates of h. influenzae from clinical infections belong to clonal division i ( 7 , 11 ) . all encapsulated h. influenzae strains , whether division i or ii , contain common genes for the production of their respective polysaccharide capsules ( cap genes ) found within the cap locus that is divided into three functionally distinct regions ( 9 , 10 ) . region i contains four genes , bexa to bexd , which play a key role in capsular polysaccharide export . region ii , flanked by regions i and iii , includes the genes bcs1 to bcs4 involved in the biosynthesis of the serotype - specific polysaccharide in hib ( 9 , 12 , 13 ) . region iii comprises genes referred to as hcsa and hcsb , which share significant homology with genes in a number of other encapsulated pathogens , including neisseria meningitidis ( lipa and lipb ) , escherichia coli k1 and k5 ( kpsc and kpss ) , mannheimia ( pasteurella ) haemolytica ( wbra and wbrb ) , p. multocida a : 1 ( phya and phyb ) , p. multocida b : 2 ( wcba and wcbo ) , burkholderia mallei and burkholderia pseudomallei . collectively , the haemophilus influenzae type b hcsa and hcsb gene products have complementary functions involved in the transport of capsular polysaccharide across the outer membrane and are essential for virulence . surprisingly , the hcsa and hcsb gene products may be viable targets for antimicrobial development . in division i type b strains , these three loci are flanked by three 771 bp insertion elements , is1016 , whereas the capsulation locus in division ii type b strains is not flanked by is1016 . the presence of the insertion element is1016 increases the copy number of the cap locus . in fact , an increase in the copy number ( up to 6 copies per cell ) has been detected in clinical isolates ( 14 , 15 ) . the aim of this study was to determine the genotypes of hib strains isolated from clinical samples , and to explore strategies to improve vaccine efficacy . a total of 50 clinical isolates of h. influenzae originated from blood , nasopharynx , eye , csf and bronchoalveolar lavage fluid from hospitalized patients were used in the current study . all isolates were collected during the years 2010 to 2012 from milad , imam khomeini and mofid hospitals in tehran , iran . they were examined for morphological characters , biochemical reactions and the requirements for x and v factors ( 16 ) . the samples were cultured on chocolate agar plates , and shipped to the department of bacteriology , pasteur institute of iran , tehran . afterwards , the h. influenzae strains were cultured on chocolate agar containing 10 % sterile sheep blood , and then incubated overnight at 37c in a humidified 5 % co2 incubator . the serotypes of the strains were also determined by polymerase chain reaction ( pcr ) as described by falla et al . after 24 hours of incubation on chocolate agar , an inoculating loop of bacteria was gently scraped from each of the chocolate agar plates and individually suspended in 150 l of double - distilled water ( ddw ) . the mixture was briefly mixed on a vortex mixer , placed in a boiling water bath for 7 min and then centrifuged at 12,000 g for 5 min . a 50 - l aliquot of the supernatant was transferred to a sterile tube and stored at 20c until pcr testing ( 17 ) . h. influenzae type a ( atcc 9006 ) , h. influenzae type c ( atcc 9007 ) and nontypeable h. influenzae ( nthi ) ( atcc 49766 ) were used as positive control for genotype ii , positive control for genotype i and negative control , respectively in pcr assays . the control samples were obtained from the microbial collection of the department of bacteriology , pasteur institute of iran , tehran , iran . to confirm species identification , pcr amplification was performed to detect the omp6 gene from genomic dna ( 18 ) . additionally , the pcr amplification was further carried out using the primer pair specific to bexa genes ( hi - 1 and hi - 2 ) to distinguish encapsulated h. influenzae strains from nthi strains . for capsular typing of encapsulated h. influenzae , six primer sets specific for capsule types a through f were used for all strains , which recognize sequences in capsule - specific genes located within region 2 of the cap locus ( 17 ) . isolates containing both the bexa gene and one of the cap - specific genes are designated as the specific capsule type . in contrast , isolates lacking both bexa and any of the cap genes are considered as nthi , and those containing a cap gene but not bexa are designated as capsule - deficient h. influenzae type b or hib strains ( 19 ) ( all primers are listed in table 1 ) . the primer sets used in this study to determine the capsular genotypes , or phylogenetic relationships , of the hib strains , pcr amplification was performed with two sets of primers designed by leo schouls et al ( 18 ) . in thisregard , two oligonucleotide primer pairs hihcsa12667f - i and hihcsa13116r - i , and hihcsa12668f - ii and hihcsa13484r - ii were used to detect capsular genotypes i and ii of h. influenzae type b , respectively . the primers hihcsa12667f - i and hihcsa13116r - i permitted the amplification of a 450 - bp dna fragment , whereas another set of primers , hihcsa12668f - ii and hihcsa13484rii , allowed the amplification of an 817 - bp fragment ( table 1 ) . to discriminate between the two capsular genotypes , type i and type ii , two separate pcr amplifications were performed for each h. influenzae type b strain . the pcr reactions were carried out in a final volume of 25 l containing 2.5 l of 10 pcr buffer , 1.5 l of 25 mm mgcl2 , 0.2 l of 5 u / l taq dna polymerase ( genet bio , korea ) , 0.5 l of each 10 m primer , 0.5 l of 10 mm dntp ( genet bio company , korea ) , 17.3 l of double - distilled water and 2 l of genomic dna . pcr conditions were as follows : an initial denaturation at 95c for 15 min , 30 cycles of denaturation at 95c for 30s ; annealing at 52c for 1 min ; elongation at 72c for 1 min , and a final extension step at 72c for 7 min .6 l of pcr products mixed with 2 l of loading buffer were loaded into individual wells of 1 % agarose gel , and electrophoresis was performed at 100 v for 45 min . further , the sizes of the amplicons were measured by comparison with 3l of the 100 - bp dna ladder ( pars tous biotechnology company , iran ) . the resulting pcr products were stained with ethidium bromide for 20 min and visualized under uv illumination . to confirm whether the amplified bands corresponded to hcsa type i or hcsa type ii fragments , one of the pcr products from each gene fragment were randomly sequenced ( tag copenhagen , copenhagen , denmark ) . a total of 50 clinical isolates of h. influenzae originated from blood , nasopharynx , eye , csf and bronchoalveolar lavage fluid from hospitalized patients were used in the current study . all isolates were collected during the years 2010 to 2012 from milad , imam khomeini and mofid hospitals in tehran , iran . they were examined for morphological characters , biochemical reactions and the requirements for x and v factors ( 16 ) . the samples were cultured on chocolate agar plates , and shipped to the department of bacteriology , pasteur institute of iran , tehran . afterwards , the h. influenzae strains were cultured on chocolate agar containing 10 % sterile sheep blood , and then incubated overnight at 37c in a humidified 5 % co2 incubator . the serotypes of the strains were also determined by polymerase chain reaction ( pcr ) as described by falla et al . after 24 hours of incubation on chocolate agar , an inoculating loop of bacteria was gently scraped from each of the chocolate agar plates and individually suspended in 150 l of double - distilled water ( ddw ) . the mixture was briefly mixed on a vortex mixer , placed in a boiling water bath for 7 min and then centrifuged at 12,000 g for 5 min . a 50 - l aliquot of the supernatant was transferred to a sterile tube and stored at 20c until pcr testing ( 17 ) . h. influenzae type a ( atcc 9006 ) , h. influenzae type c ( atcc 9007 ) and nontypeable h. influenzae ( nthi ) ( atcc 49766 ) were used as positive control for genotype ii , positive control for genotype i and negative control , respectively in pcr assays . the control samples were obtained from the microbial collection of the department of bacteriology , pasteur institute of iran , tehran , iran . to confirm species identification , pcr amplification was performed to detect the omp6 gene from genomic dna ( 18 ) . additionally , the pcr amplification was further carried out using the primer pair specific to bexa genes ( hi - 1 and hi - 2 ) to distinguish encapsulated h. influenzae strains from nthi strains . for capsular typing of encapsulated h. influenzae , sixprimer sets specific for capsule types a through f were used for all strains , which recognize sequences in capsule - specific genes located within region 2 of the cap locus ( 17 ) . isolates containing both the bexa gene and one of the cap - specific genes are designated as the specific capsule type . in contrast , isolates lacking both bexa and any of the cap genes are considered as nthi , and those containing a cap gene but not bexa are designated as capsule - deficient h. influenzae type b or hib strains ( 19 ) ( all primers are listed in table 1 ) . to determine the capsular genotypes , or phylogenetic relationships , of the hib strains , pcr amplification was performed with two sets of primers designed by leo schouls et al ( 18 ) . in thisregard , two oligonucleotide primer pairs hihcsa12667f - i and hihcsa13116r - i , and hihcsa12668f - ii and hihcsa13484r - ii were used to detect capsular genotypes i and ii of h. influenzae type b , respectively . the primers hihcsa12667f - i and hihcsa13116r - i permitted the amplification of a 450 - bp dna fragment , whereas another set of primers , hihcsa12668f - ii and hihcsa13484rii , allowed the amplification of an 817 - bp fragment ( table 1 ) . to discriminate between the two capsular genotypes , type i and type ii , two separate pcr amplifications were performed for each h. influenzae type b strain . the pcr reactions were carried out in a final volume of 25 l containing 2.5 l of 10 pcr buffer , 1.5 l of 25 mm mgcl2 , 0.2 l of 5 u / l taq dna polymerase ( genet bio , korea ) , 0.5 l of each 10 m primer , 0.5 l of 10 mm dntp ( genet bio company , korea ) , 17.3 l of double - distilled water and 2 l of genomic dna . pcr conditions were as follows : an initial denaturation at 95c for 15 min , 30 cycles of denaturation at 95c for 30s ; annealing at 52c for 1 min ; elongation at 72c for 1 min , and a final extension step at 72c for 7 min .6 l of pcr products mixed with 2 l of loading buffer were loaded into individual wells of 1 % agarose gel , and electrophoresis was performed at 100 v for 45 min . further , the sizes of the amplicons were measured by comparison with 3l of the 100 - bp dna ladder ( pars tous biotechnology company , iran ) . the resulting pcr products were stained with ethidium bromide for 20 min and visualized under uv illumination . to confirm whether the amplified bands corresponded to hcsa type i or hcsa type ii fragments , one of the pcr products from each gene fragment were randomly sequenced ( tag copenhagen , copenhagen , denmark ) . a total of 50 isolates of h. influenzae , obtained from nasopharynx ( n = 39 ) , csf ( n = 2 ) , blood ( n = 3 ) eyes ( n = 5 ) and bronchoalveolar lavage fluid ( n = 1 ) , were examined ( table 2 ) . the strains were then further characterized by pcr amplification of the omp6 gene to confirm the h. influenzae species . moreover , the primer specific for the bexa gene was used to identify encapsulated strains of h. influenzae . in pcr assays ,4 ( 8 % ) of the 50 strains were able to amplify the bexa gene ( a fragment of 343 bp in length ) . capsular types ( a f ) were determined for each of the 4 strains using specific primer pairs ( table 1 ) . out of 4 isolates of h. influenzae , 4 were typed as b , successfully amplifying the bcs3 gene ( a fragment of 480 bp in length ) . four strains of h. influenzae type b examined had been isolated from blood ( 2 patients ) and csf ( 2 patients ) specimens . in addition , two samples had been obtained from the infants at the ages of 3 months ( blood ) and 1 year ( csf ) , but the age - specific data were not available about the two other samples ( table 2 ) . characteristics of isolates used in this study bronchoalveolar lavage as mentioned previously , h. influenzae type b strains are known to belong to both phylogenetic groups , clonal divisions i and ii . in the present study , to determine which clinically isolated hib strains belong to which phylogenetic groups , specific primers to the hcsa type i and hcsa type ii genes were used to identify genotype i and ii hib strains , respectively . however , it is found that among 4 h. influenzae strains examined two strains belong to type i ( fig . pcr amplification of the hcsa type i gene : the amplified dna fragment was 450 bp in length , lane 1 and 2 : clinical isolates of h. influenzae type b containing hcsa type i , lane 3 : clinical isolate of h. influenzae type b lacking hcsa type i , lane 4 : positive control containing h. influenzae type c ( atcc 9007 ) , lane 5 : negative control containing h. influenzae type a ( atcc 9006 ) , m : marker 100 - bp . pcr amplification of the hcsa type ii gene : the amplified dna fragment was 817 bp in length , lane 1 and 2 : clinical isolates of h. influenzae type b containing hcsa type ii , lane 3 and 4 : clinical isolates of h. influenzae type b lacking hcsa type ii , lane 5 : negative control containing h. influenzae type c ( atcc 9007 ) , lane 6 : positive control containing h. influenzae type a ( atcc 9006 ) , m : marker 100 - bp . two randomly selected pcr products of hcsa type i and hcsa type ii genes were sequenced , confirming the identity of h. influenzae type b. after sequencing of pcr products , the newly determined sequences were analyzed using the chromas software . in parallel , the nucleotide sequences of hcsa type i and hcsa type ii were compared and aligned with those deposited in the genbank database using the blast algorithm ( http://blast.ncbi.nlm.nih.gov/ ) . the nucleotide sequence data of hcsa type i and hcsa type ii reported in this paper have been submitted to genbank , and assigned the accession numbers kf263489 and kf263490 respectively . a total of 50 isolates of h. influenzae , obtained from nasopharynx ( n = 39 ) , csf ( n = 2 ) , blood ( n = 3 ) eyes ( n = 5 ) and bronchoalveolar lavage fluid ( n = 1 ) , were examined ( table 2 ) . the strains were then further characterized by pcr amplification of the omp6 gene to confirm the h. influenzae species . moreover , the primer specific for the bexa gene was used to identify encapsulated strains of h. influenzae . in pcr assays ,4 ( 8 % ) of the 50 strains were able to amplify the bexa gene ( a fragment of 343 bp in length ) . capsular types ( a f ) were determined for each of the 4 strains using specific primer pairs ( table 1 ) . out of 4 isolates of h. influenzae , 4 were typed as b , successfully amplifying the bcs3 gene ( a fragment of 480 bp in length ) . four strains of h. influenzae type b examined had been isolated from blood ( 2 patients ) and csf ( 2 patients ) specimens . in addition , two samples had been obtained from the infants at the ages of 3 months ( blood ) and 1 year ( csf ) , but the age - specific data were not available about the two other samples ( table 2 ) . as mentioned previously , h. influenzae type b strains are known to belong to both phylogenetic groups , clonal divisions i and ii . in the present study , to determine which clinically isolated hib strains belong to which phylogenetic groups , specific primers to the hcsa type i and hcsa type ii genes were used to identify genotype i and ii hib strains , respectively . however , it is found that among 4 h. influenzae strains examined two strains belong to type i ( fig . pcr amplification of the hcsa type i gene : the amplified dna fragment was 450 bp in length , lane 1 and 2 : clinical isolates of h. influenzae type b containing hcsa type i , lane 3 : clinical isolate of h. influenzae type b lacking hcsa type i , lane 4 : positive control containing h. influenzae type c ( atcc 9007 ) , lane 5 : negative control containing h. influenzae type a ( atcc 9006 ) , m : marker 100 - bp . pcr amplification of the hcsa type ii gene : the amplified dna fragment was 817 bp in length , lane 1 and 2 : clinical isolates of h. influenzae type b containing hcsa type ii , lane 3 and 4 : clinical isolates of h. influenzae type b lacking hcsa type ii , lane 5 : negative control containing h. influenzae type c ( atcc 9007 ) , lane 6 : positive control containing h. influenzae type a ( atcc 9006 ) , m : marker 100 - bp . two randomly selected pcr products of hcsa type i and hcsa type ii genes were sequenced , confirming the identity of h. influenzae type b. after sequencing of pcr products , the newly determined sequences were analyzed using the chromas software . in parallel , the nucleotide sequences of hcsa type i and hcsa type ii were compared and aligned with those deposited in the genbank database using the blast algorithm ( http://blast.ncbi.nlm.nih.gov/ ) . the nucleotide sequence data of hcsa type i and hcsa type ii reported in this paper have been submitted to genbank , and assigned the accession numbers kf263489 and kf263490 respectively . haemophilus influenzae is an environmentally sensitive and fastidious bacterium , making it difficult to isolate the pathogen from human clinical samples in microbiology laboratories . the diagnosis of bacterial meningitis is based on cerebrospinal fluid biochemical findings as well as clinical features . however , there is no specific treatment proven to be effective for bacterial meningitis , and patients are randomly assigned to the treatment regimens , often resulting in misdiagnosis and improper treatment . hence , the isolation of even a single colony of h. influenzae from suspected cases will be valuable . influenzae type b remains one of the most common causes of bacterial meningitis in iran as reported by the iranian ministry of health . in tehran ( 2005 ) , among 32 csf isolates of h. influenzae with positive cultrure , 5 strains ( 15.6 % ) were hib ( 20 ) . in another study in tehran the rate of transmission of h. influenzae type b in children aged 5was reported as 7.8 % in 2007 ( 21 ) and recently in 2014 , one study reported a 28 % prevalence of h. influenzae among children 6 years old ( 22 ) . therefore , vaccination against h. influenzae type b will be included in the national immunisation program schedule to help control disease spread . in this light , the identification of h. influenzae serotypes is essential for vaccination strategies , supplied through domestic production or imports . in thisregard , two sets of primers were used to amplify the hcsa gene that could successfully discriminate between two capsular genotypes , type i and ii . in 2008 , schools et al . revealed that the type i isolates carry more surface - bound capsular polysaccharides than type ii isolates . the lower capsule production in typeii strains may have resulted in a selective disadvantage , explaining the rapid disappearance of type ii strains from the dutch hib population . type ii strains were isolated from 04 year old , non - vaccinated patients , suggesting that only type ii strains are able to cause invasive disease in hosts who have not yet mounted an antibody response against the hib capsule ( 23 ) . moreover , their results revealed that hib strains isolated from patients in different geographic regions of the world show a considerably different distribution of the type i and ii strains ; in other words , the proportion of type ii strains among the strains from the various global regions varied from 47 % for strains from the african continent , 4 % for asian strains , 8 % for australia and 43 % for cuba . furthermore , none of the hib isolates from patients in other parts of europe ( finland & switzerland ) belonged to the type ii strains ( 23 ) . on the other hands , the highest proportion of type ii strains ( 73 % ) was found among hib strains isolated from patients in the united states ( 23 ) . in the present study , the phenotypic and genotypic characteristics of hib strains suggested that 2 hib strains belonged to type i , and 2 other hib strains were type ii . it is important to note that 50 % of hib strains examined in this study belonged to the type - ii category . however , this result is inconsistent with the results reported by other investigators carried out in many parts of the world , especially in asia , because type ii and type i hib strains are completely dominant in the united states and in other countries in which the study was conducted , respectively . more importantly , these results demonstrate that the distribution pattern of hib strains from iran is closely similar to those from african countries and cuba . to develop a broadly protective hib vaccine , it would be better to use the native strains of type i prp , because a recent study by schouls et al . strongly demonstrated that type i strains produce prp twice as much as type ii stains . notably , the purified prps should be used in the development of the hib vaccine ; this leads to reduce the time and cost for vaccine development and increase the extraction yield of prps . sukupolvi - petty et al . demonstrated that the products of the hcsa and hcsb genes facilitate transport of capsular polysaccharides across the outer membrane . inactivation of hcsa alone resulted in accumulation of polysaccharides in the periplasm and a partial decrease in surface - associated polysaccharides , whereas inactivation of hcsb alone , or both hcsa and hcsb resulted in accumulation of polysaccharides in the periplasm as well as complete loss of surface associated polysaccharides . it is therefore feasible that alterations in the hcsa and hcsb genes would influence the degree of capsular polysaccharide export to the surface of the hib cells , or the efficiency of retaining the exported polysaccharides on the surface ( 12 ) . meanwhile , after analyzing the complete sequences of the type i and type ii cap b loci , they showed that the variation between the capsular gene cluster sequences of type i and type ii strains was predominantly found in the hcsa and hcsb genes . the nucleotide sequences of bex , bcs1 and bcs2 of type i and type ii were identical ( 23 ) . however , in another study , kroll and moxon compared capsule production in strains containing one or two copies of the cap b locus and observed a gene dosage effect , with twice as much polysaccharide capsule associated with two copies of the cap b locus . interestingly , despite differences in capsule production , all strains were able to produce sustained bacteremia and meningitis in the infant rat model system , suggesting that only one copy of the cap b locus is sufficient for virulence in vivo . these findings suggest that a certain threshold level of polysaccharide capsule on the bacterial surface is required for intravascular survival and virulence of h. influenzae . however , despite the presence of less polysaccharide capsule on the surface of type ii hib strains , it seems that these strains can cause long - term meningitis in humans . in summary , there are two different types of haemophilus influenzae type b strains , which differ in coding sequences of genes involved in the synthesis of a polysaccharide capsule , especially the hcsa gene . this gene plays an important role in the transport of capsular polysaccharide to the cell surface . importantly , any change or mutation in the sequence of this gene can affect on the amount of capsular polysaccharide present on the hib surface as well as pathogenicity of h. influenzae in humans . in this study , it is found that the incidence and prevalence rates of both hib types are significantly high in iran . however , type i and type ii hib strains showed significant differences in their genotype ( sequence diversity in the capsule - producing genes ) and phenotype ( the amount of capsular antigens ) as well as pathogenicity . it seems that if type i hib strains are used to produce the hib vaccine , this vaccine can not only cover type ii hib strains but also induce a strong protection against h. influenzae type b infection , offering potential advantages such as economic benefits and high - quality products .\noutput:\n" }, { "from": "agent", "value": "background and objective : haemophilus influenzae type b ( hib ) is divided into two distinct genotypes , type i and type ii , based on the structure of capsular polysaccharides . the capsulation locus of haemophilus influenzae type b consists of three functionally distinct regions , designated regions 1 to 3 . region iii contains hcsa and hcsb genes ; however , notable sequence variation in this region can be used to recognize different hib genotypes . the purpose of this study was to investigate the prevalence and genotype of the hib strains isolated from patients with invasive disease in iran.materials and methods : in the present study , 8 pairs of primers were used for identification and serotyping of encapsulated haemophilus influenzae strains , as well as confirmation of species identification . additionally , in order to identify the capsular genotypes of haemophilus influenzae type b ( type i and ii ) , two additional primer pairs were used to amplify the hcsa gene.results : out of 50 isolates of h. influenzae , four were found to be type b. interestingly , among these 4 hib isolates , 2 strains belonged to the type - ii category.conclusion : our study shows that the prevalence of both hib types i and ii seems to be high in iran ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: in the hospital setting , patients often require continuous infusions of intravenous ( iv ) regular human insulin . our standard preparation of iv insulin for infusion consists of 100 units regular human insulin added to a sufficient quantity of 0.9 % sodium chloride to yield a total volume of 100 ml . due to the physical denaturation and chemical modification occurring during insulin admixture within a polyvinylchloride ( pvc ) bag , a concentration of 100 units / 100 ml is accepted to be stable for 24 hours .13 a recent pilot analysis demonstrates insulin stability for up to 7 days when stored under refrigeration .4 in regulations set forth by the united states pharmacopeia chapter 797 ( usp 797 ) guidelines , all extemporaneous admixtures must be manufactured in a certified clean room .5 this decreases the risk of contaminants and increases the uniformity of the products produced . the maximum beyond use date allowed in the absence of end - product sterility testing is 14 days ( 336 hours ) for a given product .5 the purpose of this study was to evaluate the extended stability of extemporaneously prepared regular human insulin 100 units in 0.9 % sodium chloride at a total volume of 100 ml under refrigeration to the maximum beyond - use - date usp 797 allows . from an unopened vial of regular human insulin , 1 ml was withdrawn and added to a sufficient quantity of 0.9 % sodium chloride for injection in a pvc bag to yield a total volume of 100 ml . a total of 8 ml of overfill was removed from each pvc bag prior to the addition of insulin to account for the additional volume ( 7 ml of overfill plus 1 ml of insulin ) . this process was repeated using new , unopened insulin vials to provide a total of three iv insulin admixtures . since usp allows 10 % error on all us food and drug administration - approved products , we used different vials for each admixture to account for variance . once completed , all admixtures were affixed with labels with instructions to store under refrigeration at 2c8c ( figure 1 ) . sampling from each of the three admixtures occurred at 0 , 6 , 24 , 48 , 72 , 144 , 168 , 192 , 216 , 240 , 312 , and 336 hours . all samples were analyzed by the process of high performance liquid chromatography , which was completed by dynalabs ( saint louis , mo , usa ) . each sample underwent immediate testing in duplicate .6 the average of all samples from all three admixtures at each time point yielded the overall mean concentration . a time point was considered stable if the mean concentration of the samples exceeded 90 % of the equilibrium concentration at 6 hours .710 from an unopened vial of regular human insulin , 1 ml was withdrawn and added to a sufficient quantity of 0.9 % sodium chloride for injection in a pvc bag to yield a total volume of 100 ml . a total of 8 ml of overfill was removed from each pvc bag prior to the addition of insulin to account for the additional volume ( 7 ml of overfill plus 1 ml of insulin ) . this process was repeated using new , unopened insulin vials to provide a total of three iv insulin admixtures . since usp allows 10 % error on all us food and drug administration - approved products , we used different vials for each admixture to account for variance . once completed , all admixtures were affixed with labels with instructions to store under refrigeration at 2c8c ( figure 1 ) . sampling from each of the three admixtures occurred at 0 , 6 , 24 , 48 , 72 , 144 , 168 , 192 , 216 , 240 , 312 , and 336 hours . all samples were analyzed by the process of high performance liquid chromatography , which was completed by dynalabs ( saint louis , mo , usa ) . the average of all samples from all three admixtures at each time point yielded the overall mean concentration . a time point was considered stable if the mean concentration of the samples exceeded 90 % of the equilibrium concentration at 6 hours .710 at 6 hours , the equilibrium concentration was determined to be 0.89 units / ml ( table 1 ) . based on our definition of stability , admixtures were stable at each time point if the concentration of insulin was greater than 0.8 units / ml . all time points retained at least 90 % of the equilibrium concentration with the exception of the 168 - hour sample ( 0.790.03 units / ml ) , but at the next time point , 192 hours , the mean concentration was 0.880.03 units / ml . at 336 hours , the concentration was 0.910.02 units / ml ( figure 2 ) . to our knowledge , this is the only analysis to suggest extemporaneously prepared regular human insulin 100 units added to a sufficient quantity of 0.9 % sodium chloride to yield a total volume of 100 ml is stable for up to 336 hours under refrigeration . in our recent pilot analysis , we showed stability for up to 168 hours .4 in response to the critique of that pilot analysis , the current analysis had three modifications : ( 1 ) high performance liquid chromatography was utilized for stability testing , ( 2 ) the samples were never frozen , and ( 3 ) each sample was tested in duplicate .4 the current analysis samples extended to 336 hours , which is the maximum beyond - use - dating allowed by usp 797 . all samples underwent high performance liquid chromatography testing , which is the standard method to ensure product stability . all samples underwent immediate testing in duplicate to provide inter - sample accuracy as well as ensure precision of the values obtained , and all samples were stored under refrigeration , not frozen . previously , all iv insulin admixtures at our institution had a 7 - day expiration date .4 based on these results , we have extended the expiration date of all extemporaneously prepared bags of regular human insulin to 14 days under refrigeration . the ability to prepare and stock common medications saves time by reducing the need to prepare patient - specific medications on demand , decreasing waste from products that readily expire , and allowing for ease of availability of emergent medications . this extended stability data provides not only improved operational management , but also increased availability of medication for immediate use and urgent patient care . based on these results , regular human insulin 100 units added to 0.9 % sodium chloride for injection in a pvc bag to yield a total volume of 100 ml is stable for up to 336 hours when stored at 2c8c ( 36f46f ) .\noutput:\n" }, { "from": "agent", "value": "backgroundregular human insulin 100 units added to a sufficient quantity of 0.9 % sodium chloride , to yield a total volume of 100 ml within a polyvinylchloride bag , is accepted to be stable for 24 hours due to physical denaturation and chemical modification . the objective of this study was to evaluate the extended stability of such extemporaneously prepared regular human insulin , stored under refrigeration , to the maximum beyond - use - date allowed by united states pharmacopeia chapter 797 . methodsat time 0 three admixtures of regular human insulin were prepared by withdrawing 1 ml of regular human insulin with a concentration of 100 units / ml and adding it to a sufficient quantity of 0.9 % sodium chloride for injection in a polyvinylchloride bag to yield a total volume of 100 ml . the three admixtures were stored under refrigeration ( 2c8c [ 36f46f ] ) , and one sample of each admixture was withdrawn and tested in duplicate at 0 , 6 , 24 , 48 , 72 , 144 , 168 , 192 , 216 , 240 , 312 , and 336 hours . utilizing high performance liquid chromatography , each sample underwent immediate testing . the time points were stable if the mean concentration of the samples exceeded 90 % of the equilibrium concentration at 6 hours.resultsthe equilibrium concentration was 0.89 units / ml . time points were stable if the mean concentration was at least 0.80 units / ml . all time points retained at least 90 % of the equilibrium concentration , with the exception of hour 168 ( 0.79 0.03 units / ml ) . at 192 hours the mean concentration was 0.88 0.03 units / ml . at 336 hours the mean concentration was 0.91 0.02 units / ml.conclusionbased on these results , regular human insulin 100 units added to 0.9 % sodium chloride for injection in a polyvinylchloride bag to yield a total volume of 100 ml is stable for up to 336 hours when stored at 2c8c ( 36f46f ) ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: innate immune cells include both myeloid cells , such as neutrophils and circulating monocytes which differentiate into macrophages within tissues , and innate lymphoid cells ( ilcs ) . these cells have important functions in host defense , including the phagocytosis of pathogens , the release of antimicrobial proteases , and the secretion of cytokines and chemokines that attract and activate other immune cells . cells of the immune system encounter a range of different oxygen tensions , with lower levels in tissues than in blood , which are further reduced during inflammation . to function under hypoxic conditions , innate immune cells increase anaerobic adenosine triphosphate ( atp ) generation by upregulating glycolytic enzymes and glucose transporters .15 hypoxia also , however , has a plethora of additional effects on innate immune responses . low oxygen levels act on vascular endothelial cells to upregulate adhesion molecules and chemokines , attracting circulating monocytes and neutrophils .611 neutrophils and monocytes upregulate adhesion molecules , such as intercellular adhesion molecule 1 ( icam - 1 ) and cd18 / cd11b as they reach hypoxic regions , promoting their arrest and transendothelial or transepithelial migration toward the site of the inflammation .2,12 hypoxia also acts to retain myeloid cells at the site of injury by upregulating factors that inhibit migration .2,3,5,1316 hypoxia tends to potentiate inflammatory functions and has a prosurvival effect in neutrophils , monocytes , and eosinophils .45,15,17,18 the ability of innate immune cells to survive and function effectively under hypoxic conditions is crucial for host defense in tissues . immune cell apoptosis is , however , an important means of resolving inflammation ; prolonged survival and activation of myeloid cells under hypoxic conditions is likely to play a major role in chronic inflammation , contributing to diseases such as chronic obstructive pulmonary disease , asthma , and rheumatoid arthritis ( ra ) .1923 lack of oxygen and a reduction in oxidative phosphorylation , in favor of less efficient glycolysis , might be expected to reduce atp availability and impair cellular functions ; however , there is evidence that cardiac hypoxia inducible factor ( hif ) expression can increase atp availability despite inducing a glycolytic switch .24 this may also be the case in myeloid cells , with hypoxia enhancing many effector functions . glycolysis is critical for atp production by myeloid and endothelial cells even under normoxic conditions .25,26 inhibition of glycolysis reduces endothelial cell proliferation and impairs formation of lamellipodia , causing a defect in directional migration and vessel formation .26 potentially , therefore , glycolysis ( and its upregulation by hypoxia ) may promote migration of myeloid cells . hypoxia upregulates fc and complement receptors on macrophages and neutrophils , thereby enhancing phagocytosis .2732 it also promotes the release of antimicrobial mediators , such as - defensin by macrophages and elastase by neutrophils .3335 monocytes and macrophages upregulate proinflammatory cytokines , such as tumor necrosis factor ( tnf ) , interferon ( ifn ) , interleukin ( il ) - 1 , and several neutrophil chemoattractants in hypoxia , while downregulating chemokines associated with adaptive immunity .2,3,31,3638 macrophages precultured in hypoxia are more effective at inducing ovalbumin - specific cd8 t - cell responses , due to the upregulation of major histocompatibility complex ( mhc ) class i and costimulatory molecules , but they also produce arginase , which inhibits cd4 t - cell responses .31,39,40 many effects of hypoxia are mediated by release of hifs from suppression by the oxygen - dependent hydroxylases . these comprise prolyl hydroxylases ( phds ) , which target them for degradation , and the asparaginyl hydroxylase , factor inhibiting hif , which inhibits hif transcriptional activity . many immune - related genes are regulated by hif , either directly , via binding of hif to a hif - responsive element ( hre ) in the promoter region , or indirectly , via hif - mediated induction of other signaling molecules and transcription factors , such as nf - b . effects of hif signaling in innate immune cells in response to hypoxia and other stimuli are summarized in figure 1 . other mechanisms also play a role in hypoxia signaling ; for example , mitochondrial - derived reactive oxygen species stabilize hifs and also activate other transcription factors , such as activator protein - 1 ( ap - 1 ) , which induces cxc - chemokine ligand ( cxcl ) 8 in hypoxic macrophages .37,38,4143 hypoxia also reduces activity of the jumonji histone demethylases , resulting in increased methylation of histone h3 residues in the promoter regions of chemokine ligand 2 ( ccl2 ) , chemokine ( c - c motif ) receptor 1 ( ccr1 ) , and ccr5 , repressing their transcription by macrophages .44 though research so far has focused predominantly on myeloid cells , there is also some evidence of the effects of hypoxia on other aspects of innate immunity . for instance , mice with chronic hypoxia - induced pulmonary hypertension have reduced natural killer ( nk ) cell numbers , cytotoxicity , and ifn production .45 hypoxic nk cells downregulate the key cytotoxic mediators granzyme b and perforin and lose their ability to upregulate activating receptors in response to cytokines , thereby reducing their ability to recognize and kill infected or abnormal cells .46,47 in addition to the effects of hypoxia on innate immune responses to infection , hypoxia can also have direct effects on the pathogens themselves , such as modulating the expression of virulence factors ,48 but this is beyond the scope of this review . neutrophils are inherently adapted to low oxygen tensions , with few mitochondria and reliance on glycolysis for much of their energy demand even under normoxic conditions .25 while hif1a messenger rna ( mrna ) is present in freshly isolated neutrophils , hif - 1 protein is not expressed in unstimulated cells . it can be induced by hypoxic culture , the iron chelator desferrioxamine , or the competitive hydroxylase inhibitor dimethyloxalylglycine ( dmog ) .5,49 when cultured in hypoxia , neutrophils upregulate the glycolytic hif - 1 target genes glyceraldehyde 3 - phosphate dehydrogenase ( gapdh ) and phosphoglycerate kinase ( pgk ) , which may serve to provide additional glycolytic capacity for enhanced effector function .5 hypoxic induction of pgk expression is reduced but not abolished in hif1a neutrophils , suggesting that both hif - 1 and other factors ( possibly hif - 2 ) are involved in its induction . atp levels are substantially reduced in hif1a neutrophils and macrophages , reflecting the central role of hif - 1 in regulation of metabolic activity .50 expression of the cathelicidin - related antimicrobial peptide ( cramp ) is upregulated by hypoxia and in neutrophils lacking the von hippel - lindau protein ( vhl ) ( involved in the proteasomal degradation of hif ) , whereas hif1a neutrophils express lower levels of cramp and display reduced ability to breakdown artificial substrates for antimicrobial proteases .51 hif - 1 also promotes extracellular bacterial killing by inducing formation of neutrophil extracellular traps .52 furthermore , neutrophil hypoxic survival is mediated by hif , with hif1a neutrophils displaying a failure of hypoxia - mediated apoptosis suppression .5,49 in wild - type ( wt ) , but not hif1a neutrophils , hypoxia reverses the decline in nuclear factor ( nf ) - b and ib kinase ( ikk ) - levels observed during culture and maintains dna - binding activity of nf - b family members , which is essential for hypoxic survival . hif - 2 is also expressed by human and murine neutrophils and its expression is upregulated by hydroxylase inhibitors , bacteria or lipopolysaccharide ( lps ) .53 the respiratory burst , phagocytosis , chemotaxis , lps - induced receptor upregulation and constitutive apoptosis are unaffected by deletion of hif2a . however , hif2a inflammatory neutrophils derived from bronchoalveolar lavage ( bal ) fluid of lps - challenged mice express lower levels of the antioxidant enzyme catalase than wt neutrophils and display increased apoptosis in response to nitrosative stress . while circulating leukocytes that are attracted to a site of inflammation initially upregulate hif in response to hypoxia , cells exposed to chronic hypoxia may respond differently due to the activation of negative feedback mechanisms . for instance , hypoxia is reported to induce hif - mediated transcription of phd2 , phd3 , and vhl all negative regulators of hif expression .5457 although phds are generally understood to act upstream of hifs , promoting their degradation , in neutrophils phd3 may function downstream of hif . phd3 is upregulated during hypoxia ; this is significantly impaired in hif1a neutrophils .54 phd3 does not , however , appear to regulate hif - 1 expression , since the hypoxic upregulation of hif target genes is not affected by the deletion of phd3 . phd3 neutrophils fail to upregulate the anti - apoptotic protein b - cell lymphoma extra - large ( bcl - xl ) , as occurs in hypoxic wt neutrophils , and exhibit reduced survival during hypoxia . hypoxic macrophages upregulate hif - 1 and hif - 2 proteins in a phosphatidylinositide 3 - kinase ( pi3k ) / protein kinase b ( akt ) - dependent manner .3,58 in contrast to neutrophils , macrophages from phd3 mice exhibit higher expression of hif - 1 and nf - b than wt , produce more cytokines , and exhibit enhanced chemotactic and phagocytic responses , suggesting that in macrophages , phd3 is acting upstream of hif - 1 to degrade hif - 1 protein .59 as in neutrophils , hif - 1 has an important role in regulating macrophage metabolism under hypoxic conditions . hif1a - null or small interfering rna ( sirna ) - treated macrophages have reduced basal expression and hypoxic induction of the glycolytic genes pgk and glut1 , whereas the loss of vhl mimics hypoxic induction .3,50 release of lactate , a marker of glycolytic activity and inflammatory activation , is significantly lower in hif1a macrophages and significantly higher in vhl cells .50 hif signaling is , in turn , influenced by metabolism . for instance , the tricarboxylic acid cycle intermediate , succinate , which is generated during aerobic respiration and upregulated in response to lps stimulation , inhibits phd activity , resulting in hif - 1 stabilization and il1b transcription in macrophages .60 hypoxic upregulation of the adhesion molecule icam - 1 is inhibited by sirna targeted against hif1a or hif2a , while induction of - integrins in monocytes is abrogated by mutation of the hre in the promoter of cd18 , the subunit common to the four known 2 integrin heterodimers .3,12 hif1a macrophages display defects in chemotaxis , in their ability to penetrate the extracellular matrix , and in homotypic adhesion , a process of self - aggregation that amplifies the tissue recruitment of leukocytes .50,61 hif2a macrophages have reduced expression of the chemokine receptors macrophage colony - stimulating factor receptor and cxc chemokine receptor 4 and the adhesion molecule fibronectin - 1 , resulting in a 50 % reduction in migratory and invasive capacities .62 phagocytosis and intracellular bactericidal activity are also regulated by hifs . hypoxia induces p38 in macrophages and p38 inhibition reverses hif - 1 stabilization and enhancement of phagocytosis .32 hif - 1 induces thrombospondin - 1 and the scavenger receptor cd36 , which are involved in the recognition of apoptotic cells , therefore hypoxia enhances phagocytosis of both bacteria and apoptotic neutrophils effects that are abrogated in the presence of hif1a - directed sirna .32,63 killing of intracellular bacteria , such as streptococci and pseudomonas aeruginosa , is enhanced by iron chelators and in vhl macrophages , but impaired in hif1a macrophages , possibly due to hif -1-mediated inducible nitric oxide synthase ( inos ) induction .50,51,61 hypoxia also induces the expression of ifn , which promotes phagocytosis of opsonized cells by upregulating surface levels of the cd11b / cd18 complement receptor and the cd16 / cd32 fc receptor .31 the ifng promoter contains a functional hre and hypoxic induction of ifn and the associated upregulation of opsonic receptors are abolished by mutation of this site or by deletion or sirna knockdown of hif1a . macrophages secrete less tnf - in response to lps or group a streptococci ( gas ) and fail to upregulate tnf - when lps is administered under hypoxic conditions .50,51 hif - 1 also binds to a highly polymorphic region of the promoter encoding solute carrier family member 1 ( slc11a1 ) , a phagocyte - specific solute carrier that induces expression of cytokines , chemokines , and mhc class ii molecules .64 allelic variation affects the ability of hif - 1 to induce slc11a1 expression and has been associated with susceptibility to various inflammatory diseases . hif - 2 also appears to be involved in cytokine and chemokine transcription , since the hypoxic upregulation of il1b , il12 , cxcl2 and cxcl6 is impaired in hif2a macrophages while hypoxic expression of cxcl8 is reduced in macrophages treated with sirna targeting hif2a .3,62 in contrast to its many proinflammatory effects , hypoxia also promotes repair mechanisms and macrophage suppression of t - cells in a hif - dependent manner .65 induction of the proangiogenic factors vascular endothelial growth factor ( vegf ) and adrenomedullin is significantly reduced by sirna targeting either hif1a or hif2a .3 hif1a macrophages have reduced basal expression and hypoxic induction of vegf , whereas deletion of vhl induces vegf expression under normoxic conditions .3,50 plasminogen activator inhibitor - 1 ( pai - 1 ) , which promotes thrombosis by inhibiting plasminogen - mediated fibrinolysis , is also activated by hif - 1.66 hifs can also act as negative regulators of gene expression . for instance , hif - 1 ( but not hif - 2 ) binds to the hre of the histone deacetylase - 2 ( hdac2 ) promoter independently of the hif - 1 subunit and reduces transcription by inhibiting binding of polymerase ii .67 hypoxia , therefore , reduces mrna and protein levels of hdac2 , a suppressor of nf - b - mediated transcription , resulting in increased inflammation and corticosteroid resistance . mrna has a shorter half - life than hif2a mrna and , following intrapulmonary lps challenge , hif1a is rapidly upregulated but declines after 24 hours , whereas hif2a expression is delayed but maintained during the resolution phase .53,68 hif - 1 and hif - 2 bind to the same promoter sequence and the expression of many hypoxia - inducible genes , including vegf , il1b , cxcl8 , glut1 , adm ( adrenomedullin ) , cxcr4 , and stat4 , can be impaired by sirna targeted against either hif1a or hif2a .3 some target genes , however , such as the adenosine a2a receptor ( adora2a ) , are only regulated by one hif and not the other , which is thought to be due to interaction with different coactivators .3,69 although both hif - 1 and hif - 2 are induced by hypoxia , other stimuli such as cytokines also influence their relative expression levels . for instance , takeda et al68 reported that hif1 - mrna and protein are induced during m1 polarization of macrophages ( by ifn or lps ) , whereas hif - 2 is induced during m2 polarization ( by il - 4 or il - 13 ) and is decreased by stimulation with lps or ifn . hif1a macrophages infiltrating tumor spheroids in vitro develop a more m2 - like profile than their wt counterparts , with lower cytotoxicity and decreased production of tnf , inos , and il - 6 , suggesting that hif - 1 is important for proinflammatory responses .70 the work of imtiyaz et al62 indicates that hif - 2 also has important proinflammatory functions , since myeloid - specific hif2a deletion inhibits in vitro secretion of the proinflammatory cytokines il - 1 , il - 6 , and il - 12 in response to a combined ifn / lps stimulus and reduces serum levels of il - 1 , il - 12 , tnf , and ifn following in vivo lps stimulation . the relative levels of hif - 1 and hif - 2 may play an important role in the regulation of nitric oxide ( no ) metabolism by controlling the levels of both inos and arginase ( which competes with inos for the l - arginine substrate required for no production ) . macrophages exhibit normal hypoxic induction of inos ( nos2 ) ; however , both the basal expression and hypoxic induction of arginase 1 ( arg1 ) are attenuated .62,68 conversely , hif1a deletion dramatically reduces hypoxic inos induction , but it has a smaller effect on arginase expression .68 similar data was obtained by kobayashi et al ,71 who observed an increased inos response to lps in cells with a vhl / hif2a double knockout ( in which hif - 1 is stabilized while hif - 2 is absent ) , while vhl / hif1a double knockout mice produced more arginase in response to il - 13 stimulation . in accordance with the altered ratio of inos / arginase , mice lacking myeloid hif - 1 exhibited reduced no production 6 hours after lps treatment , while those lacking hif - 2 exhibited increased no after 24 hours .68 takeda et al68 also demonstrated decreased and increased levels of in vitro no production in ifn - stimulated hif1a and hif2a thioglycollate - elicited peritoneal macrophages respectively . however , when imtiyaz et al62 stimulated bone marrow - derived marcophages ( bmdms ) with a combination of ifn and lps , no difference was observed in no production between hif2a and wt . the discrepancy between the studies could be explained by many factors , including the sourcing of macrophages from different tissues , use of a different stimulus , and the apparent dependency of the hif2a phenotype on the level of l - arginine availability .68 mice with a myeloid - specific phd2 haplodeficiency exhibit greater infiltration of mannose receptor , c type 1 ( mrc1 ) proangiogenic / wound - healing m2 - like macrophages , which release arteriogenic factors , following femoral artery ligation .72 in comparison to wt macrophages , phd2 macrophages isolated at baseline express higher levels of m2 genes , such as arginase ( arg1 ) , cxcr4 , platelet - derived growth factor beta ( pdgfb ) , neuropilin 1 ( nrp1 ) , found in inflammatory zone 1 ( fizz1 ) and transforming growth factor beta ( tgfb ) and lower levels of the m1 genes il12 , however , following ligation , wt macrophages from the ischemic musculature upregulate m2 genes , reaching a similar level to that of phd2 macrophages , indicating hypoxia is releasing m2 genes from phd2 - mediated suppression . given the previous work indicating an association of hif - 1 with inos and hif - 2 with arginase expression ,68 this data might suggest that phd2 expression favors an m1 response by preferentially targeting hif - 2 for destruction . while hypoxia regulates hifs largely at the posttranslational level , other factors such as cytokines and infectious agents regulate its transcription , resulting in a synergistic effect when the stimuli are combined .7378 the hif1a promoter contains a binding site for nfb transcription factors .77 both the basal transcription and induction of hif1a ( but not hif2a ) in response to stimuli , such as bacteria , tnf - , or hypoxia , are dependent on nf - b. reduced hif - 1 accumulation and target gene induction are observed in ikk - deficient macrophages and in cells treated with sirna targeting members of the nf - b family .76,77 hypoxia , in turn , augments nf - b expression , phosphorylation , and target gene induction in macrophages and neutrophils .3,5,7981 hypoxic induction of mrna encoding ikk , ikk , and p65 is impaired in hif1a cells , while the increase in p65 phosphorylation is ablated by the deletion of hif2a .3,5 ikk and nf - b1 are also directly regulated by phds and factor inhibiting hif respectively .80,82 hif - 1 also binds to the tlr4 promoter and upregulates tlr4 expression , thereby increasing the macrophage response to lps .83 in addition to activating nf - b - mediated transcription , lps induces a mammalian target of rapamycin - dependent increase in hif - 1 translation in neutrophils and promotes succinate - mediated hif - 1 stabilization in macrophages , as detailed previously .52,60 oxygen consumption by bacteria , resulting in cellular hypoxia , has also been proposed as a mechanism for the upregulation of hifs during infection .84,85 immune responses in vivo may be influenced by hif expression in both leukocytes and tissue cells , and systemic modulation of hif expression affects both . myeloid - specific knockouts of hif signaling components , however , have permitted elucidation of the innate immune cell - intrinsic effects of hypoxia and hifs . administration of the hydroxylase inhibitor dmog delays inflammatory resolution following tail transection in zebrafish larvae , due to decreased apoptosis of neutrophils and their retention at the site of injury during the resolution phase .86 the effects of dmog were abrogated by injection with a hif1b morpholino or by expression of a dominant negative form of the zebrafish hif1a homolog , hif1ab . in contrast , mutation of the proline hydroxylation site targeted by phds , to create a systemic or myeloid - specific dominant active form of hif - 1b , recapitulated the effect of dmog , indicating a role for hif - 1 in delayed inflammation resolution . in a murine trauma / hemorrhagic shock model , in which gut ischemia / reperfusion injury leads to both local and systemic inflammatory responses , hif1a mice were protected against mucosal gut injury and subsequent lung damage , with reduced expression of tnf , il - 1 , and inos in the intestinal mucosa and il - 1 in the lung , further demonstrating a role for hif - 1 in promoting inflammation in vivo .87 cramer et al50 crossed mice with floxed hif1a , vegf , or vhl with lysm - cre mice to generate strains with myeloid - specific deletions of each of these genes , providing important insights into the role of hif in innate immunity . in a model of acute skin inflammation , leukocyte infiltration , myeloperoxidase production , and edemawere reduced in lysm - cre / hif1a mice and increased in lysm - cre / vhl mice . likewise , in an arthritis model , edema , synovial infiltration , pannus formation , and cartilage destruction were profoundly reduced in lysm - cre / hif1a mice . hif - 1 and vegf upregulation correlates with increased disease severity in a mouse model of allergic rhinitis and inhibition of hif using 2 - methoxyestradiol attenuates vegf production and inflammation .88 in an ova - induced murine model of allergic airway disease , inflammatory cell infiltration , levels of th2 cytokines ( il - 4 , il - 5 , and il - 13 ) , vascular permeability , fibrosis , goblet cell mucus production , ova - specific ige , and airway hyperresponsivenesswere all significantly reduced by inhibition of hif - 1 or vegf .8991 similar effects were observed in mice with a systemic hif1b deletion or a myeloid - specific hif1a deletion .89,92,93 activation of hifs may be important for antibacterial responses . following subcutaneous gas administration , lysm - cre / hif1a mice lost more weight than wt mice and developed larger necrotic skin lesions , containing approximately 1,660-fold more bacteria .51 bacterial counts in blood and spleen were also increased , indicating greater systemic spread of infection . similarly , hif -1-mediated induction of cramp in keratinocytes protects against induction of skin lesions by gas and approximately three - fold more bacteria were found in the skin ulcers of mice with a keratinocyte - specific deletion of hif1a .94 conversely , treatment with the hif agonist mimosine reduced lesion size by 50 % following subcutaneous s. aureus challenge .95 however , mice infected intraperitoneally with a mutant strain of s. aureus ( scv ) that does not activate hif - 1 survive , whereas those infected with the wt strain have 100 % mortality except when given the hif - 1 inhibitor 17 - n - allylamino -17-demethoxygeldanamycin ( 17 - dmag ) .84 this demonstrates the fine balance between controlling infection and avoiding excessive and deleterious inflammation . mice with a myeloid - specific deletion of hif2a exhibit greater survival , reduced proinflammatory cytokine production and less severe hypothermia and cardiac dysfunction during lps - induced endotoxemia .62 deletion of hif2a also decreases macrophage infiltration in a thioglycollate - induced model of peritonitis and neutrophil infiltration in the 12 - o - tetradecanoylphorbol -13-acetate - induced model of acute skin inflammation . overexpression of the dominant active zebrafish hif2a ortholog , hif2aa , did not affect neutrophil recruitment in the tail injury model described previously , but it did delay the resolution of neutrophilic inflammation .53 conversely , in a neutrophil - mediated lps - induced model of acute lung injury , mice with a myeloid - specific hif2a deletion displayed normal recruitment of neutrophils to the lung , but the clearance was more rapid , with reduced neutrophil counts after 48 and 72 hours , increased neutrophil apoptosis , and reduced markers of lung injury .53 although the majority of evidence supports a role for hifs predominantly in promoting inflammation , they may have anti - inflammatory roles under certain circumstances . for instance , renal f4 / 80 cell ( macrophage ) accumulation in a unilateral ureteral obstruction - induced kidney injury model is increased in vhl and lysmcre / vhl mice and decreased in hif and lysmcre / hif mice ( in which both hif1a and hif2a are deleted ) , suggesting that hifs are inhibiting migration toward the site of injury .71 hif signaling also has a complex role in tumor biology , including effects on the innate immune response , particularly tumor - associated macrophages ( tams ) , which preferentially accumulate in hypoxic regions of tumors .96 roda et al97 demonstrated opposing roles of hif - 1 and hif - 2 in tumor angiogenesis in a malignant melanoma model . in lysm - cre / hif1a mice , granulocyte - macrophage colony - stimulating factor treatment induced soluble vegf receptor , but not vegf , resulting in a greater reduction in tumor growth and vascularization . in contrast , myeloid hif2a deletion resulted in increased expression of vegf , but not soluble vegf receptor , and abrogated the granulocyte - macrophage colony - stimulating factor - induced reduction in tumor growth and angiogenesis observed in control mice . in a murine model of breast cancer , targeted deletion of hif1a in myeloid cells reduced tumor growth , despite vegf expression and vascularization remaining unchanged , perhaps due to the release of t - cells from hif1 -- dependent suppression by macrophages .65 hypoxia within the tumor microenvironment also confers on myeloid - derived suppressor cells ( mdsc ) the ability to suppress t - cell proliferation and ifn production and promotes their differentiation into macrophages expressing il10 , il12 , nos2 , arg1 , and il6 .96 stabilization of hif by desferrioxamine treatment mimics the enhancement in suppressive capacity , whereas hif1a mdsc are poor suppressors of t - cell proliferation . the role of hypoxia and hifs in macrophage polarization in the context of tumor biology remains subject to debate . laoui et al98 suggest that hypoxia is not an important driver of macrophage polarization , as it induces hif - 1 and hif - 2 simultaneously , therefore promoting the expression of factors associated with both m1 and m2 responses . tumors of phd2 mice , in which tumor oxygenation is increased , display a similar relative abundance of mhcii and mhcii tam subsets ( corresponding to m1 and m2 phenotypes , respectively ) to that seen in wt mice , and the expression of hypoxia - regulated genes associated with both m1 and m2 responses is reduced in tam infiltrating phd2 tumors . data is also beginning to emerge regarding the role of other components of the hif signaling pathway , such as phds . for example , in an lps - induced acute lung injury model , where rapid neutrophil influx is followed by resolution , phd3 and wt mice recovered equally well in normoxia . with coexisting hypoxia , however , phd3 mice had lower bal neutrophil counts and higher neutrophil apoptosis .54 increased apoptosis and reduced neutrophil numbers were also observed in bowel submucosa following dextran sulfate sodium - induced colitis , a neutrophil - dominated inflammatory model that involves tissue hypoxia . in a fatal model of abdominal sepsis , however , phd3 mice exhibited increased macrophage proinflammatory cytokine production and decreased survival , due to an overwhelming innate immune response .59 hypoxia and hif activation are features of many human diseases , including infection , cancers , and a variety of inflammatory conditions . immune cells are an important feature of these conditions , as are the tissue cells , and their relative and context - specific expression of the hif pathway components may modify clinical outcomes . in skin biopsy samples from patients with a variety of cutaneous infections ( including gram - positive and gram - negative bacteria , parasites , and viruses ) , a strong nuclear hif - 1 signal is detected in keratinocytes , dermal capillaries , neutrophils , lymphocytes , and macrophages , which is absent in uninfected biopsies .84 biopsies from damaged intestinal mucosa of patients with inflammatory bowel disease exhibit increased hif - 1 expression in lamina propria macrophages , compared to those from undamaged sections .63 the level of hif - 1 in damaged mucosa correlates with the expression of the scavenger receptor cd36 , suggesting that hif - 1 might promote macrophage phagocytosis of microbes and / or apoptotic cells within the colon . hif - 1 is also found in central hypoxic regions of human atherosclerotic plaques and colocalizes with unc5b and netrin - 1 , proteins that are induced in macrophages by hypoxia and low - density lipoprotein , promoting cell survival and inhibiting migration away from the plaque .15 sirna knockdown of hif1a in u937 monocytic cells inhibits foam cell formation and reduces the expression of 57 of the 70 atherosclerotic genes that are induced by oxidized low - density lipoprotein , including ptgs2 , il1b , icam1 , and vcam1 , suggesting that myeloid hif - 1 may have an important role in atherosclerosis .99 hif - 2 expression is increased in peripheral blood neutrophils of inflammatory arthritis patients compared to those from healthy controls .53 strong nuclear hif - 2 and cytoplasmic vegf immunostaining is also found in both neutrophils and neovasculature in lesions of patients with pyoderma gangrenosum , an inflammatory skin condition thought to involve a defect in resolution of neutrophilic inflammation following an inflammatory stimulus .100 although hypoxia might be expected to activate hif equally in all cell types present in diseased tissue , this is not always the case . hif2 - is expressed in neutrophils infiltrating the airway of chronic obstructive pulmonary disease patients , but not in the epithelium .53 likewise , hif - 2 protein is expressed in tams in the majority of uterine cervical cancer specimens , whereas 10 % of specimensexhibit tumor cell hif - 2 expression .101 tams infiltrating lung tumors also exhibit strong hif - 2 immunostaining in the absence of hif - 2 expression in the tumor cells themselves .102 the frequency of clusters of hif - 2 tam in breast carcinomas correlates with increased density of microvessels and appears to be associated with a reduced overall survival rate .103 in cervical cancer patients , the overall macrophage count in tumor biopsies does not affect the chance of disease - free survival ; however , the higher the percentage of tumor - associated macrophages that express hif2 , the greater the risk of local recurrence and the lower the probability of disease - free survival following radiotherapy .101 in many types of cancer , including breast , ovarian , colon , and pancreatic adenocarcinomas , hif - 1 and hif - 2 are expressed in the tumor cells themselves .102 this might induce factors , such as chemokines , that attract monocytes and mdsc and promote their differentiation into immunosuppressive macrophages that inhibit t - cell responses , as evidenced by murine models . urothelial carcinomas with higher expression of hif - 1 in tumor cells exhibit higher tam infiltration and these patients have a reduced disease - free survival rate .104 hif1a , hif2a , phd2 and phd3 transcripts are increased in peripheral blood neutrophils of ra patients .53,54 hif - 1 is highly expressed in synovial fibroblasts and infiltrating macrophages in the inflamed ra joint , where it enhances tnf -- and il -1-driven activation of the p38 and extracellular signal - regulated kinase signaling pathways , resulting in increased il - 33 expression .105,106 il - 33 , in turn , upregulates hif - 1 expression in synovial fibroblasts .105 synovial fibroblasts derived from osteoarthritis or ra patients subcutaneously engrafted into immunodeficient mice induce significantly greater myeloid cell infiltration and angiogenesis than fibroblasts derived from healthy individuals .107 this effect is dependent on both hif and vegf , since it can be reversed by hif1a sirna or by pharmacological inhibition of either hif - 1 or vegf . chronically low levels of oxygen may result in the downregulation of hifs under certain circumstances . for example , po2 is reduced in the skin of systemic sclerosis patients , yet hif - 1 expression in epidermal keratinocytes is lower than that of controls , perhaps due to increased phd levels , following induction of negative feedback loops .54,55,57,108 patients with mutations in components of hif signaling pathways are beginning to shed light on their role in humans . neutrophils from erythrocytosis patients with a gain of function mutation in hif2a express higher levels of the target genes pai1 and phd3 and undergo lower rates of apoptosis ex vivo ; however , phagocytosis and respiratory burst are unaffected .53 neutrophils derived from patients who are heterozygous for a mutation in the vhl gene exhibit lower rates of apoptosis and enhanced bacterial phagocytosis under normoxic conditions , resembling the phenotype normally seen in hypoxia , indicating the importance of proteasomal degradation in hif regulation in human neutrophils .109 given the large number of inflammatory diseases in which both hypoxia and hif upregulation occur , and the important role of hif in determining inflammatory responses , targeting the hif pathway may be a promising avenue for therapies , although a number of important issues require addressing . chronic hypoxia is a feature of many human diseases , yet most research so far has focused on acute responses . one important area for future study will be comparing the effects of acute versus chronic hypoxia and investigating the role of negative feedback mechanisms such as hif - mediated induction of phd and vhl transcription in chronic activation of the hif / hydroxylase pathway . more detailed studies of the effects of hypoxia on circulating leukocytes compared with resident immune cells derived from different tissues are also warranted . for instance , specialized populations of macrophages exist in tissues , which may well differ from each other and from circulating monocytes in their responses to hypoxic and inflammatory stimuli . given that certain organs , such as the lungs , have a higher basal level of oxygen than others , macrophages derived from these tissues may exhibit greater responses when exposed to hypoxia , due to lower hif - mediated transcription of negative regulatory proteins . furthermore , the study of hypoxic responses and hif signaling in the innate immune system has largely focused on monocytes , macrophages , and neutrophils , whereas research into other cell types , such as ilcs , eosinophils , and basophils , has been somewhat limited . efficacy of hif - 1 inhibition in dampening asthmatic inflammation has recently been demonstrated in vivo , suggesting that inhibition of hif signaling could be beneficial in chronic inflammatory diseases .8991 however , given the importance of hif - 1 for antimicrobial responses , care must be taken to ensure that treatments directed at the hif pathway do not result in susceptibility to infection . pharmacological augmentation of hif - 1 activity by mimosine has been proposed as a means of boosting innate immune responses and promoting bacterial clearance during infection , since mimosine was found to enhance myeloid cell bactericidal activity and to inhibit the development of necrotic skin lesions following s. aureus challenge in mice .51,95 augmentation of either hif - 1 or hif - 2 also enhances angiogenesis and wound healing , which may be beneficial in diabetes or ischemic disease .110,111 however , it is not clear whether this can be done safely in humans without inducing excessive inflammation , which could exacerbate tissue damage or induce shock . hif - 1 is upregulated more rapidly than hif - 2 and appears to be more important for the acute response to infection , whereas hif - 2 expression dominates during the resolution of inflammation .53,68 therefore , the targeting of hif - 2 might be useful in dampening chronic inflammation while preserving acute responses . the hif - 2 per - arnt - sim domain contains a cavity that will accommodate small molecule ligands which modulate its ability to form active heterodimers with hif - 1 , and thus provides an avenue for potential pharmacological manipulation .112 however , further investigation into the regulation of hif - 2 and the immune functions it modulates ( and how these differ from hif - 1 ) is required to determine the likely effects of modifying its expression or activity . suppression of downstream targets of hif might also be a means of delivering therapies that target specific aspects of the hypoxic response while preserving those that are protective . phd3 has been suggested as a therapeutic target in neutrophils , owing to its specific effects on hypoxic survival in this cell type . evidence from animal models indicates that the inhibition of phd3 would preserve neutrophil antimicrobial function , but encourage the resolution of neutrophilic inflammation in hypoxic tissues once the infection is cleared .54 however , it is important to consider the impact of any potential therapy targeting phd3 on other cell types , as its role in macrophages appears to be different to that in neutrophils . while modulation of the hif pathway has had beneficial effects in animal models , further work is required to determine the most appropriate way of manipulating the pathway to promote resolution of infections and to treat inflammatory diseases without causing deleterious side effects . nonetheless , the crucial role of hifs in controlling innate immune responses , in response to hypoxia as well as other factors , makes this pathway a promising target for further investigation and potential therapies .\noutput:\n" }, { "from": "agent", "value": "leukocytes recruited to infected , damaged , or inflamed tissues during an immune response must adapt to oxygen levels much lower than those in the circulation . hypoxia inducible factors ( hifs ) are key mediators of cellular responses to hypoxia and , as in other cell types , hifs are critical for the upregulation of glycolysis , which enables innate immune cells to produce adenosine triphosphate anaerobically . an increasing body of evidence demonstrates that hypoxia also regulates many other innate immunological functions , including cell migration , apoptosis , phagocytosis of pathogens , antigen presentation and production of cytokines , chemokines , and angiogenic and antimicrobial factors . many of these functions are mediated by hifs , which are not only stabilized posttranslationally by hypoxia , but also transcriptionally upregulated by inflammatory signals . here , we review the role of hifs in the responses of innate immune cells to hypoxia , both in vitro and in vivo , with a particular focus on myeloid cells , on which the majority of studies have so far been carried out ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the world health organization ( who ) estimates that 90 % of the 285 million visually impaired people in the world live in low - income countries .1 the major causes of visual impairment are uncorrected refractive errors ( 43 % ) followed by cataract ( 33 % ) , but the main cause of blindness is due to lens opacities ( 51 % ) .23 in west africa , the prevalence of cataract in adults is 40 years and older range from 21 % to 62.1 % .4 the difficulties for national governments to effectively reduce the backlog in cataract surgery has led to the organization of mass surgical campaigns by nongovernmental organizations and charity foundations .5 phacoemulsification is accepted as the technique of choice for cataract surgery in developed countries . however , the ideal procedure for surgical campaigns in low - income countries remains controversial . the high cost of equipment and supplies , the dependence on technical assistance , and the complexity of the cases ( hypermature cataracts with poor pupil dilation , zonular instability , and corneal opacities ) are arguments against phacoemulsification as the best or at least the only technique for the majority of cases .6 intracapsular cataract extraction ( icce ) has been used for many years in mass campaigns because it is a fast , cheap and easy technique that is sometimes carried out by trained local health agents ( doctors or specialized nurses ) .47 however , the rate of postoperative complications and in general , the optical problems derived from aphakia , with a total dependence on spectacles and difficulties related to anisometropia represent serious limitations in broad application of icce . extracapsular cataract extraction ( ecce ) replaced the in toto removal of the cataract for more than two decades in most developed countries . this technique is inexpensive , requires few technologic resources and many ophthalmic surgeons over 40 years are trained to perform this technique . alternately , corneal or corneoscleral incisions of 8 - 10 mm expose the eye to surgical complications ( e.g. , expulsive hemorrhage , capsular ruptures , etc . manual small incision cataract surgery ( msics ) was first described by kansas in 1990 . in this technique , the nucleus is dislodged through a 6 - 6.5 mm scleral tunnel using several of the advantages of phacoemulsification ( closed chamber procedure , no sutures needed , satisfactory control of astigmatism ) , avoiding use of advanced technology , and is relatively inexpensive . hence , msics is becoming the technique of choice in mass surgical campaigns in low - income countries .8910 in addition , msics has been proposed as a technique of choice for advanced cataracts even in developed countries because the outcomes are comparable to phacoemulsification in almost all aspects except postoperative astigmatism .111213 as many of the surgeons who participate in charity programs are trained in ecce but usually perform phacoemulsification in their home countries , the learning curve for msics has to be acquired during the campaigns . although the outcomes of msics and phacoemulsification performed by ophthalmology trainees have been compared ; 14 there are no references in the literature comparing the results obtained by surgeons who change their technique from ecce to msics in special circumstances such as surgical campaigns for charity or humanitarian purposes . the goal of the present study is to compare the safety and visual outcomes obtained by two experienced surgeons who changed the cataract extraction technique from ecce to msics during an international campaign for the prevention of blindness in two low income countries . this was a retrospective comparative cohort study of consecutive patients who underwent two different surgical settings in tertiary hospitals in kenya and burkina faso . two surgeons - with over 15 years of experience in cataract surgery and who had been trained in the ecce technique in spanish hospitals between 1993 and 1998 - used this technique during the first week of december 2008 in bobo - diulasso ( burkina faso ) on one eye of 93 consecutive cataract patients ( ecce group ) . inclusion criteria for the surgical campaign were : corrected distance visual acuity ( cdva ) 20/80 ( 0.6 logarithm of the minimum angle of resolution [ logmar ] ) in the best eye due to cataract and low income ( checked by a local partner who helped arrange the surgical camps ) . patients were excluded from the surgery if they had any other ophthalmic disease thought to be the main cause of blindness . patients were excluded from the present study if they did not attend any of the postoperative visits . both surgeons used the same criteria to include 98 consecutive cases in the campaign in thika ( kenya ) during the last week of may 2013 using the msics technique ( msics group ) for the first time after theoretical instructional courses in cataract and refractive surgery meetings . the outcome measures of this study were the rate of complications related to surgery and visual outcomes including uncorrected distance visual acuity ( udva ) , cdva , spherical equivalent , and vector analysis of corneal astigmatism . study subjects were recruited by qualified local staff ( nurses specialized in ophthalmology ) in the bobo - dioulasso and thika areas before the arrival of the surgical team . this study adhered to the tenets of declaration of helsinki and informed consent of the surgical procedures and participation in the study was obtained from each patient before surgery . postoperative visual acuities were classified into good outcomes ( va 20/60 ) , borderline outcomes ( va between 20/80 and 20/200 ) , or poor outcomes ( va 20/200 ) according to the who 's prevention of blindness program guidelines . patients for inclusion in the study were selected by qualified local staff in a screening exam which included , udva measurement , in daylight , using a snellen tumbling - e chart at 6 m and torchlight anterior segment examination before surgery . as the great majority of cases were hypermature white cataracts where refraction could not be obtained , the same mean values were considered for cdva . preoperative examinations were subsequently performed were performed by our team at the hospital on the operative day . preoperative examination included a slit lamp examination ( 91102242 by bobes , spain ) , rebound tonometry icare ( tiolat oy , helsinki , finland ) , keratometry ( helmholtz by bobes , spain ) , a scan biometry ( a - scan by otitm , spain ) . topical and peribulbar anesthesia were administered . all surgeries were performed by two spanish surgeons ( jje and tmc ) in the operating rooms of the district 22 hospitals at bobo - dioulasso and in the hospital at thika . for the ecce group , ecce with intraocular lens ( iol ) power calculations were performed and rigid polymethylmethacrylate ( pmma ) iols were implanted . a limbal incision of 8 - 9 mm at the 12 oclock position was performed . a circular continuous capsulotomy ( ccc ) was attempted , in many cases under trypan blue staining of the anterior capsule ( in white hypermature cataracts ) . z - hyalin 1 % sodium hyaluronate ( carl zeiss , jena , germany ) was used as an ocular viscoelastic device . if capsular calcification or other anterior segment anomalies prevented this manoeuvre , a discontinuous anterior capsulotomy was performed using a cystotome or scissors . after extraction of the nucleus and cortical cleaning , an iol was implanted in the posterior chamber . all cases were targeted for emmetropia . if an exact power was not available for a case , we the residual myopic value closest to myopia . continuous sutures were performed using 10/00 black monofilament after injecting 0.1 ml ( 1 mg ) of cefuroxime solution in the anterior chamber . for the msics group , two 1.5 mm limbal paracenteses were created at 2 and 10 oclock to create a ccc using the same methods as described above . subsequently , a superior fornix - based conjunctival dissection was created followed by thermal coagulation of bleeding vessels . a stainless 2.5 mm bevel down crescent knife ( beaver - visitec international , inc . , waltham , usa ) was used to create a 7 mm 2.5 mm superior scleral tunnel which was to remove the nucleus and for implanting the same rigid pmma iol model as the ecce group . after removing the ophthalmic viscoelastic device , a tight self - sealing incision was verified and no sutures were applied in any of the cases . conjunctival flaps were sutured with a single vicryl ( polyglactin 910 ) suture ( ethicon , inc . , somerville , new jersey , usa ) . after each procedure , a surgical report was created , recording the possible incidences following the criteria defined in the oxford cataract treatment and evaluation team ( octet ) protocol .15 ctet was also used for the evaluation of the postoperative complications . all cases were performed as a same - day surgery , with the patients leaving the clinic after compressive occlusion of the operated eye and with a postoperative appointment for the following day . topical medication was given to the patients , and they were instructed on postoperative ocular care . sutures , corneas , iols , and pupils were assessed at 1 day postoperatively with a handheld slit lamp . examination at the 3 months postoperative visit included measurement of udva cdva , slit lamp examination , rebound tonometry , keratometry , retinoscopy , and refraction . near distanceobjective refraction was done with a retinoscope ( 3.5 v halogen hpx streak retinoscope , model 18200 ; welch allyn , skaneateles falls , ny , usa ) , followed by a subjective examination with a trial box and glasses . all examinations and refractions were performed by two spanish optometrists and one local ophthalmic nurse . the incidence and type of intraoperative and postoperative complications were also noted . intermediate examinations at 1 week and 2 weeks postoperatively were performed by local health workers affiliated with the program . the data corresponding to this visit have been omitted because visual acuity data were not collected . arithmetic means , medians , standard deviations ( sds ) , and standard errors were calculated for udva and cdva ( after converting the values to logmar ) , sphere , cylinder , spherical equivalent , and defocus equivalent were calculated for each eye at every visit . based on these data , refractive efficacy and safety indexes were calculated using the following formula : equation 1 : efficacy = udva at 3 months postoperatively / preoperative cdvaequation 2 : safety = cdva at 3 months postoperatively / preoperative cdva . equation 1 : efficacy = udva at 3 months postoperatively / preoperative cdva equation 2 : safety = cdva at 3 months postoperatively / preoperative cdva . these results were plotted based on previous refractive literature .161718 the refractive efficacy index expresses the ability of the procedure to provide a good udva . the safety index indicates the capability of the surgery to preserve or improve the best spectacle cdva . visual acuity was recorded on a decimal scale and converted into logmar for mathematical and statistical analysis . as efficacy and safety indexes are calculated using a mean value usually expressed on a decimal scale , the data were calculated after the conversion of the arithmetical means of spontaneous and udvas ( udva and cdva , respectively ) expressed in the logmar scale . the changes in corneal astigmatism after cataract extraction was evaluated using the vector method proposed by thibos and horner ( power vector ) .19 an advantage of this mathematical approach is that astigmatism is represented in rectangular vector form . hence , conventional scalar methods can be applied to each vector component , and this allows the application of standard multivariate statistics in order to compute population means and variances , define confidence intervals and test hypotheses . another characteristic of this vector methodology is the mathematical independence of each power vector component , called orthogonality . given orthogonality , statistical analysis can be applied to each component separately . with this method , after decomposing each corneal cylinder in a horizontal ( j0 ) component and vertical ( j45 ) component , they can estimatemean corneal astigmatism vector before and 3 months after each type of surgical procedure . a graph of polar representation of the mean corneal astigmatism vectors calculated before and 3 months after surgery was designed to provide a more intuitive representation of the impact of surgery on the corneal cylinder . data were tabulated using a spreadsheet ( microsoft excel , windows xp professional , microsoft corp . this was also used to perform the calculations for spherical equivalent and the equivalent defocus for each case . statistical analysis was performed using the sigmaplot 11.0 for windows ( systat software , inc . , san jose , ca , usa ) for descriptive statistics of continuous variables for the description of the samples such as mean , sd , median , minimum , maximum , and range ; descriptive statistics for categorical variables , obtaining frequencies , and percentages of the categories . comparison tests of means or ranges ( t - test or mann - whitney test ) after using the kolmogorov - smirnov test on the samples for determining if continuous data were normally distributed . patients for inclusion in the study were selected by qualified local staff in a screening exam which included , udva measurement , in daylight , using a snellen tumbling - e chart at 6 m and torchlight anterior segment examination before surgery . as the great majority of cases were hypermature white cataracts where refraction could not be obtained , the same mean values were considered for cdva . preoperative examinations were subsequently performed were performed by our team at the hospital on the operative day . preoperative examination included a slit lamp examination ( 91102242 by bobes , spain ) , rebound tonometry icare ( tiolat oy , helsinki , finland ) , keratometry ( helmholtz by bobes , spain ) , a scan biometry ( a - scan by otitm , spain ) . topical and peribulbar anesthesia were administered . all surgeries were performed by two spanish surgeons ( jje and tmc ) in the operating rooms of the district 22 hospitals at bobo - dioulasso and in the hospital at thika . for the ecce group , ecce with intraocular lens ( iol ) power calculations were performed and rigid polymethylmethacrylate ( pmma ) iols were implanted . a limbal incision of 8 - 9 mm at the 12 oclock position was performed . a circular continuous capsulotomy ( ccc ) was attempted , in many cases under trypan blue staining of the anterior capsule ( in white hypermature cataracts ) . z - hyalin 1 % sodium hyaluronate ( carl zeiss , jena , germany ) was used as an ocular viscoelastic device . if capsular calcification or other anterior segment anomalies prevented this manoeuvre , a discontinuous anterior capsulotomy was performed using a cystotome or scissors . after extraction of the nucleus and cortical cleaning , an iol was implanted in the posterior chamber . if an exact power was not available for a case , we the residual myopic value closest to myopia . continuous sutures were performed using 10/00 black monofilament after injecting 0.1 ml ( 1 mg ) of cefuroxime solution in the anterior chamber . for the msics group , two 1.5 mm limbal paracenteses were created at 2 and 10 oclock to create a ccc using the same methods as described above . subsequently , a superior fornix - based conjunctival dissection was created followed by thermal coagulation of bleeding vessels . a stainless 2.5 mm bevel down crescent knife ( beaver - visitec international , inc . , waltham , usa ) was used to create a 7 mm 2.5 mm superior scleral tunnel which was to remove the nucleus and for implanting the same rigid pmma iol model as the ecce group . after removing the ophthalmic viscoelastic device , a tight self - sealing incision was verified and no sutures were applied in any of the cases . conjunctival flaps were sutured with a single vicryl ( polyglactin 910 ) suture ( ethicon , inc . , somerville , new jersey , usa ) . after each procedure , a surgical report was created , recording the possible incidences following the criteria defined in the oxford cataract treatment and evaluation team ( octet ) protocol .15 ctet was also used for the evaluation of the postoperative complications . all cases were performed as a same - day surgery , with the patients leaving the clinic after compressive occlusion of the operated eye and with a postoperative appointment for the following day . topical medication was given to the patients , and they were instructed on postoperative ocular care . sutures , corneas , iols , and pupils were assessed at 1 day postoperatively with a handheld slit lamp . examination at the 3 months postoperative visit included measurement of udva cdva , slit lamp examination , rebound tonometry , keratometry , retinoscopy , and refraction . near distance visual acuities were not recorded . objective refraction was done with a retinoscope ( 3.5 v halogen hpx streak retinoscope , model 18200 ; welch allyn , skaneateles falls , ny , usa ) , followed by a subjective examination with a trial box and glasses . all examinations and refractions were performed by two spanish optometrists and one local ophthalmic nurse . the incidence and type of intraoperative and postoperative complications were also noted . intermediate examinations at 1 week and 2 weeks postoperatively were performed by local health workers affiliated with the program . the data corresponding to this visit have been omitted because visual acuity data were not collected . arithmetic means , medians , standard deviations ( sds ) , and standard errors were calculated for udva and cdva ( after converting the values to logmar ) , sphere , cylinder , spherical equivalent , and defocus equivalent were calculated for each eye at every visit . based on these data , refractive efficacy and safety indexes were calculated using the following formula : equation 1 : efficacy = udva at 3 months postoperatively / preoperative cdvaequation 2 : safety = cdva at 3 months postoperatively / preoperative cdva . equation 1 : efficacy = udva at 3 months postoperatively / preoperative cdva equation 2 : safety = cdva at 3 months postoperatively / preoperative cdva . these results were plotted based on previous refractive literature .161718 the refractive efficacy index expresses the ability of the procedure to provide a good udva . the safety index indicates the capability of the surgery to preserve or improve the best spectacle cdva . visual acuity was recorded on a decimal scale and converted into logmar for mathematical and statistical analysis . as efficacy and safety indexesare calculated using a mean value usually expressed on a decimal scale , the data were calculated after the conversion of the arithmetical means of spontaneous and udvas ( udva and cdva , respectively ) expressed in the logmar scale . the changes in corneal astigmatism after cataract extraction was evaluated using the vector method proposed by thibos and horner ( power vector ) .19 an advantage of this mathematical approach is that astigmatism is represented in rectangular vector form . hence , conventional scalar methods can be applied to each vector component , and this allows the application of standard multivariate statistics in order to compute population means and variances , define confidence intervals and test hypotheses . another characteristic of this vector methodology is the mathematical independence of each power vector component , called orthogonality . given orthogonality , statistical analysis can be applied to each component separately . with this method , after decomposing each corneal cylinder in a horizontal ( j0 ) component and vertical ( j45 ) component , they can estimatemean corneal astigmatism vector before and 3 months after each type of surgical procedure . a graph of polar representation of the mean corneal astigmatism vectors calculated before and 3 months after surgery was designed to provide a more intuitive representation of the impact of surgery on the corneal cylinderdata were tabulated using a spreadsheet ( microsoft excel , windows xp professional , microsoft corp . , this was also used to perform the calculations for spherical equivalent and the equivalent defocus for each case . statistical analysis was performed using the sigmaplot 11.0 for windows ( systat software , inc . , san jose , ca , usa ) for descriptive statistics of continuous variables for the description of the samples such as mean , sd , median , minimum , maximum , and range ; descriptive statistics for categorical variables , obtaining frequencies , and percentages of the categories . comparison tests of means or ranges ( t - test or mann - whitney test ) after using the kolmogorov - smirnov test on the samples for determining if continuous data were normally distributed . the right eye was operated in 47.30 % of cases . there were 98 patients in the msics group ( 34.69 % females ) . the right eye underwent surgery in 43.96 % of cases . there were no significant between - group differences in preoperative udva or cdva 3 months postoperatively . the mean refractive efficacy / safety indexes at 3 months postoperatively were 22/48 , respectively , for the ecce group and 20/37 for the msics group . preoperative and 3 months postoperative data of patients who underwent extracapsular cataract extraction with intraocular lens implantation or manual small incision cataract surgery with intraocular lens implantation good udva was achieved in 69 % of eyes in the msics group and 49 % of eyes in the ecce group [ figure 1a ] . three eyes lost one line of cdva in the ecce group , and 88 % of eyes gained three or more lines . in the msics group , two eyes lost two lines of cdva , one eye lost one line , and 87.5 % gaining three or more lines [ figure 1b ] . ( a ) the efficacy ( top ) ; ( b ) safety ( middle ) and ( c ) predictability ( bottom ) over the time of the surgical procedures 3 months after surgeries are shown in standardized graphs for reporting refractive surgery data the spherical equivalent at 3 months postoperatively ranged between 1 and + 1 din 55 % versus 43 % of eyes in the msics and ecce groups , respectively [ figure 1c ] . there were statistically significant differences in the changes in j0 and j45 from baseline to three postoperatively in the ecce group ( mann - whitney p = 0.001 and p 0.001 , respectively ) . there were no statistically significant changes in j0 and j45 from baseline to 3 months postoperatively in the msics group ( mann - whitney p 0.05 in both cases ) . there were greater changes in mean corneal cylinder vectors from baseline to 3 months postoperatively in the ecce group [ figure 2 ] . polar representation of the mean corneal astigmatism vectors ( being the vector 's length the magnitude of corneal astigmatism in diopters as seen in the horizontal and vertical axes of the graph ) calculated before and 3 months after procedures for both series eighty - seven ( 93.5 % ) ecce surgeries and 91 ( 92.8 % ) msics procedures were performed uneventfully . moderate to severe intraoperative complications of patients who underwent extracapsular cataract extraction with intraocular lens implantation or manual small incision cataract surgery with intraocular lens implantation the most common postoperative complication was transient corneal edema on the first day after surgery in 38 ( 40.86 % ) eyes and 19 ( 19.38 % ) eyes in the ecce and msics groups , respectively [ table 3 ] . hyphema occurred in one eye in the ecce group and two eyes in the msics group . in these eyesmoderate to severe postoperative complications in patients who underwent extracapsular cataract extraction with intraocular lens implantation or manual small incision cataract surgery with intraocular lens implantation there were no other preexisting pathologies that could cause poor vision postoperatively . there were no significant between - group differences in preoperative udva or cdva 3 months postoperatively . the mean refractive efficacy / safety indexes at 3 months postoperatively were 22/48 , respectively , for the ecce group and 20/37 for the msics group . preoperative and 3 months postoperative data of patients who underwent extracapsular cataract extraction with intraocular lens implantation or manual small incision cataract surgery with intraocular lens implantation good udva was achieved in 69 % of eyes in the msics group and 49 % of eyes in the ecce group [ figure 1a ] . three eyes lost one line of cdva in the ecce group , and 88 % of eyes gained three or more lines . in the msics group , two eyes lost two lines of cdva , one eye lost one line , and 87.5 % gaining three or more lines [ figure 1b ] . ( a ) the efficacy ( top ) ; ( b ) safety ( middle ) and ( c ) predictability ( bottom ) over the time of the surgical procedures 3 months after surgeries are shown in standardized graphs for reporting refractive surgery data the spherical equivalent at 3 months postoperatively ranged between 1 and + 1 din 55 % versus 43 % of eyes in the msics and ecce groups , respectively [ figure 1c ] . there were statistically significant differences in the changes in j0 and j45 from baseline to three postoperatively in the ecce group ( mann - whitney p = 0.001 and p 0.001 , respectively ) . there were no statistically significant changes in j0 and j45 from baseline to 3 months postoperatively in the msics group ( mann - whitney p 0.05 in both cases ) . there were greater changes in mean corneal cylinder vectors from baseline to 3 months postoperatively in the ecce group [ figure 2 ] . polar representation of the mean corneal astigmatism vectors ( being the vector 's length the magnitude of corneal astigmatism in diopters as seen in the horizontal and vertical axes of the graph ) calculated before and 3 months after procedures for both serieseighty - seven ( 93.5 % ) ecce surgeries and 91 ( 92.8 % ) msics procedures were performed uneventfully . moderate to severe intraoperative complications of patients who underwent extracapsular cataract extraction with intraocular lens implantation or manual small incision cataract surgery with intraocular lens implantation the most common postoperative complication was transient corneal edema on the first day after surgery in 38 ( 40.86 % ) eyes and 19 ( 19.38 % ) eyes in the ecce and msics groups , respectively [ table 3 ] . hyphema occurred in one eye in the ecce group and two eyes in the msics group . in these eyesmoderate to severe postoperative complications in patients who underwent extracapsular cataract extraction with intraocular lens implantation or manual small incision cataract surgery with intraocular lens implantation there were no other preexisting pathologies that could cause poor vision postoperatively . msics is becoming more common in cases when phacoemulsification is unavailable due to technical or financial reasons . msics has almost the same efficacy and is more efficient than phacoemulsification in some high volume eye care hospitals .620 similarly , some studies have reported that msics can be more effective8 and more economical than ecce .921 these studies support the use of msics for international prevention of blindness campaigns when technology is unavailable and financial resources are limited . hence , in our study , the surgeons trained in ecce who wanted to transition to msics faced a learning curve in the special conditions of a mass campaign . applying the stringent conditions of scientific research is sometimes difficult during charity programs as geographic accessibility may be limited and hence , the study sample may be limited . therefore , designing a prospective , randomized , and controlled trials in the setting of prevention of blindness campaign is tenuous at best . however , despite the limitations of a retrospective cohort study performed over different populations , the aim of the present study was to analyze , as reliably as possible , a practical concern of surgeons who try to improve their skills and practice in these special conditions . there were no statistically significant differences between groups in udva or cdva at 3 months postoperatively . however , 69 % of eyes in the msics group had good udva ( va 20/60 ) postoperatively , compared to 49 % in the ecce group . this could indicate that the refractive efficacy of msics was similar or slightly higher than ecce in our study . in a high volume eye hospitalsetting , gogate et al . found that both , msics and ecce were safe and effective techniques requiring similar equipment but with msics providing better uncorrected vision .8 although the who recommendations for visual improvement after cataract surgery implies higher levels of cdva , it has been reported that the circumstances which affect the patients ( including cultural level ) in mass campaigns developed in low - income countries may affect the visual records .4 although postoperative spherical equivalent with both procedures was similar , a better refractive efficacy of msics in our series can be explained by a smaller amount of induced astigmatism when compared to ecce . our observations concur with studies that have reported a smaller impact on corneal astigmatism with msics compared to ecce .2223 the inability of obtaining subjective refraction in patients with hypermature cataracts led us to use corneal cylinder as a more reliable parameter to evaluate the changes in astigmatism . the instability of the corneal cylinder produced by the loss of tension of the sutures can induce refractive changes in the operated eye . this refractive change is especially undesirable for patients with economic difficulties who need to buy spectacles . in addition , very similar percentages of eyes gained lines of cdva in both groups . taken together , similar refractive safety between ecce and msics has been previously reported .8 the octet grading system was created to compare the outcomes and complications of different cataract surgery techniques . the systematic approach andthe grading system and scoring depending on the consequences of the possible incidences make octet , especially pertinent for our study .2425262728 notably , both surgeons had been trained for ecce in the past and not msics , but the rate of intraoperative and postoperative complications were similar . taking into account ethical considerations , it must be emphasized that these surgeons were well experienced having performed more than 5000 anterior segment procedures each . expulsive hemorrhage is a severe and very uncommon intraoperative complication and the risk of it increases the longer the difference between pressures in the vitreous and anterior chamber is maintained . as msics is a more closed procedure because of the self - sealing tunnel incision , the risk of this complication seems to be greater in ecce . previous comparisons of msics and ecce performed by trained surgeons have reported lower rates of vitreous loss for msics despite disruption of the posterior capsule .8 this observation was likely due to better maintenance of an adequate pressure in the anterior chamber8 contrary to our experience . however , the rare occurrence of a collapsed anterior chamber could explain the significantly smaller incidence of transient corneal edema seen at the early postoperative period in the msics group in our study . the learning curve for the transition from ecce to msics in experienced surgeons who operate in cooperation programs is safe , as the rate of complications is similar for both techniques even during the early learning phase . slightly better visual and refractive outcomes can be achieved from the beginning due to the lower induction of corneal astigmatism .\noutput:\n" }, { "from": "agent", "value": "purpose : to compare the safety and the visual outcomes of two experienced cataract surgeons who converted from extracapsular cataract extraction ( ecce ) to manual small incision cataract surgery ( msics ) during a campaign for the prevention of blindness.methods : two surgeons used the ecce technique ( ecce group ) during a campaign in burkina faso on 93 consecutive cataract patients with a corrected distance visual acuity ( cdva ) < 20/80 in the best eye . both surgeons used msics for the first time on 98 consecutive cases in another campaign in kenya after theoretical instructional courses.results : there were no significant differences in cdva at 3 months postoperatively . there were 69 % of eyes with uncorrected distance visual acuity 20/60 in the msics group and 49 % eyes in the ecce group . spherical equivalents ranged between 1d and + 1d in 55 % of the msics group versus 43 % in the ecce group . there were significant differences in the changes in the vertical component of astigmatism ( j45 ) but not the horizontal ( j0 ) component . there were no significant differences in the intraoperative complications . the most common postoperative complication was corneal edema on the first day in 40.86 % and 19.38 % of the ecce and msics groups , respectively.conclusion : transitioning from ecce to msics for experienced cataract surgeons in surgical campaigns is safe . the rate of complications is similar for both techniques . slightly better visual and refractive outcomes can be achieved due to the decreased induction of corneal astigmatism ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: genus arcanobacterium comprises the species arcanobacterium haemolyticum , arcanobacterium hippocoleae , arcanobacterium pluranimalium , and arcanobacterium phocae . more recently a. canis and a. phocisimile were described as novel species of this genus . arcanobacterium pyogenes together with arcanobacterium bernardiae , arcanobacterium bonasi , and arcanobacterium bialowiezense was reclassified to the newly described species trueperella . the original description of a. phocisimile was based on physiological and biochemical characteristics , chemotaxonomic analysis , and 16s rdna sequencing results of two strains isolated with several other bacterial species from a vaginal swab and an anal swab of two free living harbour seals of the german north sea . in the present study bothinitially described a. phocisimile strains and three additional strains obtained from three harbour seals were identified and further characterized phenotypically by maldi - tof ms analysis and genotypically by amplification and sequencing of various molecular targets . the a. phocisimile strains used in the present study included the previously described type strains a. phocisimile 2698 ( lmg 27073 ; ccm 8430 ) and a. phocisimile 4112 . additionally investigated a. phocisimile 3047 was isolated ( post mortem ) together with bacillus spp . , enterococcus spp . , erysipelothrix rhusiopathiae , and - haemolytic streptococci in the year 2005 from the lung of a female harbour seal with bronchopneumonia and perforation of stomach . the harbour seal was found dead in rantum , sylt of the german north sea . also investigated a. phocisimile - haemolytic streptococci from an anal swab and a. phocisimile 4125 together with pseudomonas spp . and - haemolytic streptococci also from an anal swab of two apparently healthy female harbour seals , respectively . a. phocisimile 4113 and a. phocisimile 4125 were isolated in 2007 during a monitoring program of free living harbour seals of the german north sea . all three newly investigated a. phocisimile strains were initially characterized phenotypically and by 16s rdna sequencing . both a. phocisimile strains previously mentioned in the species description and the three a. phocisimile strains of the present study were further analysed by maldi - tof ms and genotypically by amplification and sequencing of the previously described molecular target 16s - 23s rdna intergenic spacer region ( isr ) and the genes rpob and gap . all three strains newly characterized in the present study could reliably be identified as a. phocisimile by phenotypic properties and by 16s rdna sequencing . the phenotypic properties appeared to be almost identical to both previously characterized a. phocisimile strains ( table 2 ) . however , a positive pyrazinamidase reaction of a. phocisimile seems to be the only reliable biochemical property for differentiation of a. phocisimile from pyrazinamidase negative a. phocae . as shown by numerous authorsmaldi - tof ms is a powerful tool for species characterization of a broad spectrum of gram - positive and gram - negative bacteria . this technique had previously been successfully used for rapid and reliable identification of bacteria of genera arcanobacterium and trueperella . the maldi - tof ms analysis of the present study revealed that by using the current bruker data base , all five strains of this hitherto unknown species could not be identified to species level . however , using the maldi biotyper 3.1 software package the log ( score ) values of a. phocisimile 4112 , a. phocisimile 3047 , a. phocisimile 4113 , and a. phocisimile 4125 matched against a. phocisimile 2698 with log ( score ) values between 2.69 and 2.74 indicating that all five strains belong to this newly described species . inclusion of a. phocisimile in the bruker reference database will allow for the identification of this new species in future . a dendrogram analysis of the maldi - tof ms results is presented in figure 1 . the genotypic classification by 16s rdna sequencing revealed that the three novel a. phocisimile strains of the present study yielded 100 % identity to both a. phocisimile strains described previously , also including the type strain a. phocisimile 2698 ( figure 2 ) . comparable to previously described a. canis all five a. phocisimile from the present study could additionally be classified by amplification and sequencing of isr ( fn563000 , fn563002 , hg316083 , hg316084 , and hg316085 ) , gene rpob ( hg316078 , hg316079 , hg316080 , hg316081 , and hg316082 ) , and gene gap ( hf679531 , hg316074 , hg316075 , hg316076 , and hg316077 ) yielding for all three molecular targets an identity of 99.4 % , 99.8 % , and 99.8 % , respectively , for all five strains among each other . a typical dendrogram using the sequencing results of the target genesthe results of the present study revealed that phenotypic properties , the determination of peptidic spectra by maldi - tof ms , and the various genotypic targets allow for a reliable identification of a. phocisimile and a further differentiation of a. phocisimile from closely related a. phocae which could also be isolated from marine mammals . however , all a. phocisimile strains of the present study were isolated together with various other bacteria , partly from obviously healthy animals , indicating that the pathogenic importance of this species for marine mammals remains unclear . arcanobacterium phocisimile type strain and four additional a. phocisimile strains isolated from harbour seals were identified phenotypically , by matrix assisted laser desorption ionization time of flight mass spectrometry ( maldi - tof ms ) , by sequencing 16s rdna , and , as novel molecular targets , by sequencing 16s - 23s rdna intergenic spacer region and the genes rpob and gap indicating that maldi tof ms and the molecular targets might help to identify this novel species .\noutput:\n" }, { "from": "agent", "value": "arcanobacterium phocisimile , a newly described species with the type strain a. phocisimile 2698 t isolated from a vaginal swab of a harbour seal and four additional a. phocisimile strains also isolated from four harbour seals could reliably be identified by phenotypic properties , by matrix assisted laser desorption ionization time of flight mass spectrometry ( maldi - tof ms ) , and by sequencing the genomic targets 16s rdna and 16s - 23s rdna intergenic spacer region and the genes rpob and gap . the a. phocisimile strains investigated in the present study were isolated together with several other bacterial species indicating that the pathogenic importance of a. phocisimile remains unclear . however , the detection of peptidic spectra by maldi - tof ms and the presented phenotypic and genotypic approach might help to identify a. phocisimile in future ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: major depression is a highly prevalent condition as well as a debilitating psychiatric illness that has a negative impact on individual and community health .1 antidepressant drugs are the mainstay of the treatment of depression ; however , their efficacy is still lower than desired , and many patients present subsyndromal residual symptoms after the initial clinical response . up to 15 % of cases will remain significantly depressed even after multiple pharmacological approaches ,2 with a negative impact on clinical course .3 since a partial response to treatment represents a widespread condition among depressed patients and should be readily identified to decide the most appropriate treatment plan , many helpful systems for staging levels of treatment resistance have been proposed for major depression .4 in this way , rush et al describeddifficult - to - treat depression as a clinical condition which includes both those patients who do not respond adequately to one or more established treatments and those in whom a successful treatment is prevented by concomitant conditions , precluding the optimal delivery of potentially effective treatments . such circumstances mainly involve limited adherence to treatment , adverse side effects preventing an adequate dose or duration of treatment , and comorbid axis i , ii , or iii conditions .5 hence , difficult - to - treat depressed ( dtd ) patients form a clinical population of vulnerable subjects , representing a common medical challenge for clinicians who often have to develop individualized therapeutic decisions based on limited scientific evidence . many augmentation strategies have been developed to increase the efficacy of antidepressant treatments , and alternative strategies based on multidisciplinary competences are probably essential . among safe and less - demanding treatment strategies , a growing number of evidence supports the usefulness of chronotherapeutic interventions , such as bright light therapy ( blt ) , in the management of patients suffering from mood disorders . when combined with antidepressants , blt hastens recovery with improvements since the first week of treatment .6,7 clinical benefits are well known for unipolar depressed patients , but despite the amount of data provided by benedetti8 on combined chronotherapeutic intervention , only few trials have looked at blt alone as an augmentation of pharmacotherapy for bipolar depression .9,10 because of brief latency of action , blt alone11 ,12 has been little studied in the vulnerable clinical population of dtd patients . hence , the main aim of our study was to explore the effects of blt augmentation on clinical outcome of these patients , and compare unipolar and bipolar subjects . we tested blt combined with ongoing medication as a first - line choice for both more vulnerable patients ( with concomitant medical and / or psychiatric comorbidity that preclude the optimal delivery of the ongoing treatment ) and patients with stage i treatment - resistant depression ( trd ) ( those who failed to achieve a remission after the first pharmacological trial at an adequate dose ) . finally , we observed the effectiveness of such an approach both in the acute phase and after blt discontinuation over 8 weeks . thirty - one depressed outpatients ( 16 unipolar and 15 bipolar without seasonal pattern ) were enrolled in the study . a total of 110 outpatients referred for the treatment of depressive episode at the institute of psychiatry of the agostino gemellithe population consisted of 18 women and 15 men with a mean age of 47.6 years . subjects were included if they 1 ) met diagnostic criteria for a major depressive episode according to diagnostic and statistical manual of mental disorders , fourth edition , text revision ( dsm - iv - tr ) , 2 ) had a baseline 21 - item hamilton depression rating scale ( hdrs - 21 ) score of 15 or higher ,13 and 3 ) had a condition of difficult - to - treat depression that , as determined by rush et al ,5 included both patients partially responding to at least a 5 - week open - label trial of an adequate dose of antidepressant monotherapy and those in whom a successful treatment is prevented by concomitant medical or psychiatric conditions . subjects who did not respond to two or more different classes of adequate antidepressant trials according to the classical definition of stage ii trd were excluded . other exclusion criteria were 1 ) a diagnosis of non - affective psychotic disorder , 2 ) a diagnosis of substance use disorders within the last year , 3 ) a diagnosis of dementia or other cognitive disorders , 4 ) electroconvulsive therapy ( ect ) within 1 year prior to enrollment , 5 ) recent history of suicide attempts , and 6 ) ocular disease ( glaucoma , cataracts , retinal detachment , retinopathy ) . subjects having general medical conditions or personality disorders affecting treatment adherence or tolerability were not excluded . the local ethics committee approved the study , and a written informed consent was obtained from all subjects . the psychopathological status was assessed by the same experienced rater blind to the week of study and the study design . at baseline , severity of mood disorder was evaluated with hdrs - 21 and mania rating scale ( mrs ) ; 14 in order to identify a specific antidepressant effect on depression core items , a secondary outcome measure , the six - item hamilton depression rating scale ( hdrs - 6 ) , was used .15 the snaithhamilton pleasure scale ( shaps ) 16 was used to assess anhedonia , whereas the depression retardation rating scale ( drrs ) 17 was used for psychomotor retardation . in order to evaluate treatment outcomes , hdrs - 21 , hdrs - 6 , and mrs were repeated at week 1 , week 3 , week 4 , and week 8 after onset of blt . responders were defined by a decrease of at least 50 % in the hdrs - 21 total score from baseline . autumn / winter and spring / summer were taken together as the two seasons with a shorter and longer photoperiod , respectively . blt was added to the ongoing medication treatment after recruitment , and nothing was altered in psychopharmacotherapy during the experiment . at baseline , all subjects were required to be on a stable dose of their psychotropic medication for at least 4 weeks prior to enrollment . unipolar patients were taking antidepressant drugs ( ademetionine , escitalopram , duloxetine , agomelatine , clomipramine , fluoxetine , citalopram , sertraline , amisulpride , nortriptyline , amitriptyline , and trazodone ) . bipolar patients were required to take at least one mood stabilizer , with the exception of a patient who was pregnant ( lithium carbonate , lamotrigine , and valproic acid ) . patients on lithium or valproic acid had plasma levels higher than 0.4 meq / l and 50 mg / ml , respectively . six bipolar patients were taking antidepressants ( duloxetine , agomelatine , nortriptyline , sertraline , venlafaxine , clomipramine ) . once enrolled , no change in the dosage of any psychotropic medication was allowed , and any photosensitizing medication was prohibited . ten patients took benzodiazepines ( up to 2 mg of lorazepam - equivalents per day ) or sleeping drugs ( zolpidem 510 mg or zaleplon 510 mg ) for insomnia . patients were instructed to undergo daily treatment in their own homes between 5.45 am and 8.15 am , for 3 weeks , and the regimen was carefully explained to each subject . the exact time schedule for light therapy sessions was defined following a predictive algorithm based on morningnesseveningness questionnaire scores .1822 according to most studies , we chose an exposure of 30 minutes at approximately 10,000 lx for 3 weeks . after the first week of treatment , partial or no responders were instructed to increase the exposure to 45 minutes / day for the next 2 weeks .23,24 light therapy was administered by means of the daylight simulator day - light classic model ( uplift technologies inc , nova scotia , canada ) . this device measures 31.8 cm 40.6 cm 7.6 cm , with a lens material of high - impact polycarbonate , 99.3 % uv filter , and three 36 w fluorescent light tubes of 4,000 k color temperature , with height - adjustable legs and two light intensity settings of 10,000 lx and 7,000 lx at 12 in ( 30.5 cm ) . subjects were instructed to place the box on a desk or tabletop at an angle of 15 , adjust the height so that the center of the box would be at eye level , and use the 10,000 lx . descriptive analyses were carried out using student s t - test , test , and the one - way or repeated - measures analysis of variance ( anova ) . assessment scale scores before and after treatment were compared using paired samples t - test or wilcoxon signed - ranks test . the trends in the mean scores in individual assessment scales and the influence of factor affecting course of symptoms were determined using repeated measures anova with multiple comparison correction ( bonferroni adjustment ) . comparisons of response rates between unipolar and bipolar patients and between seasons of treatment have been estimated using a 22 crosstab and test . all tests were two - tailed , and significance was set with an alpha value of 0.05 . data were analyzed using spss 15.0 ( spss 15.0 , chicago , il , usa ) . blt was added to the ongoing medication treatment after recruitment , and nothing was altered in psychopharmacotherapy during the experiment . at baseline , all subjects were required to be on a stable dose of their psychotropic medication for at least 4 weeks prior to enrollment . unipolar patients were taking antidepressant drugs ( ademetionine , escitalopram , duloxetine , agomelatine , clomipramine , fluoxetine , citalopram , sertraline , amisulpride , nortriptyline , amitriptyline , and trazodone ) . bipolar patients were required to take at least one mood stabilizer , with the exception of a patient who was pregnant ( lithium carbonate , lamotrigine , and valproic acid ) . patients on lithium or valproic acid had plasma levels higher than 0.4 meq / l and 50 mg / ml , respectively . six bipolar patients were taking antidepressants ( duloxetine , agomelatine , nortriptyline , sertraline , venlafaxine , clomipramine ) . once enrolled , no change in the dosage of any psychotropic medication was allowed , and any photosensitizing medication was prohibited . ten patients took benzodiazepines ( up to 2 mg of lorazepam - equivalents per day ) or sleeping drugs ( zolpidem 510 mg or zaleplon 510 mg ) for insomnia . patients were instructed to undergo daily treatment in their own homes between 5.45 am and 8.15 am , for 3 weeks , and the regimen was carefully explained to each subject . the exact time schedule for light therapy sessions was defined following a predictive algorithm based on morningnesseveningness questionnaire scores .1822 according to most studies , we chose an exposure of 30 minutes at approximately 10,000 lx for 3 weeks . after the first week of treatment , partial or no responders were instructed to increase the exposure to 45 minutes / day for the next 2 weeks .23,24 light therapy was administered by means of the daylight simulator day - light classic model ( uplift technologies inc , nova scotia , canada ) . this device measures 31.8 cm 40.6 cm 7.6 cm , with a lens material of high - impact polycarbonate , 99.3 % uv filter , and three 36 w fluorescent light tubes of 4,000 k color temperature , with height - adjustable legs and two light intensity settings of 10,000 lx and 7,000 lx at 12 in ( 30.5 cm ) . subjects were instructed to place the box on a desk or tabletop at an angle of 15 , adjust the height so that the center of the box would be at eye level , and use the 10,000 lx . descriptive analyses were carried out using student s t - test , test , and the one - way or repeated - measures analysis of variance ( anova ) . assessment scale scores before and after treatment were compared using paired samples t - test or wilcoxon signed - ranks test . the trends in the mean scores in individual assessment scales and the influence of factor affecting course of symptoms were determined using repeated measures anova with multiple comparison correction ( bonferroni adjustment ) . comparisons of response rates between unipolar and bipolar patients and between seasons of treatment have been estimated using a 22 crosstab and test . all tests were two - tailed , and significance was set with an alpha value of 0.05 . data were analyzed using spss 15.0 ( spss 15.0 , chicago , il , usa ) . two unipolar and four bipolar subjects dropped out ( 19 % of total sample ) : one ( unipolar ) patient had an incoming adverse event not related to treatment ( patient decided to stop blt after starting an antibiotic therapy for a toothache ) and five ( one unipolar and four bipolar ) patients did not comply with the treatment procedures ( not properly respecting wake - up time or instructions on light exposure ) . twenty - five patients ( 14 unipolar and eleven bipolar ) completed the 3 weeks of treatment ( figure 1 ) . , patients showed a moderate burden of depressive symptoms ( mean hdrs - 21 standard deviation = 19.54.4 ) , relevant psychomotor retardation ( score 10 on the drrs ) , and / or anhedonic features . no significant differences were observed at basal evaluation between unipolar and bipolar patients ( table 2 ) . depressive symptoms improved significantly during adjunctive blt in the overall study sample . a repeated - measuresanova determined that mean hdrs - 21 total scores significantly differed between time points ( f = 16.306 ; p 0.001 ) ( figure 2 ) . a bonferroni correction showed a statistically significant reduction in hdrs - 21 scores since the first week of therapy ( p = 0.001 ) . a statistically significant effect of time was observed since the first week on the hdrs - 6 scores , as well ( f = 14.875 ; p 0.001 ; bonferroni correction , p = 0.009 ) ( figure 2 ) . twenty - three patients received extra daily exposure of light ( shifting from 30 minutes to 45 minutes ) after first week of treatment , but this did not have an independent effect over the course of depressive symptoms ( f [ 2.719 , 62.538 ] = 0.964 ; p = 0.409 ) . during the overall treatment period , no significant changes were reported in mrs scores , and no patient presented clinical signs of a ( hypo ) manic switch . a repeated - measures anova determined that mean mrs total scores did not significantly change between time points ( f [ 2.804 , 56.087 ] = 2.025 ; p = 0.125 ) . although mrs scores increased in bipolar group , no statistically significant difference was found between time points ( wilcoxon signed - ranks test : z = 0.4921 ; p = 0.623 ) . after 1 week from blt discontinuation ( at week 4 of the study ) , seven patients ( 28 % ) showed a treatment response . after another month ( at week 8 of the study ) , they were still responders , and two more patients achieved this treatment outcome ( in total nine patients ; 36 % ) . as reported by hdrs - 21 scores , we observed a substantial clinical improvement , in both unipolar and bipolar groups ( figure 3 ) . although bipolar patients showed a more severe psychopathological burden throughout the treatment period , bipolarity did not seem to have an independent effect over the course of depressive symptoms ( f = 14.850 ; p = 0.826 ) . however , when considering differences between mean hdrs - 21 scores , unipolar patients showed a significantly better outcome as from week 3 until the end of the study ( figure 3 ) . at the end of the study , unipolar patients also showed a significantly better response rate than bipolar patients ( 8 and 1 , respectively ; = 6.173 ; p = 0.013 ) . in order to determine the role of other demographic , clinical , and treatment variables in the course of depressive symptomsconcerning season of treatment , at the end of follow - up , patients in the spring / summer season had a significantly higher remission rate ( hdrs score 8 ; = 4.427 ; p = 0.035 ) . we checked for confounding between type of depression and season of treatment , but no significant differences in uni - / bipolarity were found in the distribution of patients over spring summer and autumn winter ( = 1.924 ; p = 0.165 ) ( figure 4 ) . no significant changes in anhedonic features were observed at the end of the study in the overall sample ( wilcoxon signed - ranks test : z = 0.514 ; p = 0.607 ) . conversely , comparison of drrs scores at baseline and at the end of the study ( 14.59.3 and 8.16.8 , respectively ) showed a statistically significant improvement of psychomotor retardation ( wilcoxon signed - ranks test : z = 3.327 ; p = 0.001 ) . no statistically significant differences in shaps or drrs scores were found in comparing unipolar and bipolar patients ( table 2 ) . previous trials on the efficacy of chronotherapeutic interventions in treatment - resistant depressed patients mainly focused on the combined chronotherapeutic intervention25 ,26 or were mostly conducted during hospitalization .27 to the best of our knowledge , this is the first study addressing the blt augmentation of psychopharmacotherapy , not combined to other chronotherapeutics , in the management of dtd outpatients , including both bipolar and unipolar subjects . in our experience , this therapeutic approach appeared not only helpful but also simple and safe for such a vulnerable , still not well - studied , clinical population . our study also seems to confirm an improvement of depressive core symptoms during blt , as measured by hdrs - 6 subscale , supporting the hypothesis of its genuine antidepressant effect .7 significant changes in depressive symptoms were observed since the first week of therapy in keeping with previous findings on seasonal and nonseasonal depression .6,7,11 this improvement endured throughout the continuation phase , and all patients who responded to blt augmentation still maintained the favorable outcome after 5 weeks from blt discontinuation ; therefore , we supposed that blt augmentation in our patients could boost the antidepressant effect of ongoing treatment . according to previous observations in trd , more than one - third of our sample ( 36 % ) still showed a clinical response at the end of the study .25,26 although both unipolar and bipolar patients showed a substantial clinical improvement , the outcome and the maintenance of therapeutic benefits were significantly better in the unipolar group . up to date , only few trials on blt , not in combination with other chronotherapeutics , have specifically looked at patients with bipolar depression ,9,10 and their findings suggested that blt might also be helpful in nonseasonal bipolar depression .28 these results did not clearly emerge in our study , since unipolar patients showed a greater improvement ( as from week 3 ) and a significantly better response rate after week 8 ( eight unipolar vs one bipolar ) . more in general , blt appeared to be useful and safe for both unipolar and bipolar subjects , since none of our patients experienced side effects or ( hypo ) manic switches or significant changes in mrs scores . considering the effect of season of treatment on the course of illness , patients treated during springsummer period appeared to have a significantly better remission rate ( hdrs - 21 score 8 ) at the end of follow - up ( figure 4 ) . previous studies focusing on the role of the season in blt augmentation reported that during autumn and winter , blt timing early in the morning was associated with a better response in unipolar depressed patients , while during spring and summer , the clinical response was unrelated to blt timing during the day .18 according to our results , we hypothesized that the differences reported might have been influenced by seasonal changes of the photoperiod , with an increased daylight exposure during spring and summer extending the therapeutic benefit of blt . although our findings are in line with the previous observations in nonseasonal major depressed patients ,2931 they must be interpreted with caution because of the limitations of our study . first , the open - label design and the lack of a placebo or active control group might bias our results . therefore , we can not exclude that high response rates observed in our sample were partially driven by the placebo response , even if more severe depressed patients are less likely to show a placebo effect .3235 we tried to reduce observer bias and eventual halo effects by keeping the patient rater blind to diagnosis and treatment .36 another major limitation is the relatively small number of subjects recruited . finally , our results might also have been influenced in an unpredictable way by the psychometric evaluation that has not yet been specifically validated for trd .37 according to different psychopathological dimension analyses , anhedonic symptoms persisted after blt augmentation , regardless of clinical remission . this observation is in keeping with previous findings on anhedonic symptoms that are particularly difficult to treat38 and might predict a poor treatment outcome39 due to some possible dysfunctions in the neurobiological mechanisms of hedonic response and reward processing that may persist , irrespective of mood state40 and clinical changes .41 on the contrary , in our sample , blt augmentation led to a significant improvement of psychomotor retardation as reported by drrs score changes . this is in agreement with martiny et al who found that the retardation score ( item 8 of hdrs ) was the most sensitive item in discriminating the effect of blt compared to the placebo treatment group .7 accordingly , recent literature on parkinson s disease also shows a positive effect of blt not only on mood but also on motor function .4244 basal ganglia through a dysfunctional dopaminergic neurotransmission probably play a crucial role in pathophysiology of psychomotor changes of mood disorders .4548 striatal dopamine metabolism seems to be regulated by clock proteins , and stimulation of dopamine receptors affects the rhythm of expression of clock genes in the striatum .43,4951 dopamine also regulates the rhythmic expression of melanopsin in retinal ganglion cells , thereby influencing the entrainment of the circadian rhythm by light .52 although the mechanism of action is still unknown , our evidence might suggest a specific dopamine - increasing activity of blt . in conclusion , in our experience , blt augmentation appeared to be a simple , safe , well - tolerated , and low - cost strategy in outpatient settings , for both unipolar and bipolar patients . blt augmentation was particularly helpful for unipolar dtd patients adding the assumption that during autumn and winter , it might be necessary to increase the intensity of blt ( ie , longer exposure or more lux ) in order to achieve satisfying results . this augmentation strategy might also have a clinically significant influence on depressive core symptoms and on psychomotor retardation , a key feature of depression suggesting a specific dopamine - increasing activity of blt . these preliminary findings deserve further investigation in this complex clinical population who requires tailored combined treatment approaches . when considering the major limitations of our study , these results need to be confirmed in placebo - controlled , randomized , double - blind clinical trial on a larger sample .\noutput:\n" }, { "from": "agent", "value": "objectiveswe investigated the clinical benefits of bright light therapy ( blt ) as an adjunct treatment to ongoing psychopharmacotherapy , both in unipolar and bipolar difficult - to - treat depressed ( dtd ) outpatients.methodsin an open - label study , 31 depressed outpatients ( 16 unipolar and 15 bipolar ) were included to undergo 3 weeks of blt . twenty - five completed the treatment and 5 - week follow - up.main outcome measuresclinical outcomes were evaluated by the hamilton depression rating scale ( hdrs ) . the snaith hamilton pleasure scale and the depression retardation rating scale were used to assess changes in anhedonia and psychomotor retardation , respectively.resultsthe adjunctive blt seemed to influence the course of the depressive episode , and a statistically significant reduction in hdrs scores was reported since the first week of therapy . the treatment was well - tolerated , and no patients presented clinical signs of ( hypo ) manic switch during the overall treatment period . at the end of the study ( after 5 weeks from blt discontinuation ) , nine patients ( 36 % , eight unipolar and one bipolar ) still showed a treatment response . blt augmentation also led to a significant improvement of psychomotor retardation.conclusionblt combined with the ongoing pharmacological treatment offers a simple approach , and it might be effective in rapidly ameliorating depressive core symptoms of vulnerable dtd outpatients . these preliminary results need to be confirmed in placebo - controlled , randomized , double - blind clinical trial on larger samples ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the present issue of critical care features a publication by min tan and colleagues from the affiliated hospital of north sichuan medical college in china on the use of probiotics in severe traumatic brain injury patients . critically ill trauma patients have many reasons to develop infectious complications when admitted to the icu . trauma causes a massive inflammatory response during which a first phase dominated by pro - inflammatory cytokines is follow by a second phase of immunosuppression in which anti - inflammatory cytokines prevail ( immunoparalysis ) . trauma in many cases disrupts the mechanical barriers that prevent micro - organisms from entering the body . of perhaps even greater impactprobiotics have the potential to reduce the infectious complications of these patients because they can limit the mucosal barrier dysfunction and regulate the balance of cd4effector t lymphocytes . because probiotics are , by definition , live bacteria , there has been hesitation in using them for critically ill patients . bynow , many studies have demonstrated the safety of probiotics for a variety of clinical conditions maybe with the exception of acute pancreatitis complicated by multiorgan failure [ 4 - 6 ] . the efficacy of probiotics for critically ill patients is debated because both positive as well as negative results have been published . with regard to the prevention of ventilator - associated pneumonia in critically ill patients admitted to the icu , morrow and colleagues reported a positive effect , while in the study of barraud and colleagues no effecttan and colleagues now present the results of a pilot study on the immunomodulatory as well as clinical effects of a multispecies probiotic preparation in patients with severe brain trauma . their study is important because it is the first one in this patient category that includes biomarkers of the immune system . trauma itself is known to cause a depression of the t helper 1 ( th1 ) cytokines il -12 p70 , and interferon - . il - 12 is the major th1 driving cytokine while interferon - potentiates cellular immunity as well as macrophage function . during the first weekno differences in cytokine levels were found between the intervention and control groups , but afterwards , il - 12 p70 , and interferon - returned to normal faster in the probiotics group . serum levels of il - 6 and c - reactive protein at days 15 to 21 were lower in the probiotics group . the probiotics significantly reduced the length of icu stay ( from 10.7 to 6.8 days ) . they also reduced the frequency of ventilator - associated pneumonia ( from 68 to 44 % ) and mortality ( from 19 to 11 % ) , but with a relatively small group size the study was underpowered to detect differences in these outcome parameters . larger , preferably multicenter studies are now needed to confirm these encouraging results . for those studies it will also be important to decide on the choice of probiotics . not all probiotics are the same - in fact , they are all different . even between different strains of the same species considerable differencesmay exist . in the study of morrow and colleagues , lactobacillus rhamnosus gg ( lgg ) was used in a dose of 210colony forming units ( cfu ) per day . barraud and colleagues used a multispecies preparation consisting mainly also of lgg as well as lactobacillus casei , lactobacillus acidophilus , and bifidobacterium bifidum in a total dose of 210cfu per day . the multispecies combination of tan and colleagues was composed mainly of bifidobacterium longum as well as lactobacillus bulgaricus and streptococcus thermophilus and was used at a total dose of 10cfu per day . maintenance ( or even improvement ) of th1 cytokine - mediated immune functions can be of decisive importance for severe trauma patients . probiotics selected to fulfill that function may therefore be optimally suited to support the clinical outcome of this category of patients .\noutput:\n" }, { "from": "agent", "value": "probiotics are live micro - organisms with a health promoting effect . because of their immunomodulating capacity as well as improvement of gut barrier function , probiotics have the capacity to prevent infectious complications in a variety of clinical settings . now selected probiotics show potential for improving the clinical outcome of severe trauma patients ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: study area and experiment animals : this study was conducted on 5 pregnant asian elephants which were domesticated in a semi - captive condition in the ayuttaya elephant palace camp in pranakornsri - ayuttaya province , thailand . all elephants in this study were chosen randomly from a mixed group . they varied in age between 21 and 37 years , had no reproductive problems and had not calved for at least 3 years previously . the animals were habituated to humans and used for tourist treks outside of the camp in the early morning or late afternoon . they were brought back to the camp for forage and supplementary feeding each evening . during their working period , they were given a variety of foods , such as banana , sugar cane and hay from tourists . in addition , they had access during this time to water ad libitum and natural grass . in camp , the elephants were divided into different groups according to age ( calves , sub - adult , adult and old adult ) . the cows were separated from the bulls except during the breeding period . during this time , the bulls were walked to detect estrus for 30 to 60 min , 3 to 5 times per week in the early morning . when the cows were found to be in standing heat , they were allowed to mate until , they refused mounting . pregnancy diagnosis was determined monthly by transrectal ( linear transducer ; 5.0 to 12.0 mhz ) and transabdominal ( convex transducer ; 2.0 to 8.0 mhz ) ultrasonography scanning ( model medison portable ultrasound machine ; version sonoace r3 , samsung medison co. , ltd . , california , u.s.a . ) between the 2nd and the 4th month after the last mating . under their general management schedule , the elephants were dewormed and looked after by a veterinarian from the elephant camp . these experiments were approved by the animal care and use committee , faculty of veterinary medicine , mahanakorn university of technology , nong - chok , bangkok , thailand ( project : vet - mut008 / 2553 ) . sample collection : blood and feces samples were collected monthly during the pregnancy period ( beginning 30 days after the last mating ) for routine progestagen ( progesterone hormone and its metabolite ) and glucocorticoid hormones and their metabolites analysis . the samples were collected twice a day ( around 7.00 to 9.00 am and 16.00 to 18.00 pm ) , one day per month from each of the five pregnant elephants . blood samples of around 10 ml were collected from the ear vein , while the cows were controlled by a mahout . blood samples were kept for 8 to 16 hr at 4c in a sealed box with ice packs , while the blood was transported to a laboratory . in the laboratory , the blood samples were centrifuged for 5 min at 1,500 g. the serum was collected and stored at 20c until analysis . the fecal samples were collected from each elephant on the same day as the blood samples , 1 hr after blood sample collection . the fecal samples were taken from the rectum or chosen from the middle of a bolus of freshly dropped feces and were approximately 50 g. fecal samples were packed in resealable plastic bags and kept for 8 to 16 hr at 4c in a sealed box during transport and then stored at 20c until analysis . serum and fecal hormone analysis : serum and fecal progestagens , cortisol , corticosterone hormones and their metaboliteswere analyzed by enzyme immunoassay ( eia ) at conservation research and animal health , khao - kheow open zoo , cholburi province , thailand . serum , feces extraction and eia analysis were conducted following the standardized protocol used by brown et al . . the concentrations of progestagen were determined using monoclonal antibody ( dilution 1:10,800 ; quidel clone no .425 ; supplied by coralie munro ( cm ) , university of california ( uc ) davis , ca , u.s.a . ) against 100 % progesterone hormone and cross - reacted with various progesterone metabolites . horseradish peroxidase ( hrp ) conjugated antibody was used on already treated and visualized progestagens ( dilution 1:60,000 ; supplied by cm , uc davis ) which were examined with a elisa plate reader ( tecan sunrise absorbance reader ; tecan austria gmbh , grdig , austria ) for quantitative progesterone detection by comparison with progesterone standard levels . the sensitivity of this assay was 0.02 ng / ml , and the inter - assay coefficients of variation ( cv ) for high and low concentration controls were 9.39 % and 10.22 % , respectively . the intra - assay cv for high and low concentration controls were 5.12 % and 4.57 % , respectively . cortisol hormone and its metabolite assays used polyclonal cortisol antiserum ( dilution 1:8,500 ; quidel clone no . r4866 ; supplied by cm , uc davis ) , against cortisol -3-carboxymethyloxime , linked to bovine serum albumin and cross - reacted with cortisol ( 100 % ) , prednisolone ( 9.9 % ) , prednisone ( 6.3 % ) , cortisone ( 5 % ) and 0.1 % with androstenedione , androsterone , corticosterone , desoxycorticosterone , 11 - desoxycortisol , 21 - desoxycortisone and testosterone . the horseradish peroxidase ( hrp ) conjugated antibody was labeled cortisol ( dilution 1:20,000 ; supplied by cm , uc davis ) , and the use of the elisa plate reader was for quantitative cortisol detection by comparison with cortisol standard levels . the sensitivity of this assay was 0.08 ng / ml . the inter - assay cv for high and low concentration controls and the intra - assay cv for high and low concentration controls were 8.23 , 8.28 , 4.75 and 4.93 % , respectively . corticosterone hormone and its metabolite assays were conducted by using polyclonal corticosterone antiserum ( dilution 1:30,000 ; quidel clone no . cjm06 ; supplied by cm , uc davis ) , 100 % binding with corticosterone hormone and cross - reacted with 14.25 % desoxycorticosterone and 0.9 % tetrahydrocorticosterone ( cm , uc davis ) . the horseradish peroxidase - conjugated antibody was labeled corticosterone ( dilution 1:40,000 ; supplied by cm , uc davis ) and used with the elisa plate reader for quantitative corticosterone detection . the sensitivity of this assay was 0.08 ng / ml . the inter - and intra - assay cv for high and low concentration controls were 8.56 , 9.82 , 5.81 and 6.08 % , respectively . statistical analysis : correlations between serum and fecal progestagens , cortisol and their metabolites and corticosterone and their metabolites were analyzed using spearman s correlation test , using spss ( spss 10.0 for windows , spss inc . two of the pregnant elephants calved at about 21.5 months , and the other 3 pregnant elephants gave birth after approximately 22 months within 2 to 7 days after the last blood and feces samples collection ( last sample collections were at day 21 of the 22nd month ) . the average serum progestagen concentration profile during gestation in all pregnant elephants was 12.083.87 ng / ml . overall , mean serum progestagen gradually rose from the 1st month to the 4th month and then slightly decreased in the 5th month of pregnancy ( fig . 1fig .1 . the mean ( sd ) of serum and fecal progestagens concentration level profiles in asian elephants during pregnancy ( 22 months ) . ) . after this , it increased rapidly from over 12 ng / ml in the 6th month to a peak concentration of 18.442.28 ng / ml in the 11th month ( mid - gestation ) . it remained 12 ng / ml until the 18th month and then began to decline to its lowest level ( 2.110.60 ng / ml ) in the 22nd month shortly before parturition ( 2 to 7 days ) . fecal progestagen concentration varied from 1.180.54 to 3.350.45 g / g with an average of 2.500.71 g / g during pregnancy until the prepartum period and was highest during the 12th month ( mid - gestation ) of pregnancy ( fig . 1 ) . fecal progestagen levels showed a significant positive correlation with serum progestagen in all five asian pregnant elephants ( r = 0.88 , p 0.001 , table 1table 1 . correlations between serum and fecal progestagens , cortisol and their metabolites and corticosterone and their metabolites analyzed using spearman s correlation testcorrelation between hormone sortscorrelation coefficient ( r ) p - valueserum and fecal progestagens0 .8800.001 serum corisol and fecal cortisol metabolite0 .1790.425 serum corticosterone and fecal corticosterone metabolite0 .4870.021 serum progestagen and serum cortisol0 .7190.001 serum progestagen and serum corticosterone0 .2060.357 serum cortisol and serum corticosterone0 .4380.042 fecal progestagen and fecal cortisol metabolite0 .0910.687 fecal progestagen and fecal corticosterone metabolite0 .0570.801 fecal cortisol metabolite and fecal corticosterone metabolite0 .6050.003 ) . in a pattern similar to serum progestagen , fecal progestagen rose slowly from the 1st month to the 4th month and then decreased a little in the 5th month of pregnancy . fecal progestagen remained higher than 3 g / g from the 7th until the 15th month and then declined rapidly to reach its lowest level in the 22nd month of pregnancy ( on average 2 to 7 days before calving ) . the mean ( sd ) of serum and fecal progestagens concentration level profiles in asian elephants during pregnancy ( 22 months ) . the serum cortisol concentration profile during gestation in all five pregnant elephants was 6.052.48 to 18.545.73 ng / ml ( averaging 9.102.72 ng / ml ) . overall , serum cortisol concentrations remained relatively stable almost the whole period from the 1st month to the 20th month of pregnancy and then rapidly increased until parturition ( fig .2 . the mean ( sd ) of serum cortisol and fecal cortisol metabolite concentration level profiles in asian elephants during pregnancy ( 22 months ) . ) . the fecal cortisol metabolite concentration level ranged from 10.32.74 to 20.683.09 g / gin general , fecal cortisol metabolite concentration levels fluctuated from the 1st to the 21st months of pregnancy and then rose to reach a peak in the 22nd month of pregnancy ( fig . serum cortisol concentrations showed no significant correlation with fecal cortisol metabolite levels in all five asian pregnant elephants ( table 1 ) . serum corticosterone concentration levels during gestation in all 5 pregnant elephants ranged from 1.420.63 to 12.352.21 ng / ml ( averaging 4.772.67 ng / ml ) , and fecal corticosterone metabolite concentrations varied from 64.8126.45 to 127.0729.04 g / g ( averaging 95.4415.76 g / g ) . generally , both serum corticosterone and fecal corticosterone metabolite concentrations fluctuated almost the whole period from the 1st month to the 20th month of pregnancy and then reached a peak in the last month of the gestation period ( fig . 3fig .3 . the mean ( sd ) of serum corticosterone and fecal corticosterone metabolite concentration level profiles in asian elephants during pregnancy ( 22 months ) . ) . serum corticosterone and fecal corticosterone metabolites concentration levels showed a significant positive correlation ( table 1 ) . the mean ( sd ) of serum cortisol and fecal cortisol metabolite concentration level profiles in asian elephants during pregnancy ( 22 months ) . the mean ( sd ) of serum corticosterone and fecal corticosterone metabolite concentration level profiles in asian elephants during pregnancy ( 22 months ) . the present study obviously demonstrated that serum glucocorticoid and fecal glucocorticoid metabolite concentrations in the last month of pregnancy ( the 22nd month ) archived their peak levels , while progestagens were in their lowest levels . these results could be specifically explained by the fact that serum and feces collections in the last period of pregnancy were done shortly ( 2 to 7 days ) prior to parturition . our findings were similar to a previous report , in that the dramatically increased serum cortisol and the sharply decreased progestagens levels around 5 days before calving and the highest serum cortisol and the lowest serum progestagens levels were observed on the day of parturition . brown and lehnhardt reported a gradual decline of serum progesterone and an increase of cortisol concentrations during the last month of gestation in asian elephant . thereafter , 2 days before parturition , the serum progesterone was obviously decreased to non - detectable levels , while the serum cortisol concentrations increased to reach the peak on the day of parturition . for fecal glucocorticoid metabolites and progestagens , our results did not agree with the other study by foley et al . who presented that the fecal corticoid metabolites pursued fecal progestagens during periparturition until postpartum if a dietary effect of seasonal changes was responded in free - ranging african elephants . in our study , the elephants were domesticated in semi - captive condition which they were fed with optimal diets . in addition , the high glucocorticoid concentrations could be due to a calving stress response resulting in increased concentration levels in serum and feces shortly before parturition . this means that measuring serum or fecal glucocorticoid concentration levels as an indicator of stress could be used to monitor the progestagen profile indirectly in the short period of periparturition . however , the prediction of parturition required more frequent sample collections during the last month of gestation period . although the number of elephants ( 5 pregnant elephants ) and the frequency of sampling collections ( 1 day per month ) were limited , the present study could demonstrate a gestation length of 21.5 to 22 months , similar to that found by other studies . there would be only a minimal disruption of the pregnant elephant s habitat and working routines . the monthly samplings , however , were carried out twice a day in order to increase the sample number and reduce the possibility of error in the hormone concentration levels readings . the serum progestagen concentration profile in our study was similar to the serum concentration profiles of progesterone , 5 - p - 3oh and 5 - dhp ( progesterone metabolites ) in pregnant african elephants that were reported previously . moreover , the serum progestagen concentration profile in our research could indicate that luteal activity was at its highest level in mid - gestation ( in order to maintain pregnancy ) and then declined to its lowest level from 7 to 2 days prior to calving , which is supported by the serum progesterone concentration profiles of pregnant elephants found in other studies . the average fecal progestagen concentration in this study was lower than the 5 - p - 3oh ( major progesterone metabolite in elephant feces ) concentration that was found previously . that study used a 100 % specific antibody , while our study used a 64 % specific antibody with 5 - p - 3oh ( monoclonal antibody quidel clone no .425 ) . however , the fecal progestagen concentration profile in this study was quite similar to the fecal progesterone , 5 - p - 3oh and 5 - dhp concentration profiles found in a previous study of pregnant african elephants . a significant positive correlation with serum progestagen concentrations could mean that high concentration levels of progesterone in serum during pregnancy are excreted mainly in the form of progesterone metabolites in feces . if so , assays of fecal progesterone metabolites could be useful as an indicator of luteal activity for assessing the pregnancy status of asian elephants according to other studies . glucocorticoid hormones ( cortisol and corticosterone ) were measured to evaluate stress responsiveness in the elephants in this study . it was found that the serum cortisol concentration profile was relatively similar to a previous study . fecal cortisol metabolite concentration levels during pregnancy in our study , however , were lower than the levels in the pregnant african elephants reported previously . normally , serum glucocorticoid ( cortisol and corticosterone ) hormone is rapidly and extensively changed into the form of metabolites before excretion in feces . therefore , the correlation between serum cortisol and fecal cortisol metabolites should be positive . but , serum cortisol and fecal cortisol metabolite concentration patterns in this study showed no significant correlation ( table 1 ) . this could be because the polyclonal antiserum used in this study ( r4866 ) had a limited cross - reactivity with 10 % fecal cortisol metabolites . this could cause a reduction in the detection of fecal cortisol metabolites and help account for the lack of correlation between these concentration levels and those of serum cortisol . in this study , however , there were significant positive correlations between serum corticosterone and fecal corticosterone metabolites and serum cortisol and corticosterone and fecal cortisol metabolites and corticosterone metabolites ( table 1 ) . the average fecal corticosterone metabolite concentration was about 7 times higher than the fecal cortisol metabolite concentration during gestation in all five pregnant elephants . an increase of corticosterone metabolites concentrations in feces during pregnancy was also reported previously . our research found that serum progestagen was negatively correlated with serum cortisol and an inclination ( non significant ) with serum corticosterone according to meyer et al . . furthermore , in our study , fecal progestagen did not correlate with fecal glucocorticoid that it was different from a previous study which showed a positive correlation in african elephants . one explanation could be that our study had a relatively low sampling frequency ( twice a day and one day a month ) . a second explanation could be that glucocorticoid metabolite concentrations are significantly correlated with season . they are highest in the dry season , but our research did not control for dry season influences . moreover , excited or stressful behavior of elephants during pregnancy could lead to an increase in glucocorticoid levels which , in turn , could cause abortion or parturition according to dobson and smith . in conclusion of our study , it was found that during pregnancy , the progestagen level increased and only returned to low levels in the short period before calving . the glucocorticoid level , in contrast , fluctuated from low to medium throughout the pregnancy up until the last month shortly before calving when it increased dramatically . these findings may help for evaluating and managing the pregnancy status and stress condition in order to decrease the rate of fetal loss and predicting parturition in asian elephants .\noutput:\n" }, { "from": "agent", "value": "abstractthe study was to find patterns of progestagen ( progesterone and its metabolite ) and glucocorticoid and their metabolite concentrations in serum and feces of pregnant asian elephants ( elephas maximus ) . the 5 female asian domestic elephants were naturally mated until pregnancy . after that , blood and feces samples were collected monthly during pregnancy for progestagen , glucocorticoid and their metabolites analysis by enzyme immunoassay ( eia ) . the results showed the serum progestagen concentration during gestation was 2.11 0.60 to 18.44 2.28 ng / ml . overall , serum progestagen concentration rose from the 1st month to reach peak in the 11th month , after which it declined to its lowest level in the 22nd month of pregnancy . fecal progestagen concentration varied from 1.18 0.54 to 3.35 0.45 g / g during pregnancy . in general , fecal progestagen concentration increased from the 1st month to its highest level in the 12th month . after this , it declined reaching its lowest point in the 22nd month of pregnancy . glucocorticoid hormones and their metabolite concentrations both in serum and feces fluctuated from low to medium throughout almost the entire pregnancy period and then rapidly increased around the last week before calving . our study suggests that this profile of progestagen and glucocorticoid hormones and their metabolite concentration levels in serum and feces can be used to assess the pregnancy status of asian elephants . if serum and fecal progestagen concentrations were found in very low levels and glucocorticoid and their metabolite concentrations were found in very high levels , it was indicated that the cow elephant would calve within 7 days ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: infection with dengue virus ( denv ) causes dengue and severe dengue ( formerly dengue fever and dengue haemorrhagic fever ) . denv is an enveloped virus , and its genome consists of a positive polarity , single - stranded rna of around 11 kb that encodes ten proteins . denv can replicate in several types of cells , including dendritic cells , b and t lymphocytes , endothelial cells , hepatocytes , and neuronal cells . however , monocytes / macrophages are the primary target during in vivo infection . viral entry into these cells enables the virus to spread to different tissues and induces the presentation hla molecule - associated viral antigens . the presentation of viral antigens by macrophages to memory t cells induces t cell activation and , consequently , the proliferation and production of cytokines such as tnf - , ifn , and il - 2 . this set of cytokines and chemokines induces endothelial dysfunction and plasma leakage , both of which are characteristic of more severe manifestations of the disease . several studies have addressed the relationship between human genes and the susceptibility to dengue virus infection . for example , the hla - a * 0203 allele correlated with dengue fever ( df ) in thai children , while hla - a * 0207 correlated with dengue haemorrhagic fever ( dhf ) . moreover , the alleles hla - b44 , b62 , b76 , and b77 confer protection against dhf in secondary infections . other polymorphisms associated with dhf have been found in the genes for dc - sign1 , tnf - , fc - receptors , vitamin d receptors , and mannose binding lectin . in addition to these host factors , there is evidence that denv serotypes 2 and 3 cause dhf more frequently , supporting the belief that both host and virus factors can affect the clinical outcome of patients . recent studies have identified the oligoadenylate synthetase 1b ( oas1b ) gene as being responsible for susceptibility / resistance to west nile virus ( wnv ) infection in mice , and it is therefore a potential candidate gene for the flv locus . these seminal works found a non - sense mutation ( c820 t ) in the oas1b gene , exon 4 , that was linked to susceptibility to wnv infection . this mutation replaces an arginine with a stop codon , producing a truncated protein lacking the c - terminal domain . knock - in of a normal oas1b allele induced resistance to yellow fever virus infection in a susceptible mouse strain , which was comparable to the resistance observed in resistant congenic mice . these results led to the conclusion that the oas1b gene conferred resistance against flavivirus infection . however , a neuronal cell line expressing the complete form of the oas1b protein showed only a slight reduction in virus yield and was not significantly different from the same neuronal cell line expressing the truncated form . likewise , transfecting cdna from the complete oas1b gene into susceptible embryonic fibroblasts did not induce a complete reversion to the resistant phenotype . together , these results suggest that murine resistance to flavivirus infection is not completely understood in vitro and that other cellular and animal models should be studied . this work evaluated the permissiveness to denv infection and evaluated the presence of the c820 t polymorphism in the oas1b gene obtained from different rodent species , including three strains of mouse , rat , hamster , and guinea pig . experiments with animals were approved by the universidad el bosque 's ethics committee following the national legislation . different 68 - week - old rodent species were used and were obtained from the colombian national institute of health 's animal facility . the animals used were balb / c inbred mice ( mus musculus ) , nih swiss outbred mice , cd1 ( icr ) swiss outbred mice , syrian hamsters ( mesocricetus auratus ) , wistar rats ( rattus norvegicus ) , and hartley strain guinea pigs ( cavia porcellus ) . two millilitres of 1.5 % carboxymethylcellulose was injected intraperitoneally into two animals from each species and this was done twice in different days . after 48 hours , the animals were euthanized , and a peritoneal wash was made with rpmi 1640 medium plus 10 % foetal bovine serum , 100 u / ml penicillin , 10 g / ml streptomycin , and 2,5 g / ml amphotericin ( complete medium - cm ) . the medium was collected and centrifuged , and the cell pellet was then suspended in cm . then , 200,000 cells were seeded into 12 - well culture dishes and 10,000 cells were seeded in 24 - well culture dishes using round glass coverslips . nonadherent cells were removed 48 hours later , and the culture of adherent cells continued for a further 5 days to allow for cytokine clearance . the virus was obtained by infecting c6 / 36 ht cells with a denv serotype 2 ( col - 789 ) isolate donated by dr . jairo mndez from the colombian institute of health 's virology group and titrated on llcmk - 2 cells . the virus was placed in contact with the macrophages for 1 hour at 37c at a multiplicity of infection ( moi ) of 1 and 0.1 ; it was then removed , fresh medium was added , and the cells were kept for 24 , 48 , and 72 hours , at which time they were processed . a capsid gene fragment amplified from denv2 rnawas used to construct a plasmid as published previously , and a dilution having 10 copies / l was prepared . rna was extracted from infected and uninfected macrophage supernatants and monolayers using trizol ls and trizol reagents , respectively , ( invitrogen ) and reverse - transcribed using the m - mlv enzyme and random primers . the sybr green and the geneamp 5700 sequence detection system ( perkin - elmer corporation ) were used for the real - time pcr assay . a denv capsid gene fragment was amplified using dv2c - l and dv2c - r primers . samples lacking cdna were used as negative controls , and cdna obtained from viral inoculums was used as positive controls . the data obtained from the monolayers were analysed using the relative quantification method based on the assumption of ideal amplification efficiency with a doubling product every cycle , followed by twofold changes in fluorescence intensity ( which could be calculated using the 2 formula ) and - actin as the housekeeping gene . absolute quantification was used for analysing the data obtained from the supernatants by producing a six - point standard curve ( 1010 copies / l ) from the pdv2core plasmid ( 1010 molecules ) that was obtained as previously described . this curve was simultaneously processed with the samples and evaluated 24 , 48 , and 72 hours p.i . data were analysed using anova and a least significant difference post hoc test and p 0.05 was considered significant . two independent experiments were done , and two animals were used from each species in each one . independent duplicates of cells were seeded for each animal ( n = 8 ) ; each sample was processed by duplicate in qpcr experiments . infected and noninfected cells were fixed with 4 % paraformaldehyde for the same defined periods and then permeabilised with 0.1 % triton x-100 . infected cells were detected by using monoclonal antiflavivirus antibody ( chemicon , mab8744 ) . biotinylated anti - mouse igg antibody was used as the secondary antibody and detected with peroxidase - coupled streptavidin , and 0.05 % diaminobenzidine and 0.01 % h2o2 were used as the developing reagents . other cultures were incubated with biotinylated dutp and the tdt enzyme for detecting dna fragmentation ( as an apoptotic indicator ) ; after being washed , samples were incubated with cy3 - coupled streptavidin . one - way anova was done , and when the overall anova resulted in a p value less than 0.05 , least significant difference ( lsd ) test was carried out for comparing infected cell counts and values from viral rna quantification . brain dna was obtained from each rodent species using phenol / chloroform extraction and precipitated with sodium acetate and ethanol . this dna was used to amplify an oas1b gene exon 4 fragment using oas - 1br : 5 - ctg gga gta tgg gag tcg ag - 3 and oas - 1bl : 5 - gct gtt ggt gca ggt att ca - 3 primers , which amplify the gene region between nucleotides 771925 . the number of viral copies released by the macrophages into the supernatant was quantified by real - time pcr analysis of the rna obtained from the supernatant of cells infected for 24 , 48 , and 72 hours at two different mois . figure 1 ( a ) shows that the viral copy number obtained from balb / c - derived macrophage supernatants infected with denv at an moi of 0,1 in all post - infection ( p.i . ) times was 425 times larger than that obtained from nih - and icr - derived mouse macrophages . the differences in the number of viral copies were significant at 24 and 48 hours p.i . ( p 0.01 ) , while the number of viral copies obtained in balb / c - derived macrophages was similar to that obtained in nih - and icr - derived mouse macrophages at 72 hours . similar findings were established in macrophages from taxonomically different rodent species , such as rats , hamsters , and guinea pigs , where highly significant differences were found ( p 0.01 ) . when the macrophages were infected at an moi of 1 ( figure 1 ( b ) ) , significant differences were observed 24 hours p.i . when balb / c donors were compared to nih mice , hamsters , and guinea pigs ( p 0.01 ) . no difference in the viral copy number were found in the supernatants at 48 and 72 hours p.i . a larger number of viral rna copies were found in balb / c - derived macrophage supernatants from cells infected with an moi of 0.1 than with an moi of 1 ( figure 1 ( a ) versus figure 1 ( b ) ) . there were no differences among viral copies when the infection was carried out at an moi of 0.1 or 1 in the other animals ( p 0.05 ) . relative rna viral quantitation was carried out from macrophage monolayers and showed that the amount of virus found in cells was proportional to the amount of virus released to the supernatant . the relative viral rna quantity was significantly larger in balb / c macrophages , from 4-fold ( balb / c versus hamster ) to 5400-fold ( balb / c versus icr ) higher at an moi of 0,1 , and from 4-fold ( balb / c versus hamster ) to 8100-fold ( balb / c versus icr ) at an moi of 1 ( p 0.05 , see figure 2 ) . differences in relative expression levels were much more marked than the differences found in the absolute quantification of the supernatants . the data obtained from the other rodent species did not reveal any significant differences when comparing different mois , nor when comparing the three p.i times . with the exception of the lower relative viral rna levels found in nih mouse macrophages , the levels of viral rna tended to decrease as the p.i . immunocytochemistry was used to detect viral antigens in macrophages from the six different rodent species studied . as previously described , specific immunoreactivity was observed that corresponded to viral antigens in the infected cell cytoplasm ( having punctiform characteristics ) in the perinuclear region . a significantly larger number of infected macrophages was found in balb / c - derived macrophages compared with other rodent macrophage cultures ( figure 3 ( c ) ) . approximately 43 % of the macrophages from balb / c mice inoculated with an moi of 1 showed evidence of infection 24 hours p.i . ; an 81 % infection of macrophages was reached at an moi of 0.1 , but only at 72 hours p.i . infection percentages were much lower in cells from the other animals ( see table 1 ) . a large number of positively stained extracellular vesicles were also observed in balb / c - derived macrophages ( figure 3 ( b ) ) , but they were not observed in macrophages from other species ( figure 3 ( c ) ) . macrophages inoculated with denv at an moi of 1 presented a high percentage of dna fragmentation , as demonstrated by tunel . other than balb / c , the percentage of tunel - positive cells was similar to that found in control cells that had not been infected with denv ( table 1 ) . an interesting finding was that the apoptotic percentages in macrophages from balb / c mice inoculated with denv at an moi of 0,1 did not correlate with the percentages for denv - positive cells . while 79 % of the cells had become infected 48 hours after - infection , only 8 % were apoptotic ; the same phenomena occurred at 72 hours ( 81 % versus 5 % ) . analysing the sequences from the oas1b gene exon 4 fragment obtained from balb / c mouse genomic dna revealed that they were consistent with those reported previously . the tga stop codon mutation inserts a premature translation stop in the oas1b gene in these mice . interestingly , the other rodent species analysed also had the c820 t mutation , which leads to the translation of a truncated protein in all cases . the sequences from this oas1b fragment from guinea pigs , hamsters , and nih and icr mice had not been previously identified and were reported to genbank ( cavia porcellus accession number ef081023 , rattus norvegicus accession number ef081022 , mus musculus nih strain accession number ef081021 , mus musculus icr strain accession number ef081020 , mesocricetus auratus accession number ef081019 , mus musculus balb / c strain accession number ef081018 ) . genetic markers for host susceptibility to infection could provide answers for questions concerning why not all individuals infected by denv become ill and why they do not all have similar symptoms if they do become ill . the clinical manifestations of dengue virus infection range from undifferentiated fever to severe systemic compromise , encephalitis , and haemorrhagic syndrome . the reason why infection with denv ( and the flavivirus in general ) causes clinical manifestations in only a small percentage of infected individuals remains unknown . however , it has been suggested that the host 's genetic factors could be involved . the resistance of some mice strains to infection by some flavivirus has been described since the beginning of the twentieth century ( reviewed in ) , and it was initially found that flavivirus resistance to infection was inherited as a dominant trait . it is known that the monocyte / macrophage system is the primary in vivo cellular target for denv , and the peritoneal macrophage model has also been used to study flavivirus resistance and susceptibility . in this work , it was found that macrophages from balb / c mice had higher permissiveness to denv2 infection using qpcr and immunocytochemistry . sequence analysis of the oas1b gene demonstrated that all four rodent species studied had the c820 t mutation , leading to the supposition that the production of a truncated protein by this genotype does not affect denv susceptibility . with the exception of balb / c mice , all rodent strains and species of macrophages studied have a low capacity to support denv2 replication because infection with the virus did not cause large amounts of rna to assemble or be released as virions . this finding could contradict the suggestion of a protective mechanism involving viral packaging , as has been previously proposed . the results found in nih mouse - derived macrophages could suggest that these cells not only have a cellular mechanism that reduces permissiveness but also have a more efficient viral clearance process . nevertheless , it is important to clear that these results are only relevant for dengue virus serotype 2 ; it is probable that different results could be found for other dengue serotypes . like other studies , we did find more viral copies in supernatants in any of the cultures that had been inoculated with an moi of 0.1 relative to those with an moi of 1 . brinton suggested that this finding could be due to the presence of defective interfering ( di ) particles found in greater amounts at a higher moi . the production of di particles could be facilitated by some mechanism in resistant cells , while highly susceptible cells will mainly produce infectious virus . in turn , this higher virus production leads to greater cell death in highly susceptible cells . the theory is supported by the work done by espina et al . , who used human monocytes as their model . despite the infected cell percentage in balb / c - derived macrophages is similar with both mois , infection at an moi of 1 induced a significantly higher number of tunel - positive cells . it seems that the infection of cells with a high moi activates proapoptotic molecular routes as a mechanism to block viral replication and dissemination during viral infection , thereby explaining this finding . however , the virus could be activating anti - apoptotic routes at a low moi and improving cell survival . it has been previously established that denv induces apoptosis in different cell types ( e.g. , endothelial cells , hepatocytes , dendritic cells , monocytes , and neuroblastoma cells ) . the proapoptotic mechanisms that are related to denv infection include apoptosis activation by the extrinsic route ( via ligands such as tnf - and apo2 / trail ) and the intrinsic route ( described in neuroblastoma cells having phospholipase a2 activation , superoxide anion production , cytochrome c release , followed by caspase 3 activation ) . a mechanism related to apoptosis has not been previously proposed in work studying resistance and susceptibility to flavivirus infection . the results of the present study displayed a clear relationship between lower susceptibility to infection and decreased apoptosis . this finding suggests that the control of apoptosis - inducing mechanisms may represent a macrophage protection strategy in addition to it control of viral replication , a phenomenon that deserves more investigation . it would also be necessary to consider in the study of these cells susceptibility to dengue virus infection , the recent findings of kwan et al . , in which monocyte - derived dermal macrophages were capable of internalizing live denv but they displayed an inherent resistance to viral growth because virus particles accumulate into poorly acidified phagosomes , which prevents release of the nucleocapsid into the cytoplasm , and therefore its later replication . together , these results suggest an additional level of complexity in the genetic control of flavivirus replication . this work can conclude that balb / c mice macrophages had higher permissiveness to denv2 infection as it showed higher viral copies when measuring by using qpcr and immunocytochemistry . besides , sequence analysis demonstrated that balb / c , nih , and icr mice as well as rat , hamster , and guinea pig had the c820 t mutation in oas1b gene . it is needed to carry out more studies to clarify which is the molecular pathway involved in this higher permissiveness and if it is related to some apoptotic pathway .\noutput:\n" }, { "from": "agent", "value": "infection with dengue virus presents a broad clinical spectrum , which can range from asymptomatic cases to severe cases that are characterised by haemorrhagic syndrome and / or shock . the reason for such variability remains unknown . this work evaluated the in vitro permissiveness of mouse , rat , hamster and guinea pig macrophages to infection by dengue virus 2 ( denv2 ) . the results established that macrophages derived from the balb / c mouse strain showed higher permissiveness to denv2 infection than macrophages from other rodent species , although all rodent species studied had the c820 t mutation in the oligoadenylate synthetase 1b gene , indicating no relationship to the different in vitro susceptibilities of mouse cells at this locus . other molecular mechanisms related to flavivirus susceptibility remain to be explored ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: with an ever increasing disease prevalence , aortic valve stenosis is the most common valve disease in the developed world . , aortic valve replacement ( avr ) via a median sternotomy approach , has been largely shown to be safe and long - term efficacious , and thus currently represents the gold - standardthe number of avr interventions has dramatically increased with outcomes that have improved despite the increasing age of patients that carry a growing burden of comorbidities . , nevertheless , data from euro heart survey have suggested that 30 % of patients with severe aortic stenosis are not referred to surgery because deemed inoperable due to presence of multiple comorbidities . this observation has recently triggered the development of minimally invasive interventions such as percutaneous transcatheter aortic valve implantation ( tavi ) . compared to optimal medical therapy , tavi has shown to provide a 26.8 % absolute reduction in mortality at 3 - year follow - up in inoperable patients , , and has demonstrated great potential for high - risk surgical candidates . while the uptake and growth for tavi has been enthusiastic and widespread in europe and north america , concerns still exist surrounding paravalvular leakage , vascular complications , stroke , optimal access sites , long - term valve durability and economic sustainability meaning that the optimal treatment of high - risk operable patients remains controversial and requires further long - term follow - up and critical assessment . over the last years , minimally invasive techniques are progressively challenging traditional approaches for aortic valve surgery . minimally invasive incisions , by allowing reduced surgical dissection , may lead to lower blood loss , wound complications , postoperative pains , improved postoperative respiratory recovery , earlier mobilization and functional recovery . in thissetting , recent technological developments have led to an alternative minimally invasive surgical option which avoids the placement and tying of sutures , known as sutureless or rapid deployment aortic valves . while the sutureless concept of aortic valve implantation came up in the early sixties , new sutureless valve prostheses have been redeveloped in the last few years based on modern experience with tavi . sutureless or rapid deployment aortic valve replacement ( su - avr ) , by avoiding placement and tying of sutures after annular decalcification , has shown to minimize cross - clamp and cardiopulmonary bypass ( cpb ) durations . , shortened operational durations of su - avr may help reduce post - operative mortality and morbidity and improve cost - effectiveness , particularly in high risk patients as well as in those undergoing complex or concomitant procedures . sutureless and rapid deployment aortic valves are biological , pericardial prostheses that anchor within the aortic annulus with no more than three sutures . there are two types of sutureless aortic prostheses which are currently available on the market , including perceval s ( sorin , saluggia , italy ) and intuity elite ( edwards lifesciences , irvine , usa ) sutureless valves . it comprises a biological component of bovine pericardium fixed in a metal cage made of a super - elastic alloy . the cage design is characterized by two ring segments , on the proximal and distal end , and 9 vertical struts , with the dual task of supporting the valve and holding it in place without any permanent suture . its elastic properties allow the stent to adapt to the anatomy of the aorta and to follow its movements , relieving the stress on the leaflets . the valve is collapsed with an atraumatic device compression , assuring that the valve leaflets are not affected . perceval is lowered until the correct position and then self - expands back to its original diameter ( figure 1a ) . the design of the edwards intuity elite valve , ce approved in 2012 , is based on the perimount valve family . a balloon expandable stainless steel cloth - covered frame is incorporated into the inflow aspect of the valve . the valve is implanted with the aid of a delivery system , which incorporates a balloon catheter used to expand the frame within the left ventricular outflow tract . the expandable frame works in conjunction with the sewing ring to position and stabilize the valve at implant . the system reduces to three the number of sutures required to secure the valve , while establishing the seal between the aortic annulus and the frame ( figure 1b ) . minimally invasive incisions involve the upper mini - sternotomy , extended to the 2 , 3 or 4 intercostal space , or the right anterior mini - thoracotomy , usually at the 2 intercostal space . similarity to the traditional avr , su - avr does not avoid cpb and aortic cross - clamping ( figure 2 ) . after cardioplegic arrest , the diseased valve is excised and the annulus is accurately decalcified to allow for the sutureless prosthesis to be deployed and positioned . the nature of sutureless valves is that these do not require extensive placement and tying of sutures . therefore , subsequent to diseased valve excision , the sutureless and rapid deployment valve prostheses are sized and deployed using delivery systems that make the procedure extremely rapid ( figure 3 ) . this may translate into reduced operation duration , especially when a minimally invasive access is used to approach the aortic valve , the latter traditionally associated with longer operative times due to increased surgical complexity in narrow working spaces and learning curve . the sutureless surgical approach provides direct visualization of the implantation and target orifice location , in contrast to tavi where visualization is achieved indirectly via the use of fluoroscopy . both in su - avr and tavi , an accurate valve sizing is pivotal to avoid catastrophic complications such as paravalvular leaks , valve migration , and root dehiscence . during su - avr procedure , this is performed under direct vision using standard surgical valve sizers , which seems to be more accurate than ct - derived measurements used for tavi moreover tavi protocols do not involve excision of the diseased calcified aortic valve , in contrast to su - avr . calcium remove in sutureless aortic valve surgery may be effective in reducing paravalvular leaks and brain embolic showers and injuries in comparison to tavi ; however , this hypothesis remains to be demonstrated in clinical studies . whilst sutureless valves are in principle based on a similar technology to tavi prosthesis , the former do not require crimping of the pericardium , which may translate in superior long - term valve durability . the former is performed under direct vision with a still heart in contrast to tavi where the deployment is performed under fluoroscopy and rapid pacing ( table 1 ) . ( a ) : perceval sutureless aortic valve ( sorin , saluggia , italy ) ; ( b ) : edwards intuity elite rapid deployment aortic valve ( edwards lifesciences , irvine , usa ) ( a ) : minimally invasive su - avr through an upper j ministernotomy extended to the 3 intercostal space ; ( b ) : aortic valve exposure . ( a ) : sizing of the aortic valve annulus ; ( b ) & ( c ) : guiding sutures placement and valve seating ; ( d ) : valve deployment . cpb : cardio - pulmonary bypass ; su - avr : sutureless aortic valve replacement ; tavi : trans - catheter aortic valve implantation . in cardiac surgery , prolonged cpb and cross - clamp durations are strong independent risk factors for post - operative mortality and morbidity . , their detrimental effect becomes further amplified when operations are performed in patients burdened by advanced age and other serious comorbidities . in a recent retrospective analysis of 979 patients with aortic valve stenosis , ranucci , et al , showed that aortic cross - clamp time was a significant independent predictor of cardiovascular morbidity . the cross - clamp time reduction decreased the risk of operative mortality , acute kidney injury , stroke and low postoperative cardiac output . therefore , any technique that shortens cross - clamp or cpb time will have the potential to decrease the risk of complications and reduce long - term mortality . the sutureless prostheses , by avoiding the passage and the tying of the sutures , significantly reduce operative times and may improve outcomes . in a recent meta - analysis , phan , et al . reported a pooled cross - clamp and cpb duration for su - avr of 56.7 and 33 min , respectively , showing that sutureless valves , compared to sutured valves , halves cpb and cross clamping times with interesting positive prognostic implications for elderly and high risk patients . therefore , the indication for su - avr is appealing in higher risk patients and may become standard of care once long - term results have demonstrated efficacy and durability . additionally , the use of su - avr may be particularly reasonable in higher risk patients who need to undergo avr with concomitant cardiac surgery or complex operations with multiple interventions to minimize operational durations and improve outcomes . minimally invasive aortic valve replacement ( mi - avr ) has been introduced in the nineties and has slowly gained acceptance as a less traumatic alternative compared to median sternotomy . , however , due to the technical challenges involved and the lack of data showing a substantial survival benefit and a reduced occurrence of major post - operative complications from mi - avr over conventional management , , , this approach has not been universally adopted . opponents of minimally invasive avr claim that potential advantages ( reduced surgical chest trauma and improved cosmesis ) are counterbalanced by longer cross - clamp and cpb duration , which are associated with poorer outcomes . in a recent meta - analysis , phan , et al . showed that , despite longer operative times , mi - avr is associated with reduced transfusion incidence , postoperative renal failure , intensive care stay , and hospitalization . in terms of mortalitymi - avr was not inferior to conventional avr , but there was no data suggesting it was superior . in mi - avr , the placement and tying of sutures may be challenging and time consuming compared to standard approach . in this setting , sutureless and rapid deployment aortic valves , by avoiding sutures and minimizing cross - clamp and cpb times may simplify the mi - avr procedure and improve outcomes , particularly in critically ill patients at the highest operative risk . recently , a prospective , multicentric , randomized trial comparing outcomes in patients undergoing minimally invasive su - avr using edwards intuity elite valve , with those undergoing conventional full sternotomy avr revealed a significant cross - clamp time reduction in patients undergoing su - avr , despite the minimally invasive approach . consistent with the data reported by others , borger and colleagues , also demonstrated excellent hemodynamic performance of the su - avr prostheses compared to conventional avr . at three months , the mean gradient was significantly lower for the su - avr prosthesis than for the conventional valves ( 8.5 vs. 10.3 mmhg ; p = 0.04 ) the authors speculated that the balloon - deployable frame , which is expanded in the inflow aspect of the left ventricular outflow tract , combined with the lack of annular suture material , allows for maximum hemodynamic performance of this prosthesis . moreover , no severe patient - prosthesis mismatch ( ppm ) was observed for the su - avr group compared to six patients ( 15 % ) in the conventional avr group ( p = 0.01 ) . patient - prosthesis mismatch , as is know , has been associated with worse haemodynamic function , less regression of left ventricular hypertrophy , more cardiac events , and an increase in all - cause and cardiac - related mortality over long - term follow - up . , as such , aortic root enlargement and use of stentless prostheses may assist in reducing ppm complications ; however , these interventions add technically complexity , and certainly extend operative duration significantly , thus translating into increased surgical risk . therefore , as stated in a recent expert consensus document with regard the use of sutureless , rapid deployment valves and stented bioprosthesis in avr , su - avr should be considered for isolated avr in patients with comorbidities , old age , small aortic anulus , delicate aortic wall conditions such as calcified root , as well as for concomitant procedures to reduce cross - clamp time . there is a contraindication for bicuspid valves only for type 0 ( according to sieveres , et al . ) and for annular abscess or destruction due to infective endocarditis . current evidence on su - avr is limited to observational studies with short - term follow - up . in the largest institutional study comparing 164 mini - thoracotomy versus 117 mini - sternotomy su - avr patients , it was found that in - hospital mortality ( 0.7 % ) , strokes ( 1.8 % ) and overall survival rate ( 90 % ) over one - year follow - up was acceptable and safe . cardiopulmonary bypass ( 81 min ) and cross - clamp ( 48 min ) durations were low and excellent mean postoperative gradients were achieved . in a large multicentric study on sutureless valves , analysis of314 patients showed acceptable early survival in high - risk patients ( 1 - year survival : 90.5 % ) and low paravalvular leak rates ( 0.6 % ) . despite the above retrospective analyses , there is still a paucity of prospective data , propensity - score matched analyses and randomized controlled trials on su - avr to adequately determine long - term survival outcomes and to compare between different minimally invasive interventions . haverich , et al . reported on 287 patients with aortic stenosis , enrolled in a prospective multicentric study , underwent rapid deployment avr using edwards intuity elite valve . the main complications included stroke ( 2.8 % ) and major paravalvular leak ( 0.7 % ) . at three yearsrecently , shrestha , et al . reported the combined results of three multicentre , prospective , non - randomized clinical trials designed to evaluate the sutureless perceval aortic valve prosthesis in 731 elderly patients . no structural valve degeneration was found during follow up . in a propensity - matched study by d'onofrio , et al . , 38 matched pairs of su - avr versus tavi showed that both approaches were equally efficacious , but su - avr was associated lower incidence of paravalvular leak and similar transprosthetic gradients . in a similar study by santarpino , et al . su - avr demonstrated a significantly higher survival rate than the tavi group , lower paravalvular leak incidence , shorter procedural durations and non - significant increase in permanent pacemaker implantations . gilmanov , et al . published a propensity - matched analysis of 133 pairs of patients undergoing mi - avr , using conventional and sutureless prostheses . cpb and cross - clamp time was significantly shorter in the sutureless group , whilst in - hospital mortality , perioperative strokes and pacemaker implantations were comparable . at median follow - up of 21 months , there was similar actual survival rate for all patients , but survival was 2-fold higher in octogenarian patients with sutureless compared to sutured valves ( 100 % vs. 50 % , p = 0.02 ) . this is likely due to this group susceptible to high mortality risk and morbidities under the duress of conventional avr compared to more rapid minimally invasive sutureless surgery . in another propensity - matched analysis of 164 pairs receiving sutureless and conventional sutured valves , pollari , et al . demonstrated reduced procedural time in the su - avr cohort , that significantly correlated with shorter hospitalization , reduced postoperative atrial fibrillation , respiratory complications and hospital costs . the only randomized multicentric trial published to date on minimally invasive su - avr vs. conventional avr , showed that su - avr was associated with significantly lower cross - clamp durations ( 41.3 vs. 54 min ) , but similar cpb time ( 68.8 vs. 74.4 min ) . there was no difference in early clinical outcomes , but su - avr patients had superior mean transvalvular gradients . in a recent meta - analysis pooled results from 1037 patients undergoing su - avr were analyzed . cross - clamp and cpb duration for isolated su - avr was 56.7 and 46.5 min , respectively . several experienced valvular centers have reported cross - clamp and cardiopulmonary bypass durations as low as 22 and 46 min , respectively . these operative durations are much shorter compared to the reported durations of isolated conventional avr , and suggest potential benefits from sutureless technology in different settings : higher risk or elderly patients , complex or time - consuming combined operations , and minimally invasive surgery . pooled 30 - day and 1 - year mortality rates were 2.1 % and 4.9 % , respectively , while the incidences of strokes ( 1.5 % ) , valve degenerations ( 0.4 % ) and paravalvular leaks ( 3.0 % ) were satisfactory . on the other hand , there have also been reports of post - operative conduction disorders following implantation of the perceval s sutureless valve . shrestha , et al . reported a pacemaker implantation rate of 6 % ( 44/731 ) . in an observation study of 31 patients who underwent perceval s implantation , four patients ( 13.3 % ) required permanent pacemaker implantation due to total atrioventricular blockfurthermore , there are also concerns around stent fatigue in sutureless valves , which may lead to longer - term paravalvular leak complications . however , the relative paucity of clinical data on the long - term safety , efficacy and hemodynamic profiles of su - avr requires further critical assessment . current evidence suggests su - avr may be a safe and effective alternative to conventional avr allowing for shortened cpb and cross - clamp times . sutureless and rapid deployment prostheses seem to provide excellent haemodynamic results together with reduced surgical trauma by facilitating minimally invasive approach . however there is still a paucity of robust , evidence - based data on the role and performance of sutureless avr on the long term . therefore , strongest long - term data , randomized studies and registry data are required to adequately assess the durability and long - term outcomes of su - avr .\noutput:\n" }, { "from": "agent", "value": "aortic valve stenosis is the most common valve disease in the western world . over the past few years the number of aortic valve replacement ( avr ) interventions has increased with outcomes that have been improved despite increasing age of patients and increasing burden of comorbidities . however , despite such excellent results and its well - established position , conventional avr has undergone great development over the previous two decades . such progress , by way of less invasive incisions and use of new technologies , including transcatheter aortic valve implantation and sutureless valve prostheses , is intended to reduce the traumatic impact of the surgical procedure , thus fulfilling lower risk patients ' expectations on the one hand , and extending the operability toward increasingly high - risk patients on the other . sutureless and rapid deployment aortic valves are biological , pericardial prostheses that anchor within the aortic annulus with no more than three sutures . the sutureless prostheses , by avoiding the passage and the tying of the sutures , significantly reduce operative times and may improve outcomes . however , there is still a paucity of robust , evidence - based data on the role and performance of sutureless avr . therefore , strongest long - term data , randomized studies and registry data are required to adequately assess the durability and long - term outcomes of sutureless aortic valve replacement ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: aqueous solvent plays a significant role in dynamical processes of biological molecules , such as conformational changes , molecular recognition , and molecular assembly , that control cellular functions of underlying biological systems . implicit - solvent models are efficient descriptions of such dynamics of biomolecular interactions in an aqueous environment . in such a model , the solvent is treated implicitly as a continuum and the effect of individule solvent molecules are coarse grained . a large class of implicit - solvent models are based on dielectric boundaries that separate charged solutes from the solvent . such description of a biomolecule in water using a dielectric solutesolvent interface is rather natural , as it has long been realized that there is indeed a vapor liquid - like interface separating a biomolecule from the solvent . moreover , electrostatic properties of biomolecules can presumably be accurately described by dielectric boundaries , as the dielectric environment of biomolecules is quite different from that of the aqueous solvent . recent studies have shown that , with properly defined and estimated surface tension and other coarse - grained quantities , solutesolvent dielectric interfaces are crucial in the accurate description of biomolecular hydrophobic interactions . it is therefore clear that , with an implicit solvent , dielectric solute solvent interfaces are fundamental in the accurate and efficient prediction of biomolecular interfacial properties , electrostatic interactions , and solvation free energies . providing such predictions by properly defining and precisely locating dielectric boundaries is one of the main goals of a recently developed variational implicit - solvent model ( vism ) . the principle of vism is to minimize a free - energy functional of all possible solute solvent interfaces . such a free - energy functional consists of the surface energy , solute solvent van der waals ( vdw ) interaction energy , and electrostatic interaction energy , all depending on the solute solvent interface . the minimization of vism free - energy functional determines stable equilibrium solute solvent dielectric boundaries and solvation free energies . for years , we have developed a level - set method to numerically minimize such a vism free - energy functional . with such a method , we begin with a large surface that encloses all the solute atoms and then evolve the surface in the direction of steepest descent of the vism free energy . the surface evolution is tracked by solving numerically a partial differential equation of a level - set function that represents the surface . our extensive computational results have demonstrated that the level - set vism can capture polymodal hydration states , describe well the curvature and charge effect to the dry - wet transition , and provide accurate estimates of solvation free energies . we believe that vism is the first implicit - solvent model that can capture multiple hydration states including hydrophobic cavities and dry - wet transitions of charged molecules in water that are important in protein ligand binding . such pockets are hard to be described by traditional and popularly used , fixed - surface , implicit - solvent models , where a van der waals surface ( vdws ) , solvent - excluded surface ( ses ) , or solvent - accessible surface ( sas ) is used as the dielectric boundary . in this work , boltzmann ( pb ) theory of continuum electrostatics into our vism formulation of the solvation free energy . this will improve our previous work using the coulomb - field approximation ( cfa ) for electrostatics that does not describe the effect of ionic charges in the solvent . the pb theory is a well - established continuum description of electrostatic interactions of biomolecules in an aqueous solvent . to couple the pb theory into vism , here we develop robust numerical methods to solve the pb equation with arbitrarily shaped dielectric boundaries and to calculate the effective dielectric boundary force ( dbf ) that is the electrostatic part of total force as the negative variation of the vism functional with respect to the location change of dielectric boundary . the concept of dbf only arises in the variational approach to implicit solvation . in our previous work , we derived the formula of dbf . our numerical method generalizes the coupling interface method ( cim ) to have a compact discretization scheme . our compact cim ( ccim ) has high accuracy for solving the pb equation and computing the dbf , required to evolve numerically the dielectric boundary during the relaxation dynamics . we test the convergence and accuracy of our numerical algorithm by considering a single charged particle in ionic solvent for which analytical results are available . we then apply our level - set vism with pb theory to several systems . first , we study the solvation of single ions and compare our level - set vism results with experimental data . second , we apply our vism to study the potential of mean force of the solvent mediated interaction between two charged particles along their center - to - center distance . third , we consider the hydrophobic interaction of two parallel plates in water with differently charge patterns and compare our vism calculations with existing molecular dynamics ( md ) simulations . finally , we apply our level - set vism with pb theory to the study of the hydration behavior , charge effect , and binding affinity of the hostour extensive numerical calculations show that the level - set vism with the pb theory is able to capture multiple local minimizers of the vism free - energy functional that correspond to different hydration states . moreover , we find that the electrostatic interaction has a strong influence on the conformation and solvation free energy of charged molecules in solvent . in particular , our studies of the host guest system also show that the vism with pb theory can provide reasonably good estimates of the system solvation free energies . we notice that other theories and models that are related to our vism approach exist in literature . in some of these works , geometrical partial differential equations coupled with the pb equationwe relax our vism functional to find stable equilibrium structures by computing the effective boundary force that includes the dbf . we also use our approach to analyze in detail some model systems in terms of the multimodal character of the potentials of mean force and the strong charge effect on hydration . ii , we present the vism free - energy functional with the pb description of the electrostatic solvation free energy . in section iii , we describe briefly the level - set method for minimizing the vism free - energy functional , and numerical methods for solving the pb equation and computing the dielectric boundary force . in section iv , we apply our level - set vism to the solvation of several charged molecular systems . we consider the solvation of a charged solute molecule in an aqueous solvent that is treated implicitly as a continuum . we assume that the solute consists of n atoms that are located at x1 , ... , xn and carry partial charges q1 , ... solvent interface separates the solute region , m , from the solvent region , w , cf . figure 1 . in the variational implicit - solvent model ( vism ) , one minimizes the solvationfree - energy functional ii .1 among all possible solutesolvent interfaces . schematic view of a solvation system with an implicit solvent . a solutesolvent interface separates the solvent region w from the solute region m that can have multiple components . the dielectric coefficients of the solute and solvent regions are denoted by m and w , respectively . the first term in eq ii .1 , proportional to the volume of solute region m , describes the work it takes to create a solute cavity in the solvent . the second term is the surface energy , where is the surface tension . it is known that at the molecular scale the surface tension depends on local geometry of the surface . here , we use = 0 ( 12h ) , where 0 is the surface tension for a planar interface , is the curvature correction coefficient or the tolman length , and h is the mean curvature defined as the average of the two principal curvatures . we denote by ggeom the sum of the first two terms in ( ii .1 ) and call it the geometrical part of the solvation free energy . xi | ) in eq ii .1 is the van der waals ( vdw ) type interaction potential between the solute particle at xi and a solvent molecule at x that is coarse grained . the summation term represents the vdw interaction between the solute and solvent , where w is the bulk density of the solvent . we define ui to be the lennard - jones ( lj ) potentialthe parameters i of energy and i of length can vary with different solute atoms as in a conventional force field in molecular dynamics ( md ) simulations . we denote by gvdw this summation term in ( ii .1 ) , and call it the vdw part of the solvation free energy . the last term gelec in ( ii .1 ) is the electrostatic part of the solvation free energy . it is given byii .2 here , = ( x ) is the electrostatic potential , reac = ref is the reaction field , and ref is the potential for the reference statewith 0 being the vacuum permittivity and m the dielectric coefficient of solutes . we have assumed here that there are m ionic species in the solvent , with cj and qj being the bulk concentration and charge for the jth species . in eq ii .2 , = kbt with kb the boltzmann constant and t the absolute temperature . the first term in eq ii .2 is the electrostatic potential energy corresponding to the fixed solute charges q1 , ... , qn , and the others terms in eq ii .2 are the free energy of electrostatics due to the mobile ions in the solvent . the potential = ( x ) solves the boundary - value problem of the poisson , w is the dielectric coefficient of solvent , [ [ u ] ] = u | w u | m denotes the jump across of a function u from m to w , = ( x ) takes the value m in m and w in w , respectively , the unit normal n at points from m to w ( cf . figure 1 ) , and 0 is a given boundary value which is often given in practice bywhere = ( 0wkbt / j = 1mcjqj2 ) is the inverse debye length . in our numerical computations , we solve the following equations for the reaction field reac , instead of eq ii .3 for : ii .4 we minimize the free - energy functional ( eq ii .1 ) by evolving an initial surface in the direction of steepest descent of the free energy . the evolution of the surface is therefore driven by the ( normal component of the ) effective boundary force , fn , defined to be fn = g , the negative variational derivative of the free - energy functional g with respect to the location change of the boundary . with our convention that the unit normal vector n = n ( x ) for a point x on the boundary points from the solute region m to the solvent region w , we have the effective boundary forceii .5 where k = k ( x ) is the gaussian curvature , defined as the product of the two principal curvatures at a point x on . here fnelec ( x ) is the electrostatic part of the boundary force , the dielectric boundary force ( dbf ) . note by eq ii .3 that the normal component of the electric displacement / n and the tangential component of the electric field ( i n n ) are both continuous across . note also from eq ii .6 that fnelec ( x ) 0 for any point x on , since in general m w . this implies that the dbf always points from the solvent to the solute region . to compare with md simulationspreviously , we found that an optimal vism surface often corresponds to the surface with the first peak of water density determined using the position of oxygen atoms in water molecules . such a surface is not necessary the best choice of dielectric boundary . this is because the center of charge of a polarized water molecule is displaced near a charged molecule , with the amount of displacement differing significantly between the two cases of positive and negative charges . this well - documented issue of charge asymmetry gives rise to the subtlety in defining a dielectric boundary . , if we use a vism surface as the dielectric boundary to calculate the electrostatic solvation energy , then the error can be sometimes significant . here we use an empirical method developed in our previous studies : after we obtain a vism free - energy minimizing surface , we shift it in parallel toward the solute by ( in ) and then use the shifted surface as the dielectric boundary to calculate the electrostatic solvation energy , cf . the parameter should in principle depend on the local environment such as the sign of charges near the surface . however , to avoid being too complicated , we use a uniform value of shift and usually set it to be close to 1 . consider the solvation of a solute that consists of two groups of atoms . one group of atoms are located at x1 , ... , xm and the other at xm +1 , ... we choose the distance d between the geometrical centers ( i = 1mxi ) / m and ( i = m +1 nxi ) / ( n m ) of these two groups of atoms as a reaction coordinate . also , we choose the system that two groups are infinitely far from each other as a reference state , that is , dref = . for every fixed finite d , the minimization of the vism solvation free - energy functional leads to a local minimizer , that is , a stable equilibrium solute solvent interface d . we define the ( total ) potential of mean force as the sum of three contributionsii .7 wherehere , a quantity at is understood as the sum of two separate contributionsii .8 where i and ii , both independent of d , correspond to the vism equilibrium solute solvent interfaces of those two solute groups that are treated individually . the quantity g in the above eq ii .8 can be replaced by ggeom , or gvdw , or gelec . in the above definition of gvdwpmf ( d ) , we include the contribution of the vdw interaction between the two solute groups . in the definition of gelecpmf ( d ) , we include the coulombic interaction between the two solute groups in the reference medium with the dielectric constant m . effective dielectric boundary is obtained by shifting the vism surface to the solute region by in . for a given reaction coordinate d , different initial conditions can result in multiple equilibrium interfaces , corresponding to different local minimizers of the vism free - energy functional . the pmf therefore may have multiple branches along the reaction coordinate d , leading to a hysteresis . we call these branches equilibrium pmfs in contrast with the ensemble pmf that is the averaged pmf weighted with boltzmann factors . numerically , we minimize the vism free - energy functional ii .1 by relaxing an initial surface that encloses all the solute atoms in the direction of steepest descent of free energy . we relax the surface by solving the level - set equationiii .1 here , = ( x , t ) is a level - set function representing the evolving surface = ( t ) at time t ; that is , ( t ) consists exactly all the points x such that ( x , t ) = 0 . the function fn = fn ( x ) is the effective boundary force given in eq ii .5 . this force is extended away from the surface so that the level - set eq iii .1 can be solved in a finite computational box or a narrow band surrounding the surface ( t ) . due to the nonconvexity of the vism free - energy functional , different initial surfaces can relax to different local minimizers with our steepest descent strategy . to capture different local minimizers , we usually start with two types of initial surfaces : a tight wrap that is a union of vdw spheres centered at solute atoms with reduced radii and a loose wrap that is a large surface loosely enclosing all the solute atoms . to discretize the level - set eq iii .1 , we rewrite it aswherethe b | | is a hyperbolic term . , we use a fifth - order weno ( weighted essential - no - oscillation ) scheme . for the a term , we first linearize a = a ( ) at that is computed in the previous time step and adjust the parameter to enforce parabolicity of the linearized equation . we use the central differencing to discretize the derivatives in a with the adjusted . typical initial surfaces of the level - set vism calculations . we use the forward euler method to discretize the time derivative in the level - set eq iii .1 : iii .2 where ( x ) and fn ( k ) ( x ) are the approximations of ( x , tk ) and fn ( x , tk ) , respectively , at time tk = kt ( k = 1,2 , ... ) and t is the time step size . we update the level - set equation by iii .2 in a narrow band surrounding the surface . to satisfy the courantfriedrichs lewy condition , we chooseiii .3 where h is the step size in space discretization , c = c ( ) is the matrix obtained in linearizing a ( x ) with respect to and is determined by a ( ) = 0c ( ) : , andthe maximum in iii .3 is taken over all the grid points in the band . to solve eq ii .4 , we use newton s iterationiii .4 where w is the characteristic function of the solvent region w , that is , w ( x ) = 1 in w and 0 otherwise , and the number of iteration p can vary from 1 to 30 . in each iteration , we solve a linear partial differential equation with two jump conditions on , cf . we solve this linearized interface problem with a compact coupling interface method ( cim ) that is an improved version of cim . to compute the dbf ( eq ii .6 ) on the interface , we approximate and by the interpolation of the potential at adjacent grid points . we use the tip4p water model to determine the parameters for water and employ the lorentz berthelot mixing rules for the lj potentials of interaction between water and individual solute atoms . we also use kbt for energy and angstrm for length . throughout our calculations , we fix t = 300 k , p = 0 bar , 0 = 0.1315 kbt / , w = 0.0331 , m = 1 , w = 78 , and = 0.76 . we consider a single particle with charge value q centered at the origin . the vism free - energy functional for this system reduces to a one - variable function of radius r : iv .1 this function can be numerically minimized with a very high accuracy . we use the lj parameters = 0.3 kbt and = 3.5 . we perform a series of test with different charge values : q = 0.0 e , 0.5 e , 1.0 e , 1.5 e , 2.0 e. in our level - set calculations , we use a 120120120 computational grid to resolve a computational box ( 4,4 ) ( 4,4 ) ( 4,4 ) . in table 1 , we show the result of our level - set calculations ( labeled as level - set ) and numerical minimization of ( iv .1 ) ( labeled as analytical ) . we compare the optimal radii , the nonpolar and polar solvation energies , and the total solvation energies for different values of q. clearly , the level - set relaxation gives very accurate results . note that the optimal radius decreases as the charge value increases due to the strong dielectric boundary force acting on the solutethe reaction potential reac becomes larger and the system thus gains more electrostatic solvation energy . meanwhile , the nonpolar part of the solvation energy also increases because of the rapidly increasing solutethe electrostatic part of the solvation energy becomes more and more dominant as the charge value increases . we also apply our level - set vism to the solvation of single ions k , na , cl , and f. we take the lj parameters for these ions from the publication . in our calculations , the dielectric boundary of the anion cl or f is obtained by shifting the vism equilibrium surface by = 1 , which is the length of the water oh bond . in table 2 , we display the nonpolar and polar parts of the solvation free energy obtained by our level - set vism calculations , and the experimental values of solvation free energy for these ions . again , we observe that the polar part of solvation free energy contributes more than the nonpolar part . we consider a system of two ions k and cl in water and in monovalent ( 1 : 1 ) ionic solution with different bulk concentrations c1 = 0.1 m , 0.5 m , and 0.8 m , respectively . the lj parameters are k = 0.2104 kbt , cl = 0.2104 kbt , o = 0.2622 kbt , k = 3.250 , cl = 3.785 , and o = 3.169 , where o means the oxygen in water . when we calculate the electrostatic solvation energy , we employ a parallel shift of the equilibrium surface by = 0.6 . this value is determined by trying several - values . for each trial - value , we compute the vism solvation energy for each of the ions . we then compare the sum of these two computed energy values with the sum of the two experimental solvation energy values of the two ions , respectively . in other words , we determine the best uniform shift = 0.6 for the two ions as they are infinitely separated from each other and use it for the system when the two ions are apart from each other with a finite distance . we choose the center - to - center distance of the two ions as the reaction coordinate and study the solvent - mediated pmf of the system . for each distance d , we minimize the vism free - energy functional to get an equilibrium solute solvent interface and compute each component of the solvation free energy with the obtained interface . the geometric part of the pmf in the upper left of the figure shows a pronounced desolvation barrier at d = 5 , where the two vism surface branches of charged particles start to merge together . solvent interface accounts for the distortion of the water molecules in the overlapping hydration shells . at a small separation , the geometric part of pmf shows water - induced attraction due to less water - accessible area . the upper right of figure 4 displays the vdw part of pmf with the soluteit shows significant repulsions as the two objects merge together and peaks at d = 6 where the two objects begin to break . different components of the pmf for the two - particle system of k and cl . hckel ( dh ) screening law for two - particle interactions are shown as references . three inset figures are effective dielectric boundaries at d = 4 , d = 6 , and d = 10 , respectively . lower right shows the total pmf gtotpmf in the mainframe and md simulation results ( with 0.5 m salt ) in the inset . in the lower left of figure 4 , we observe that the electrostatic part of the pmf varies with the ionic concentration . at a small separation d3 , the attraction between two oppositely charged particles is greatly enhanced due to the short interaction distance and weak dielectric screening in the solute region . there is a high electrostatic desolvation barrier at d = 4 , due to the concave dielectric boundary . such a barrier depicts the energy penalty of the steric depletion of polar water molecules that are originally attracted to the charged particles . in contrast , the favorable electrostatic interaction between water molecules and particles is only partially reduced at d = 5 . after two objects are completely solvated at d 5 , the effect of solvent and ionic solution comes into play . overall , the attractive interaction between the two particles is gradually screened , and the profiles converge asymptotically to the coulomb law q1q2 / 40wd and debye hckel ( dh ) screening law ( q1q2 e ) / ( 40wd ) . we see that after the two objects separate , the decay of electrostatic attraction as the separation increases is faster than that for the coulomb or dh interaction . this is due to the solvent screening and the shape change of dielectric boundary . from the snapshots in the lowerleft of figure 4 , we can see that the dielectric boundary for the particles at the distance d = 6 are not perfect spheres . they are deformed slightly in the direction of the reaction coordinate , due to the strong electrostatic interaction between two particles . as the separation becomes larger , the electrostatic interaction becomes weaker and the shape of the dielectric boundary becomes more spherical . this indicates that the nonpolar and polar contributions affect each other via the equilibrium solute solvent surface . in the lower right of figure 4 , we show the pmf obtained by our vism - pb in the mainframe and by md simulation ( for c1 = 0.5 m ) in the inset . for d 3 , both results show the repulsion that stems from the vdw interaction between the overlapping particles . near d = 3 , both capture the significant electrostatic attraction due to the weak dielectric screening and short interaction distance . at a distance close to d = 4 , solvent surface of two particles breaks apart , both pmfs again show the attraction . the md simulations show some oscillations for d 6 while our mean - field vism only predicts a monotonic pmf . overall , however , there is a remarkable agreement between our vism calculations and the md simulations . we consider the solvation of a strong hydrophobic system of two parallel paraffin plates with different charge patterns , and study the effect of charge pattern to the hydrophobic attraction , capillary evaporation between the plates , and the hysteresis of the pmf profiles . each plate contains 66 fixed atoms with the lj parameters = 0.265 kbt and = 3.532 . the two plates are placed in pure water ( labeled ps ) or monovalent ionic solutions with 0.2 m bulk concentration ( labeled pb ) . plate separation distance is chose to be the reaction coordinate to define the pmf . we define five different charge patterns : pattern i : each atom in the two plates carries a positive charge 0.2 e , cf . figure 5 a.pattern ii : one plate is positively charged and the other negatively charged . each atom in the two plates is charged with the same charge value 0.2 e , cf . figure 5a and b.pattern iii : one plate is charged as shown in figure 5c and the other plate is oppositely charged with the same value in corresponding positions.pattern iv : one plate is charged as shown in figure 5d , and the other plate is oppositely charged with the same value in corresponding positions.pattern v : one plate is charged as shown in figure 5e , and the other plate is oppositely charged with the same value in corresponding positions . pattern i : each atom in the two plates carries a positive charge 0.2 e , cf . figure 5 a. pattern ii : one plate is positively charged and the other negatively charged . each atom in the two plates is charged with the same charge value 0.2 e , cf . figure 5a and b. pattern iii : one plate is charged as shown in figure 5c and the other plate is oppositely charged with the same value in corresponding positions . pattern iv : one plate is charged as shown in figure 5d , and the other plate is oppositely charged with the same value in corresponding positions . pattern v : one plate is charged as shown in figure 5e , and the other plate is oppositely charged with the same value in corresponding positions . homogeneously ( a and b ) and heterogeneously ( c , d , and e ) charged plates . blue means a positive charge 0.2 e. red means a negative charge 0.2 e. gray means neutral . figure 6 shows the total pmf and its different components for pattern i. we observe the capillary evaporation when 611 . in this range of the plate plate separation , there are in general two branches of the pmf . the lower one corresponds to the dry state and the upper one the wet state . we observe from the upper left and upper right of figure 6 that , at a short plateplate separation , the geometric part of pmf exhibits a strong attraction due to a small water - accessible area but the vdw part ( including the solutethe dry state resulting from a loose initial leads to a higher vdw desolvation barrier . the electrostatic repulsion results from the like - charge interaction . for a wet state , the electrostatic interaction is greatly screened at the distances d 6 , due to the presence of solution between the plates . clearly , a stronger screening occurs with ionic solution ( pb ) . for a dry state , the electrostatic interaction gradually decreases as the separation increases where the solvent partially penetrates into the region between plates . the lower - right plot in figure 6 displays the total pmf of the system , with a snapshot showing the solute solvent surface of the dry state at d = 10 . we can see that the electrostatics attracts the solvent close to the charged atoms , pushing the solutewe also observe that the total pmf profile is mainly determined by the electrostatic part with small nonpolar contributions at short separations . we see that the capillary evaporation only occurs at shorter separations d 8 , due to the strong electrostatic interaction between oppositely charged plates that drags polar water molecules and ions into the inter plate region . this can also be seen from the analytical formula ii .6 of dielectric boundary force ( dbf ) : a stronger electric field leads to a larger dbf . the nonpolar contributions , both ggeompmf and gvdwpmf , show a strong sensitivity to the local electrostatics , due to the very different solutesolvent surface geometries induced by different charge patterns . for the electrostatic part , there are obvious desolvation barriers when two solute solvent surfaces of the plates begin to merge together , especially for a dry state . the polar water molecules between the charged plates are firmly attracted to the charged atoms by the strong electric field . however , they are sterically depleted away when two plates come closer than the critical distance , resulting a concave solutethe corresponding energy cost of the depletion is responsible for the high desolvation barriers in the electrostatic pmf . for a large distance , similar screening effects of the solvent and ionic solutioncan also be observed . for two plates that are charged as pattern iii , iv , and v , we focus on the electrostatic part of the pmf and the total pmf , cf . we see that the largest distance of capillary evaporation for patterns iii and iv is increased to d = 18 this is because that the electrostatic interaction is reduced by the surrounding opposite charges . again , we observe electrostatic desolvation barriers when water molecules between two plates evaporate . from the snapshots shown in figure 8solvent surfaces are concave between two plates when there are desolvation barriers . compared with the results for pattern i and pattern ii , the water molecules between the plates are easier to evaporate away from the charged plates , because of the weaker electrostatic interactions between the plates . the electrostatic desolvation barriers are therefore much lower . since the electrostatic contribution is weak , the nonpolar contribution dominates and therefore the total pmfs for pattern iii and iv are very close to each other . total pmf and its different components vs the separation distance d between the two plates that are charged as pattern i. ps denotes pure water and pb denotes ionic solutions . we can see from the bottom panel of figure 8 that the largest separation distance for capillary evaporation decreases down to d = 12 remarkably , our vism solutesolvent interface captures the stepwise cavitation for the dry state when the capillary evaporation takes place , cf . the snapshot of the solute solvent surface in bottom - right plot of figure 8 , agreeing qualitatively with the md simulations by hua et al . the electric field generated by the charged atoms at the two corners attracts polar solvent molecules , while the hydrophobic sites still keep dry . the desolvation barrier in the electrostatic pmf is consistent with this stepwise dewetting transition . for a distance between d = 9 and d = 12 , the desolvation barrier reaches its first plateau , because of the desolvation of water molecules near the hydrophobic , neutral atoms . when d 9 , the desolvation barrier goes up further with a larger magnitude , since it costs larger energy penalties to desolve the water molecules near the hydrophilic , charged atoms . the total pmf shows another different type of hysteresis , induced by the different distribution of charged atoms in pattern v. we can see that our level - set vism has accurately captured the hydrophobicdifferent components of the pmf vs separation distance d between the two plates that are charged as pattern ii . ps denotes pure water and pb denotes ionic solutions . the inset snapshot shows the solutebottom panel : pattern v. the inset snapshot shows the solute solvent surface of the dry state at d = 12 . finally , we consider the water density between the plates , defined bywhere w is the bulk water density , vsol is the solvated volume between the plates , and vtot is the total volume between the plates . figure 9 displays the water density along the reaction coordinate for dry ( loose initial ) and wet ( tight initial ) states . for loose initials , the region between the plates becomes solvated with the increasing separation for all the patterns except pattern ii where a complete solvation occurs suddenly when the separation increases from 7 to 8 . these dewetting transitions predicted by our vism calculations have also been observed in md simulations on similar two - plates systems . vism estimate of water density between the two plates for different charge patterns ( ptn means pattern ) . left : tight initials . we now apply our vism with pb theory to the solvation of a host guest system : a bicyclo [ 2.2.2 ] octane ( b2 ) binding to a synthetic host cucurbituril ( cb ) . guest system has wide applications in many fields , such as molecular machines , supramolecular polymers , gene transfection , and drug transport . we studied this system in our recent work with a coulomb - field approximation ( cfa ) of the electrostatics . here , we use our vism with pb theory to investigate the hydration behavior and the binding affinity of the host guest system . we use a parallel shift of our vism surface toward solute region by = 1 when we calculate the electrostatic solvation energy . in our calculations , the force - field parameters and coordinates are taken from an md study . to show the effect of electrostatics to the hydration and free energies , we study both charged and uncharged cases . the uncharged case is simply treated by setting the values of partial charges to be all zero . figure 10 displays our vism equilibrium surfaces of the isolated host with loose ( upper panel ) and tight ( lower panel ) initials . we observe both dry and wet states that result from loose and tight initials , respectively . moreover , vism equilibrium surfaces are tighter when charges are included . in such a case , the vism surface with the pb description is tighter than that with the cfa of electrostatics . we see that the electrostatic solvation energy is underestimated without the parallel shift of the vism surface . also , the electrostatics plays a dominant role in the solvation . without charges , the solvation free energy of a dry state corresponding to a loose initial is lower than that of a wet state corresponding to a tight initial . however , with charges , the solvation free energy with a wet state is much lower . these conclusions are in line with recent explicit md simulations of the identical nonpolar and polar systems . enhanced fluctuations are observed in md simulations due to the toroidal confinement of the host cavity , and the host is mostly found in the wet state . also , the average water density near solute atoms is much higher when the charges are included ( cf . the vism equilibrium surfaces for the bound host guest system are shown in figure 11 . for the bound system , both the loose initials and tight initials give nearly the same equilibrium surfaces . the free energies listed in table 3 also show this independence of the initial surfaces . again , we can see that the electrostatic interaction pushes the equilibrium surface to be closer to the solute atoms , and the charge effect predicted by cfa is not as strong as that by the pb description . md simulations also show that the water molecules distribute much closer to the charged atoms and water densities around atoms are much higher when charges are included . vism equilibrium surfaces of the host cb without and with charges . left : no charges . lower : tight initials . the color on the surface represents the mean curvature being convex ( red ) , the values in parentheses denote the energies obtained without shifting the solute - solvent surface . the binding affinity is described bywhereis the difference between the total pmf ( eq ii .7 ) of the bound state and that of an unbound state , gts is the entropy penalty upon binding , and gval is the valence energy differences , including the energy changes of bond - stretch , angle - bend , dihedral , etc . table 4 lists individual contributions computed with loose initials and tight initials . for comparison , those results are obtained with a second - generation mining minima ( m2 ) algorithm , in which free energies are estimated by the sum of the potential energies and implicit solvation energies at local energy wells . for the geometric contribution , both the loose and tight initials predict favorable binding energies because the water - accessible area is reduced after the host and guest are bound together . the tight initial , corresponding to a wet state of the host cavity , has a larger energy difference than the loose case , since more water - accessible area is lost upon binding . the vdw interaction between water and solutes disfavors binding , with an energy penalty of 12.1 kbt for the loose initial and 21.4 kbt for the tight initial . the reason for this energy penalty is that the favorable solute - water vdw interaction ( cf . gvdw in table 3 ) is reduced upon binding , especially for the tight case . the nonpolar part of the solvation favors the host guest binding by 17.5 kbt for the loose initial and 18.7 kbt for the tight initial . for the electrostatic part of the solvation ( gelec ) , both the loose initial and tight initial predict unfavorable energy differences . remarkably , the tight initial , which corresponds to the wet state , predicts a 4.2 kbt energy penalty , agreeing very well with 24.5 kbt reported in ref ( 83 ) . as a component of the electrostatic part of the pmf , the coulombic interaction between the host and guest in the reference state has a favorable contribution 12.2 kbt to the binding affinity . such a contribution is independent of the solute solvent interface . the electrostatic part of the pmf ( i.e. , gelecpmf = gelec + gelecr ) shows an unfavorable energy difference : 1.4 kbt energy penalty for the loose case and 12.0 kbt for the tight case , compared to 10.6 kbt presented in the work . these data indicate that the attractive coulombic interaction in the reference state partially cancels the binding penalty from the electrostatic part of the solvation , leading to a relatively weak penalty of electrostatics to the binding . guest vdw interaction in the reference state strongly drives the binding with an attraction of 38.7 kbt . . the discrepancy can be attributed to the difference in the positional coordinates of the host and guest in the bound state . since the two binding partners are treated as rigid bodies with a fixed relative orientation , we are unable to compute the entropy penalty and the valence energy changes upon binding . here , we take these data , which are shown in parentheses in table 4 , from ref ( 83 ) to complete the computation of the binding affinity . in the last row of table 4 , we show the total binding affinity of the system given by loose initials and tight initials . we can see that both of them predict a favorable binding affinity , with 24.4 kbt for the loose initial and 14.0 kbt for the tight initial . they are in line with the calculation of 20.3 kbt by the m2 algorithm and 22.6 kbt of the experimental data . overall , vism captures individual contributions to the binding affinity and predicts reasonably well binding free - energy values . means energy difference ( in kbt ) between the bound and unbounded states . unavailable data are blank cells . the numbers in parentheses are taken from ref ( 83 ) . the energy difference of the nonpolar solvation energy is gnp = gvdw + ggeom . gelecr and gvdwr are the energy differences of the coulombic interaction and vdw interaction between the host and guest in the reference state , respectively . the energy difference of the electrostatic part of the pmf gelecpmf = gelec + gelecr . in this work , we introduce the poisson boltzmann ( pb ) description of the electrostatics in the variational implicit - solvent model ( vism ) , and implement a level - set method to minimize the resulting vism free - energy functional . different types of initial surfaces in the free - energy minimization lead to different final stable equilibrium surfaces that describe multiple hydration states . one of our major efforts has been to design and implement a high - order compact coupling interface method ( ccim ) for solving the pb equation to obtain the electrostatic potential and to compute the pb dielectric boundary force ( dbf ) . we apply our theory and methods to a few charged systems that include single ions , two charged particles , two parallel plates , and a hostour extensive computational results with comparison with experiment and molecular dynamics ( md ) simulations have demonstrated that vism is able to capture multiple hydration states that lead to the hysteresis in the potential of mean force ( pmf ) and provide fairly accurate estimates of solvation free energies . it is clear that different components of the free energy all contribute to the relaxation of the system . in particular , the nonpolar parts ( i.e. , the geometrical and vdw parts ) of interaction depends sensitively on the electrostatics via the solutein fact , the analytical expression of the dbf and our numerical computations show clearly that the effective electrostatic force always pushes the solute solvent interface into the solute region . the magnitude of such force predicted by the pb theory is larger than that by the coulomb - field approximation , indicating that mobile ions enhance the charge effect . guest system cb - b , our level - set vism calculations reveal different hydration states that have been predicted by the md simulations . first , our computational results show that the boundary shift of an optimal vism surface works well for the final evaluation of electrostatic free energy . however , such a shift is inconsistent with the principle of free - energy minimization . one possible improvement of vism is then to use two boundaries : one corresponding to a solutesolvent interface and the other to a dielectric boundary . with two boundaries in the vism free - energy functional , we do not have a simple formulation of the vism functional with these two bounaries and yet that is relatively simple to implement and efficient in computation . solvent interaction in the vism description , so that the two boundaries can be unifined into one . second , solving the nonlinear pb equation in each step of level - set optimization is very costly . as typically the ionic concentrations are low in an aqueous solvent , it is reasonable to just use the linearized pb equation . moreover , we can speed up our computations by use the cfa for electrostatics in the beginning of level - set iteration . third , we have used mainly two types of initial surfaces , loose or tight initial surfaces , to relax our vism functional . in some cases , they represent two local minima of the functional that are stable equilibrium conformations of an underlying molecular system . for a simple system , such as the two parallel plates , . however , in general , we may not be able to capture all different kinds of local minima of the vism functional by using only the loose and tight initial surfaces . a relatively simple one is to design different kinds of initial surfaces based on the solute atomic positions . a complicated one is to introduce fluctuations in the model to allow the system to jump from a local minimum to another . finally , our current theory and methods do not provide a systematic way of computing the entropy of an underlying molecular system . accurate predictions of enthalpy and entropy are , however , particularly important in understanding protein ligand binding . it is therefore our goal to develop a vism compatible theory for such predictions .\noutput:\n" }, { "from": "agent", "value": "we incorporate the poisson boltzmann ( pb ) theory of electrostatics into our variational implicit - solvent model ( vism ) for the solvation of charged molecules in an aqueous solvent . in order to numerically relax the vism free - energy functional by our level - set method , we develop highly accurate methods for solving the dielectric pb equation and for computing the dielectric boundary force . we also apply our vism - pb theory to analyze the solvent potentials of mean force and the effect of charges on the hydrophobic hydration for some selected molecular systems . these include some single ions , two charged particles , two charged plates , and the host guest system cucurbit [ 7 ] uril and bicyclo [ 2.2.2 ] octane . our computational results show that vism with pb theory can capture well the sensitive response of capillary evaporation to the charge in hydrophobic confinement and the polymodal hydration behavior and can provide accurate estimates of binding affinity of the host guest system . we finally discuss several issues for further improvement of vism ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: primary hyperparathyroidism ( phpt ) syndrome is an endocrine disorder , characterized by excessive secretion of parathyroid hormone from one or more parathyroid glands . the elevation of pth usually leads to hypercalcemia and hypophosphatemia ; patients may present with classic skeletal disease , recurrent nephrolithiasis , or be asymptomatic , detected on routine biochemical screening . a dramatic increase in the incidence of phpt occurred in the late 1960s , due primarily to the introduction of the multichannel autoanalyzer . the clinical profile of phpt in the western countries had shifted from a symptomatic disorder , toward a more asymptomatic state . however , phpt has a variable clinical expression and symptomatic phpt is still the predominant form of disease in many developing countries , with skeletal manifestation ( osteitis fibrosis cystica ) being very common . earlier studies from india have attributed the greater severity of phpt to delayed diagnosis and widely prevalent vitamin d deficiency . hypercalcemia is considered to be a rare cause of pancreatitis but the true cause and effect relationship between phpt and pancreatitis remains controversial . phpt has been associated with different types of pancreatitis . despite its rarity , a cause and effect relationshipsome patients suffer from 2 or more attacks of pancreatitis before a diagnosis of phpt is made . we present a patient who had repeated admissions for acute pancreatitis , 4 episodes over a period of 15 months . a 32 - year - old man was first admitted to a district hospital with an episode of acute pancreatitis . he had elevated serum amylase and computed tomography ( ct ) abdomen revealed diffusely enlarged pancreas with irregular outline with no calcification or dilatation of main pancreatic duct [ figure 1 ] . , he suffered 3 more episodes of acute pancreatitis . during the second episode , ct abdomen revealed focal necrosis in the body ( less than 30 % ) . ct abdomen showing diffusely enlarged pancreas with irregular outline for the fourth episode of acute pancreatitis , he was admitted in our institute . he denied any history of alcohol abuse and there was no family history of pancreatitis . lipid profile was normal ( total cholesterol 157 mg / dl , triglyceride 158 mg / dl , ldl cholesterol 85 mg / dl , and hdl cholesterol 40 mg / dl ) . the serum calcium was 10.4 mg / dl ( normal range 8.8 - 10.5 mg / dl ) and serum albumin was 4.6 g / dl . during the first 3 episodes of pancreatitis , the serum calcium at the upper limit of normal gave us clue that he may be having underlying hypercalcemic disorder . repeat serum calcium was 13.1 mg / dl , phosphate 2.0 mg / dl , albumin 4.8 g / dl , and serum alkaline phosphatase was 284serum 25 - hydroxyvitamin d was 10.31 ng / ml and serum ipth was 610.7 pg / ml . ultrasonography neck revealed a hypoechoic lesion 2.11.2 cm at the lower pole of left lobe of thyroid . left inferior parathyroid adenoma was localized on a radionuclide parathyroid scan ( 99mtc mibi ) [ figure 2 ] . he denied any history of bone pains , bone fractures , neuropsychiatric symptoms , or muscle weakness . radionuclide parathyroid scan ( 99mtc mibi ) showing left inferior parathyroid adenoma parathyroid adenoma was removed . eighteen months after successful parathyroid surgery , there has been no recurrence of abdominal pain and his serum calcium is within the normal range . his current biochemical parameters are serum calcium 8.2 mg / dl ; serum phosphorus 3.9 mg / dl ; ipth 32 pg / ml , and 25 ( oh ) d329 .33 pg / ml . the mayo clinic experience between 1950 and 1975 found that out of 1153 patients with phpt , only 17 ( 1.5 % ) had coexisting pancreatitis , and alternative explanations for pancreatitis were found for several patients . but several studies have suggested a causal association between pancreatitis and phpt . the prevalence of acute pancreatitis in phpt has been estimated to be between 1.5 % and 13 % . phpt has been associated with different types of pancreatitis , such as acute , subacute , or chronic calcifying pancreatitis . a study involving 83 cases of pancreatitis combined with phpt found that about 70 % of the patients suffered from acute relapsing or chronic pancreatitis . some patients suffer from 2 or more attacks of pancreatitis before a diagnosis of phpt is made . in a study from india , pancreatitis was associated in 6 of 87 patients ( 6.8 % ) with phpt . all patients with a past history of pancreatitis had suffered two or more attacks . in our patientserum calcium estimation after the first episode of pancreatitis would have eliminated this delay . . it is important to estimate serum calcium after an episode of unexplained pancreatitis . this will minimize the delay before the diagnosis of phpt is made . despite its rarity , a cause and effect relationship is still suggested by the fact that parathyroidectomy seems to prevent recurrence of pancreatitis . nearly 100 % improvement in pancreatitis symptoms after the cure of phpt has been reported . hypercalcemia can lead to de novo activation of trypsinogen to trypsin , resulting in autodigestion of the pancreas and subsequent pancreatitis . another explanation is that hypercalcemia leads to the formation of pancreatic calculi , ductal obstruction , and subsequent attacks of acute or chronic pancreatitis . the mean calcium values among patients with phpt and pancreatic disease have been reported to be significantly higher than those in patients with phpt without pancreatic involvement .\noutput:\n" }, { "from": "agent", "value": "the association between pancreatitis and primary hyperparathyroidism ( phpt ) is controversial . we report a 32 - year - old man who presented with recurrent episodes of acute pancreatitis . primary hyperparathyroidism was diagnosed after the fourth episode of pancreatitis . he had no additional risk factors for pancreatitis . eighteen months after successful parathyroid surgery , there has been no recurrence of abdominal pain and his serum calcium is within the normal range ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: cancer is the anomalous growth of cells in our bodies that can lead to death . these cells are born due to imbalance in the body and by correcting this unevenness ; the cancer may be treated . consistent with the american cancer society , deaths arising from cancer constitute 2 - 3 % of the annual deaths recorded worldwide . cancers affecting the digestive tract are among the most common of all the cancers associated with aging . about one out of every 14 men and women in america is diagnosed with gastrointestinal cancer at some time in his / her life . alpinia galangal is widely cultivated in china , india , and southeast asian countries such as thailand , indonesia , and philippines . the rhizomes of this plant are used in traditional medicine for several purposes , such as stomachicin china , or for carminative , anti - flatulent , antifungal , and anti - itching in thailand . in chemical studies of a. galangal , was reported to possess various biological activities , such as antitumor , anti - inflammatory , pungency , antifungal , antioxidative , and xanthine oxidase inhibitory activity [ 5 - 9 ] . there is no report available on the effects of aqueous extract of alpinial galangal on gastric adenocarcinoma . the present study was designed to examine the effect of this extract on the in vitro proliferation of ags cells , originated from gastric carcinoma . in addition , we chose l929 cell lines as non - tumor cell , for comparison of the effect of extract on both cell lines . aqueous extract preparation fresh whole plants of alpinia galangal were purchased from a local market in mashhad , iran . the fresh plants were sliced and dried in a tray - dryer oven at 50c for 24h , after which they were ground in a blender ( national , mxt2gn , taiwan ) to make powder . then , the different concentrations of alpinia galangal ( 125 , 250 , 500 , 750 and 1000 g / ml ) were prepared . morphologic examinations ags and l929 cells were obtained from national cell bank of iran ( ncbi ) . cells were cultivated in a 1:1 mixture of dulbeccos modified eagles medium ( dmem ) , supplemented with 10 % fetal bovine serum ( fbs ) and 1 % penicillin - streptomycin solution . the cultured were humidified at atmosphere and fed 2 - 3 times a week until they approached confluence . trypsin activity was inhibited by adding growth medium and cells were centrifuged at 1000 rpm for 5 min . after 24h , both cells were incubated with different concentrations of the extract into the flasks . cells were observed under light inverted microscope for shape , granulation and suspension from 24 to 72h . cell viability assay the effect of aqueous extract of alpinia galangal on ags and l929 cells proliferation was determined . all five alpinia galangal extracts , at the concentration of 0 - 1000 g / ml , dissolved in dimethyl sulfoxide ( dmso ) ( sigma - aldrich ) , were added to the wells , 24h after seeding of 5103 cells per well of 96 - well plate . after 24 and 48h of incubation , 20l of 5 mg / ml mtt ( sigma chemical company ) solution was added to each well , and the plates were wrapped with aluminum foil and incubated for 4h at 37c . the purple formazan product was dissolved by addition of 100l of 100 % dmso to each well . the absorbance was monitored at 570 nm ( measurement ) and 630 nm ( reference ) using a 96 - well plate reader ( bio - rad , hercules , calif , usa ) . data were collected for each four replicates and used to calculate the means and the standard deviations . optical density of ags and l929 cells incubated in the presence and absence of the different concentrations of alpinia galangal was compared together and the percentage of surviving cells was determined using the following formula : surviving cells ( % ) in compared to the controls = statistical analysis data was analyzed by spss software version 11.5 . one way anova followed by post hoc tukey 's multiple comparison tests were used for statistical evaluation . morphologic changes after 72h , ags and also l929 cells with low concentrations ( 125 and 250 g / ml ) of extract in sense of morphology were very similar to the control . morphological effects of the extract on both cells started at concentration of 500g / ml . a complete response from the extract was seen on both cells at concentrations 750 and 1000 g / ml , so that cells appeared as round and suspended with increase granulation of cytoplasm when compared to the control . the granulation of cytoplasm also was seen on times 24 and 48 h after addition of extract . however , this effect was lower than 72h ( data not shown ) . after 24 hours , the percentage of living ags cells compared to control showed no significant decrease at concentrations of 125 and 250 g / ml . but in the rest concentrations were significant ( p 0.05 ) . the percentage of surviving l929 cells at the extract concentration of 125 g / ml just not be significant , but in the other concentrations were significant . also , there was a direct correlation between increasing in the extract concentration and decreasing of surviving ags and l929 cells . the maximum decrease in the percentage of surviving cells in the both cells was observed at the concentration of 1000 g / ml ( figure 1 ) . as shown in figure 2 , the percentage of living ags and l929 cells were significantly decreased at the last three concentrations of the extract compared with control cells ( p 0.05 ) . also , there was a correlation between increase in the extract concentration and surviving ags and l929 cells . the maximum decrease of surviving ags cells was observed at 250 g / ml while in the l929 cells was at 500 g / ml . these changes became more prominent in third day , so that percentage of surviving ags and l929 cells at concentrations of 500 , 750 and 1000 g / ml of extract showed significant decrease compared with control cells ( p 0.05 ) . the maximum decrease of surviving ags cells was at 500g / ml while in the l929 cells were in 1000g / ml . also , there was a correlation between increase in the extract concentration and decrease of surviving ags and l929 cells . effect of the alpinia galangal extract on percent of surviving ags and l929 cells after 72h is shown in figure 3 . no previous literature was found to show the effectiveness of aqueous extract of alpinia galangal on ags and l929 cells . effect of the extract was started from 24h and continued for 48h and 72h , so that maximum anti proliferative effect appeared after 72h . in mtt assay , statistical analysis indicated that the extract significantly inhibited the proliferation of both cells in concentrations higher than 500g / ml . these results demonstrated that aqueous extract of alpinia galangal can inhibit growth of human gastric tumor cell lines in vitro . but this inhibition can also occur in non - tumor l929 cells . these properties may arise from several mechanisms including inhibition of gene mutation , suppressing the formation of dna - adducts , change of enzyme activity or induction of apoptosis . various in vitro and in vivo studies in diverse cancer cell lines have showed obviously the potential of alpinia species as anticancerous plant in animal models . for instance , pinostrobin chalcone , as a new compound , has been isolated from a. mutica which displays remarkable cytotoxic potential to different human carcinoma cell lines such as mcf7 and caski cells with significant ic50 values . the first compound , showed significant cytotoxic activity against human cancer cell lines like a549 , snu638 , ht1080 , hl60 and hct116 , while , the next compound revealed specific activity against snu638 . on the other hand , cytotoxic activity has been revealed with four different compounds separated from a. officinalrum and only 7 - ( 3,4 - dihydroxyphenyl ) - 1 - ( 4 - hydroxy -3-methoxyphenyl ) -4-en-3-heptanone has notable cytotoxic activity against hepg2 , mcf - 7 and sf - 268 in some other cancer cell lines . in the work of lu et al . it was shown that a. officinarum has the whitening effects on melanin biosynthesis in b16 ( mouse melanoma cell line ) . so that , the flavonoid mixture and galangin exhibited a broad absorption band at 270 - 290 nm related to the uv - b area supporting that galangin could be a whitening agent and a capable candidate for prevention of skin cancer . additionally , acetoxychavicol acetate ( aca ) , a compound isolated from an n - pentane / diethyl ether - soluble extract of dried rhizomes , act as an antiulcer and antitumor agents as well as an inhibitor of chemically induced carcinogenesis is event . it was also shown that extract from the dried rhizomes of a. galangal showed strong protective effects against gastric lesions induced with ethanol , which it is stronger than clinically used medicines such as omeprazole , cimetidine , and cetraxate hydrochloride . in this study , using cell culture model , anti - proliferative effect of aqueous extract of alpinia galangal on human gastric tumor ( ags ) and l929 cell lines was demonstrated . in this study , using cell culture model , anti - proliferative effect of aqueous extract of alpinia galangal on human gastric tumor ( ags ) and l929 cell lines was demonstrated .\noutput:\n" }, { "from": "agent", "value": "backgroundalthough the incidence of gastric cancer is declining during the last half century , this cancer still is the second morbid cancer in the world after lung cancer . the incidence of gastric cancer is 26 per 100,000 in iran . this study evaluated the effect of alpinia galangal on ags cells ( human gastric adenocarcinoma epithelial cell line ) and l929 cells ( as a standard cell line originated from mouse fibroblast cells ) . methodsafter culturing the cells in roswell park memorial institute ( rpmi ) medium , the cells were incubated with different doses of alpinia galangal ( 0 ( control ) , 125 , 250 , 500 , 750 and 1000 g / ml ) in 24 , 48 and 72 hour periods and then , cells viability were assessed using mtt based cell proliferation assay.resultsafter 24 hours , the percentage of living ags cells compared to the control group showed no significant decrease at the concentrations of 125 and 250g / ml . but in the rest concentrations were significant ( p < 0.05 ) . only , the percentage of surviving l929 cells at concentration of 125g / ml of the extract was not significant , but these percentages in the other concentrations were significant . after 48 and 72h incubation , in the last three extract concentrations , the percentage of living ags and l929 cells significantly decreased compared to control cells ( p < 0.05 ) . conclusionwe have demonstrated , using cell culture model , anti - proliferative effect of aqueous extract of alpinia galangal on human gastric tumor ( ags ) and l929 cell lines . this effect was prominent in high concentrations ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: however , the possibility of using a folk theory for predicting others should be taken more seriously in social psychology . folk psychology consists of an array of lay theories or platitudes about how the mind works , which are believed more or less uncritically . mundane examples for widely held lay theories are : people who work hard succeed ; the longer an event lies in the past , the worse it is remembered ; people can not change their personality , moral character , or intelligence ; opposites attract ; or that happiness is a matter of wealth . lay theoriesalso include information about typical everyday settings , typical characters , and how people are expected to behave in certain contexts ( karniol , 2003 ) . the answer to krueger s question where such lay theories come from is that they are a compendium of day - to - day psychological wisdom based on various personal experiences . it takes time to develop these theories , and , like scientific theories , they are refutable and revisable ( e.g. , harris , 1992 ) . if our original article can be interpreted as saying that the basis of these lay theories is an inference from well - known people to people in general , we apologize for this misunderstanding . lay theories come from everyday experiences , irrespective of whether well - known or unknown people are involved . of course , lay theories can be enriched with information about specific people if such information exists ( nickerson , 1999 ) . for example , a social - cognitive variant of theory theory , namely karniol s ( 2003 ) self - as - distinct model , holds that general ( generic , in karniol s terminology ) knowledge can be used in predictions . specific knowledge , that is applicable only to a certain individual , can lead to an activation of the self , but this is not equal to using the self as a basis for a prediction . in sum , there is an alternative to the projection view that is theoretically plausible and empirically substantiated . our example of a choice between carrion and apples as food is only a far - fetched example to illustrate that the use of a theory can also lead to a prediction that entirely overlaps with one s own choice . most people would ( correctly ) predict a preference for cooked beef , but some people ( sometimes ) prefer raw beef ( otherwise there would be no beef tartar ) . however , for predicting this , there is no need to project your own preference . rather , you can apply the simple rule that people prefer cooked over raw meat . if you do so , a high correlation between own and predicted choice follows . krueger ( 2008 , 2012 ) correctly points out that there are ways to identify biases based on projection by using corrected correlations ( see below ) , but most of the evidence for social projection still is based on uncorrected correlations . knowledge used in predictions can be wrong , and it does not necessarily have to do anything with oneself knowledge can happen to lead to a prediction that is similar to one s own point of view , but it needs not to . therefore , correlations are hard to interpret and are unreliable indicators of social projection . however , correlations varying widely in magnitude all have been interpreted as providing evidence for social projection . krueger points out that by sampling error alone , self - other correlations will vary , and that variation is a general property of empirical evidence . meta - analysis is a suitable method to aggregate effect sizes over studies and to thereby wash away the error . while effect sizes do vary , this variation is treated differently in meta - analyses ( cf . borenstein , hedges , higgins , & rothstein , 2009 ) . under the fixed - effect model , the assumption is that there is only one true effect which underlies all studies , and differences in the effect sizes are due to sampling error only . in contrast , under the random - effects model , the assumption is that there is an array of true effects depending on the characteristics of the studies , and therefore , that there are different effect sizes that underlie the effect size variations in various studies . variations in the effect sizes are due to sampling error , in addition to true variation in effect sizes . therefore , depending on the approach , variation in the magnitude of correlations can be interpreted as a variation around a fixed - effect ( indicating the same process , i.e. , projection ) , but also as a variation that indicates different processes ( e.g. , the application of different theories ) . meta - analysis by itself does not tell you whether the effect is fixed or random ; rather this is up to the researcher to decide . a related point is which magnitude of correlation should be used as a benchmark for demonstrating projection . krueger points out that our proposal of using self - reliability has a problem : it sets a ceiling and ensures that only a bias of underprojection can be discoveredsocial projection can be justified and be statistically appropriate ( dawes , 1989 ; hoch , 1987 ) , and there are measures that capture whether a truly false consensus effect ( krueger & zeiger , 1993 ) exists , by correlating item endorsements with the difference between estimated and actual consensus . a truly false consensus effect tells us that people are getting their predictions wrong , but again , not what the source of this bias is ( i.e. , simulation vs. theory ) . the other aspect is conceptual : from the perspective of simulation theory , one can not use the self too much . either you simulate or you do nt , but this is not a matter that is related to the correctness of the prediction . simulation means that you use your own system in exactly the same way for predicting thoughts , actions , and feelings of another person as you would use it if you thought , acted , or felt yourself . krueger s observation thus is true ; by using self - reliability you could only detect underprojection , because overprojection is logically impossible . if social cognition were to use this benchmark , the conclusions probably would be quite different : that there are many cases of underprojection . taken together , additional methods that go beyond simple correlations are necessary , for example , the use of empathy gaps ( loewenstein , 1996 ) , the method of juxtaposed versus independent predictions by perner , gschaider , khberger , and schrofner ( 1999 ) , or the use of process tracing methods in addition to input output measures ( schulte - mecklenbeck , khberger , & ranyard , 2011 ) . in addition , even self - reports can be successfully used in studies on social projection ( dunning & hayes , 1996 ) . in sum , it is not that correlations should be abandoned altogether , but they should be interpreted with caution and supported by additional methods .\noutput:\n" }, { "from": "agent", "value": "in a commentary to our article on the role of theory and simulation in social predictions , krueger ( 2012 ) argues that the role of theory is neglected in social psychology for a good reason . he considers evidence indicating that people readily generalize from themselves to others . in response , we stress the role of theoretical knowledge in predicting other people s behavior . importantly , prediction by simulation and prediction by theory can lead to high as well as to low correlations between own and predicted behavior . this renders correlations largely useless for identifying the prediction strategy . we argue that prediction by theory is a serious alternative to prediction by simulation , and that reliance on correlation has led to a bias toward simulation ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: a man in his eighties with a past medical history notable for 4 primary cutaneous melanomas ( all ajcc stage ia or 0 ) , squamous cell skin cancer , and severe actinic damage presented for routine skin cancer surveillance follow - up . on the left dorsal forearm , a new 8 mm bluish nodule was detected during photographically assisted examination using total body photography digital images ( figure 1 ) . the patient was unaware of the lesion and denied the presence of any symptoms , including pain , itching , or bleeding . non - polarized contact dermatoscopic examination revealed a central blue - white veil , scale , sparse atypical blue and black dots focally at the periphery , and a surrounding pink vascular blush with focal irregular tan - brown pigmentation ( figure 2 ) . no lymph - adenopathy was present in the bilateral epitrochlear , axillary , supraclavicular , or cervical nodal basins , and there were no systemic symptoms . clinical concern for melanoma prompted an excisional biopsy . histopathologic examination of the biopsy specimen revealed a nodular basaloid tumor abutting from the epidermis with mucinous stroma , stromal retraction , and small cystic spaces filled with mucin and melanin pigment ( figure 3 ) . many atypical melanocytes were identified within the tumor as well as in the adjacent epidermis ( figures 3 and 4 ) . the nodular basaloid tumor stained with berep4 ( figure 5 ) . the atypical melanocyte population within the tumor and along the dermal - epidermal junction stained with hmb - 45 ( figure 6a and 6b ) , a103 , and sox10 . these findings were interpreted as melanoma in situ ( mis ) colonizing a nodular basal cell carcinoma ( bcc ) . surgical excision with 1 cm marginstwo additional excisions , each with 5 mm margins , were required to achieve negative histopathologic margins . cutaneous neoplasms with two or more distinct cell populations are rare but well documented entities that frequently pose a diagnostic challenge to both clinicians and pathologists . multiple unique presentations regarding the specific co - existence of bcc with melanoma or melanocytic nevi have been reported , often with confusing , overlapping , or imprecise nomenclature . based on a review of the literature , satter et al proposed simplifying the terminology used for these lesions and classifying them as collision , combined , colonized , or biphenotypic tumors . collision tumors are defined as two distinct neoplasms that occur within close proximity of each other but maintain sharp distinct boundaries . pierard et al retrospectively searched a histopathologic case series of 78,000 primary cutaneous cancers and identified 11 collision tumors of melanoma with bcc . case reports have similarly documented other examples of collisions between bcc and melanoma , but also with melanocytic nevi and blue nevi . boyd and rapini performed a retrospective evaluation of 40,000 cutaneous biopsies and found 69 examples of collision tumors . bcc with melanocytic nevus ( n = 14 ) was the most frequently identified collision tumor in their series . neoplasms consisting of two phenotypically different , yet imperceptibly intertwined populations of malignant cells are referred to as combined tumors . often immunohistochemical stains are required to appreciate the intermingling of two tumor cell populations . using the above definition , authors have suggested reclassifying some neoplasms previously reported as collision or colonized tumors , as examples of combined bcc and melanoma lesions . biphenotypic tumors are exceptionally rare neoplasms that arise from a common stem cell precursor that undergoes divergent differentiation . the tumor cell populations that arise exhibit overlapping immunohistochemical and molecular properties , such as cytoplasmic organelles normally seen in two different cell lines . rodriguez et al described two cases of cutaneous neoplasms with combined phenotypical features of bcc and melanoma , employing the term basomelanocytic tumor . nonetheless , the authors could not conclusively demonstrate tumor cells showing combined staining for keratinocytic and melanocytic markers , and these tumors are likely better classified at present as combined neoplasms . in contrast , there is a report of a biphenotypic squamomelanocytic tumor reported by rosen et al in which dual expression of both s - 100 and keratin could be detected , along with expression of both premelanosomes and keratin tonofilaments in the cytoplasm of cells by electron microscopy . a unique situation arises when mis permeates an adjacent or underlying bcc tumor . in these cases , atypical melanocytes from an adjacent misare found interspersed among , but always restricted to basaloid epithelial cell aggregates ( i.e. , no invasive melanoma component exists ) . the case presented herein represents an example of such a phenomenon ( table 1 ) . care must be used with the term colonization as this term has also been used to describe the situation where large dendritic non - neoplastic melanocytes populate various neoplasms . the discovery of colonization of bcc by melanoma cells specifically led florell et al to analyze nests of bcc using immunohistochemistry . they found that all 10 bcc tumors studied were populated by either dendritic melanocytes at the periphery ( 5/10 ) or evenly throughout the tumor ( 5/10 ) . the authors further compared the density of melanocytes in bcc tumor islands to a single example of bcc colonized by mis and found that when bcc is infiltrated by melanoma cells , the melanocyte density is higher and clusters of melanocytes can be observed . including the case presented herein , the majority of patients who have developed colonization of bcc by mis have been males ( 5/6 ) , often with significant risk factors for melanoma including a history of prior invasive melanomas , severe actinic damage , cdkn2a gene mutation , or xeroderma pigmentosum variant . anatomic sites with chronic ultraviolet light exposure including the face , ears , forearm , and scalp are most frequently affected . dermatoscopy or reflectance confocal microscopy ( rcm ) was rarely used in the evaluation of these neoplasms . recently , these two diagnostic technologies have emerged as valuable tools for the diagnosis of cutaneous neoplasms with two or more distinct cell populations . in one study of 20 benign - malignant collision tumors , dermatoscopy andrcm was successful in identifying the malignant tumor in 14 and 19 cases , respectively . in our case , the dermatoscopic features observed correlated well with histopathologic findings . the blue - white veil and blue - black dots are due to melanin and aggregates of pigmented neoplastic cells within the dermal nodule . the irregular tan - brown color at the periphery of the lesion corresponds to lentiginous proliferation of in - situ neoplastic melanocytes along the dermal - epidermal junction . colonization of bcc by mis raises important etiologic , prognostic , and therapeutic questions . we suggest an interaction theory may be a contributing factor for the colonization of bcc by mis . we believe that increased secretion of cytokines and growth factors from the bcc may create a favorable environment for the unrestrained proliferation of melanoma cells . furthermore , it is plausible that a bcc may be populated by melanoma due to poor physical cohesion of bcc cells , allowing melanoma cells to proceed without mechanical resistance . with regards to prognosis , the biologic significance of the breslow depth of melanoma cells colonizing , but restricted within a bcc tumor island remains unclear . burkhalter and white originally suggested that the bcc simply acts as a conduit for the extension of neoplastic melanocytes , similar to that seen when mis extends along adnexa , and therefore does not represent true invasion . we agree with previous authors who have similarly stated that these lesions are unlikely true invasive melanomas with metastatic potential . nonetheless , the following two cases highlight the caution that should be exercised before issuing a diagnosis of bcc colonization by mis . belisle et al report a case of an 82 - year old woman where the initial biopsy of a papule on the nose demonstrated lentigo maligna with permeation of bcc nests by melanoma cells . no atypical melanocytes were detected in the dermis outside the bcc epithelium or between collagen bundles . a subsequent re - excision , however , demonstrated true dermal melanoma invasion beyond the limits of the bcc , suggesting invasion of melanoma into the dermis from the overlying epidermis . in a similar case , taibjee et al report the presentation of a bcc with an overlying lentigo maligna on the nose of a 78 - year old man . atypical melanocytes , both as single cells and clusters , were additionally present in basaloid islands but also throughout the surrounding bcc dermal stroma . it remains unclear in this later case whether melanoma cells entered the dermis through invasion of the epidermis or via the epithelia of the basaloid tumor islands . in summary , we report a case that may best be interpreted as a melanoma in situ colonizing a bcc . we are of the opinion that these tumors developed independent of each other and the bcc served as a conduit for the extension of melanoma cells . the alternate hypothesis of a biphenotypic tumor with a common precursor diverging towards both epithelial and melanocytic differentiation seems less plausible . given the absence of adequate prospective data on outcomes , we suggest that these neoplasms should be treated on an individual case - by - case basis , taking into account the adequacy of the original biopsy , the anatomic site of the lesion , and the age and underlying comorbidities of the patient . new technologies , particularly rcm , may be useful in accurately identifying these tumors prior to skin biopsy .\noutput:\n" }, { "from": "agent", "value": "colonization of basal cell carcinoma ( bcc ) by melanoma cells is a unique and uncommonly reported cutaneous entity . we describe a bluish nodule on the left forearm found during routine skin cancer surveillance examination with suspicious dermatoscopic findings including central - blue - white veil , sparse atypical dots , and a surrounding pink vascular blush with focal irregular tan - brown pigmentation at the periphery . histopathology demonstrated a pigmented bcc with an overlying and adjacent melanoma in situ ( mis ) , as well as colonization of the bcc nodule by melanoma cells . we performed a review of the literature on the topic and discuss other presentations of cutaneous neoplasms composed of both bcc and melanoma , including collision , combined , and biphenotypic tumors . the prognostic and management challenges inherent to this distinctive neoplasm are summarized ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: removal of myoplasmic ca by this mechanism is essential for physiological cardiac relaxation ( bers , 1991 ) . in general , removal of ca by na - ca exchangeis equivalent to ca entry through l - type ca channels on a beat - to - beat basis ( bridge et al . , na - ca exchange may also serve an important role as a ca entry mechanism during cardiac excitation . several studies have demonstrated that this reverse mode of na - ca exchange can trigger sarcoplasmic reticulum ca release ( leblanc and hume , 1990 ; kohmoto et al . , 1994 ; levi et al . ,1994 ; vornanen et al . , 1994 ; wasserstrom and vites , 1996 ) . consequently , alterations in na - ca exchange function , exemplified by digitalis treatment ( lee and dagastino , 1982 ) or alterations in the intracellular na concentration ( harrison and boyett , 1995 ) , produce major effects on cardiac contractility . recently , several regulatory properties have been characterized for the cardiac na - ca exchanger , ncx1 . detailed characterization of these regulatory mechanisms has been accomplished for the native and cloned cardiac na - ca exchanger using the giant excised patch technique . regarding ionic regulation , both na and ca regulate exchange activity in addition to serving as the transport substrates ( hilgemann , 1990 ) . examination of outward ( reverse ) na - ca exchange currents reveals a complex waveform . the application of nai induces an outward current which undergoes a time - dependent inactivation . the extent of this inactivation is governed by both cytoplasmic na and ca levels . however , in the presence of a constant level of cytoplasmic ca ( e.g. , 1 m ) , both outward currents and the extent of inactivation increase as nai levels are increased . this behavior is referred to as nai - induced or i1 inactivation ( hilgemann et al . cytoplasmic ca levels regulate exchange activity by influencing the extent of nai - induced inactivation and through an apparent direct activation of the exchange molecule ( hilgemann et al . this direct pathway is referred to as i2 inactivation where removal of cytosolic ca favors entry into an inactive ( i2 ) state . both forward andreverse modes of na - ca exchange are regulated by cytoplasmic ca ( matsuoka et al . , 1995 ) , and the high affinity regulatory ca binding site has been identified for the cardiac exchanger , ncx1 ( levitsky et al . , 1994 ; matsuoka et al . , 1995 ) . the ability of other divalent cations to substitute for ca at the regulatory site has not been examined in detail . na - ca exchange has a strict specificity for na as the transported monovalent cation ( philipson and nicoll , 1993 ) . less stringency is observed for transport of other divalent cations with ba and sr being transported to varying degrees . earlier studies of this nature have used cardiac sarcolemmal vesicles to examine radioisotope fluxes for different divalent cations . from these reports , it appeared that ca and sr were transported at nearly equal rates , whereas ba transport was 20 times slower and exhibited a two - to threefold reduction in affinity for the exchanger ( trosper and philipson , 1983 ; tibbits and philipson , 1985 ) . more recent electrophysiological and fluorescence measurements yield conflicting results . in one instance , outward na - ba exchange currents were not detectable from whole cell patch clamp experiments using guinea - pig ventricular myocytes ( kimura et al . , 1987 ) . however , ba uptake through the exchanger was readily detected in cho cells expressing the bovine cardiac na - ca exchanger ( chernaya et al . , 1996 ) . an experimental limitation of all the above studies is the difficulty in discriminating between transport and regulatory consequences for this ionic substitution . however , this limitation can be circumvented by using the giant excised patch clamp . in this study , we have compared the effects of ca and ba on properties of the cloned , cardiac na - ca exchanger , ncx1 . the specific goals were to examine how ba substitution alters the transport and regulatory properties of ncx1 and to determine if these differences can provide a reasonable account for why cardiac muscle fails to relax in ba - containing media . lukas ( university of manitoba , winnipeg , canada ) and were prepared as described previously ( lukas and antzelowitch , 1993 ) . myocytes were superfused with ( in mm ) : 136 nacl , 10 hepes , 8.33 nah2po4 , 5.4 kcl , 1 mgcl2 , 1 cacl2 or bacl2 , ph 7.4 ( using naoh ) at 30c . field stimulation of myocytes at 0.5 hz ( 1.11.5 times threshold ) was performed using a grass sd - 9 stimulator ( grass instrument co. , warwick , ri ) . shortening was monitored with a video edge detection system ( crescent electronics , sandy , ut ) and recorded using axon instruments ( foster city , ca ) hardware and software as described previously ( hryshko et al . , 1989 ) . oocytes were obtained from xenopus laevis as described previously ( hryshko et al . , 1996 ) . oocytes were treated with collagenase ( 20 mg / ml ) for 1 h , washed in barth 's solution , treated with 100 mm k2hpo4 for 15 min , washed , and stored overnight in fresh barth 's solution . oocytes were injected with crna ( 5 ng / oocyte ) , and activity was measured 36 d later . na - ca exchange activity was measured using the giant excised patch clamp technique of hilgemann ( 1989 ) as described previously ( matsuoka et al . , 1995 ; hryshko et al . , pipettes were pulled from borosilicate glass and polished to a final diameter of 2040 m . pipettes were coated with a parafilm / mineral oil mixture to enhance patch stability and reduce electrical noise . for seal formation , oocytes were placed in a solution containing ( in mm ) : 100 koh , 100 mes , 20 hepes , 5 egta , 5 mgcl2 , ph 7.0 with mes . gigaohm seals were formed by gentle suction and patches were excised by progressive movements of the pipette tip . excised patches were in the inside - out configuration . for outward na - ca exchange current measurements , pipettes were filled with ( in mm ) : 100 nmg - mes , 30 hepes , 30 tea - oh , 16 sulfamic acid , 8 caco3 , 6 koh , 0.25 ouabain , 0.1 niflumic acid , 0.1 flufenamic acid , ph 7.0 ( using mes ) . outward na - ca exchange currents were elicited by switching from a li to na - based superfusate containing ( in mm ) : 100 na - or li - aspartate , 20 mops , 20 tea - oh , 20 csoh , 10 egta , 02.30 caco3 or 07.55 ba ( oh ) 2 , 11.5 mg ( oh ) 2 , ph 7.0 ( using mes or lioh ) . the amounts of ca and mg were adjusted to yield free mg concentrations of 1 mm and various free ca concentrations as indicated . maxc software was used to calculate free ca and mg concentrations ( bers et al . , 1994 ) . for inward current measurements , pipettes contained ( in mm ) : 100 na - mes , 20 tea - mes , 20 cs - mes , 10 hepes , 10 egta , 4 mg ( oh ) 2 , 0.2 ouabain , 0.1 niflumic acid , 0.1 flufenamic acid , 0.002 verapamil , ph 7.0 . inward na - ca exchange currents were activated by switching to the li - based ca containing superfusates described above for outward current measurements . current data were acquired and analyzed using axon instruments ( foster city , ca ) hardware and software . solution changes ( 200 ms ) were accomplished using a custom - built 20 - channel computer - controlled solution switcher . lukas ( university of manitoba , winnipeg , canada ) and were prepared as described previously ( lukas and antzelowitch , 1993 ) . myocytes were superfused with ( in mm ) : 136 nacl , 10 hepes , 8.33 nah2po4 , 5.4 kcl , 1 mgcl2 , 1 cacl2 or bacl2 , ph 7.4 ( using naoh ) at 30c . field stimulation of myocytes at 0.5 hz ( 1.11.5 times threshold ) was performed using a grass sd - 9 stimulator ( grass instrument co. , warwick , ri ) . shortening was monitored with a video edge detection system ( crescent electronics , sandy , ut ) and recorded using axon instruments ( foster city , ca ) hardware and software as described previously ( hryshko et al . , 1989 ) . oocytes were obtained from xenopus laevis as described previously ( hryshko et al . , 1996 ) . oocytes were treated with collagenase ( 20 mg / ml ) for 1 h , washed in barth 's solution , treated with 100 mm k2hpo4 for 15 min , washed , and stored overnight in fresh barth 's solution . oocytes were injected with crna ( 5 ng / oocyte ) , and activity was measured 36 d later . na - ca exchange activity was measured using the giant excised patch clamp technique of hilgemann ( 1989 ) as described previously ( matsuoka et al . , 1995 ; hryshko et al . , pipettes were pulled from borosilicate glass and polished to a final diameter of 2040 m . pipettes were coated with a parafilm / mineral oil mixture to enhance patch stability and reduce electrical noise . for seal formation , oocytes were placed in a solution containing ( in mm ) : 100 koh , 100 mes , 20 hepes , 5 egta , 5 mgcl2 , ph 7.0 with mes . gigaohm seals were formed by gentle suction and patches were excised by progressive movements of the pipette tip . excised patches were in the inside - out configuration . for outward na - ca exchange current measurements , pipettes were filled with ( in mm ) : 100 nmg - mes , 30 hepes , 30 tea - oh , 16 sulfamic acid , 8 caco3 , 6 koh , 0.25 ouabain , 0.1 niflumic acid , 0.1 flufenamic acid , ph 7.0 ( using mes ) . outward na - ca exchange currents were elicited by switching from a li to na - based superfusate containing ( in mm ) : 100 na - or li - aspartate , 20 mops , 20 tea - oh , 20 csoh , 10 egta , 02.30 caco3 or 07.55 ba ( oh ) 2 , 11.5 mg ( oh ) 2 , ph 7.0 ( using mes or lioh ) . the amounts of ca and mg were adjusted to yield free mg concentrations of 1 mm and various free ca concentrations as indicated . maxc software was used to calculate free ca and mg concentrations ( bers et al . , 1994 ) . for inward current measurements , pipettes contained ( in mm ) : 100 na - mes , 20 tea - mes , 20 cs - mes , 10 hepes , 10 egta , 4 mg ( oh ) 2 , 0.2 ouabain , 0.1 niflumic acid , 0.1 flufenamic acid , 0.002 verapamil , ph 7.0 . inward na - ca exchange currents were activated by switching to the li - based ca containing superfusates described above for outward current measurements . current data were acquired and analyzed using axon instruments ( foster city , ca ) hardware and software . solution changes ( 200 ms ) were accomplished using a custom - built 20 - channel computer - controlled solution switcher . the rationale and design of the different types of experiments are summarized in fig . 1 . fig . 2 illustrates the effects of replacing 1 mm extracellular ca with 1 mm ba on electrically evoked shortening in a canine ventricular myocyte . almost immediately , contraction fails and a contracture develops . upon restoration of ca to the superfusate , the contracture gradually wanes and near normal resting length and contractions resume . while numerous cellular processes are affected by this intervention , our specific goal was to determine how ba substitution affects the operation of the na - ca exchanger . in particular , we sought to distinguish between the effects of ba substitution on transport vs. regulatory aspects of na - ca exchange function .3 a shows inward na - ca and na - ba exchange currents from a single excised patch . currents were activated by the application of li - based ca - or ba - containing solutions to the cytoplasmic surface of the patch at the concentrations indicated . the pipette solution contained 100 mm na , and ca - and ba - containing solutions were applied in a random order . for ca - activation , notein contrast , at ba concentrations up to 300 m , inward currents were barely detectable . in eight patches showing robust ca - activated inward currents at 30c , three patches were also examined at 37c and did not exhibit substantial ba - activated inward exchange currents , whereas ca - activated currents were readily observed ( not shown ) . we did not routinely examine higher ba concentrations as these led to a small outward current at concentrations of 1 mm and above . this small outward current was also observed using pipette solutions containing li rather than na and may represent residual ca activated cl conductance ( see discussion ) .3 b shows pooled data from nine patches for inward current measurements activated by ca or ba . each point represents the average from between three and nine determinations with data normalized to the inward current obtained at 3 m ca . kd values are not reported as not all divalent concentrations could be examined in a single patch . for comparative purposes , currents obtained at 3 m ca ( n = 9 ) exceeded currents obtained with 100 m ba ( n = 4 ) by 17-fold and 300 m ba ( n = 6 ) by 10-fold .5 ) , the absence of inward current is not a consequence of failure to activate the exchanger with ba .4 illustrates outward currents activated by the application of 100 mm na to the cytoplasmic surface of the patch . different concentrations of regulatory ca were present before and during na application , as indicated .4 , traces a and b ) or ca ( traces c and d ) . , we observed very small currents at 30c ( 20 pa in six separate patches ) . although regulated by ca , the extent of i2 regulation appeared blunted and nai - induced ( i1 ) inactivation was not observed . at 37c , six of six patches exhibited na - ba exchange activity with regulatory properties more typical of those observed with ca - containing pipette solutions . in three patchesfor which both temperatures could be examined , a three to fourfold increase in current magnitude was observed for this 7c increase in temperature , as shown in fig .4 , a and b. recall that this striking increase in outward na - ba exchange currents was not evident for inward currents at 37c .4 , c and d ) , normal i1 and i2 regulation were observed at both temperatures .4 , c and d , shows less augmentation of current ( 3050 % increase ) at 37c than that observed for na - ba exchange . for both ba - and ca - containing pipettes , it is likely that we have underestimated the true temperature sensitivity as current rundown likely occurs during the 510 min period required to increase perfusate temperature . the activity of na - ca exchangers is regulated by the occupancy status of a high affinity ca binding site on the cytoplasmic surface of the molecule ( levitsky et al . , 1994 ; matsuoka et al . consequently , alterations in the activation of na - ca exchange activity by ba could also contribute to the reduced ability of ncx1 to transport ba . to investigate this possibility , we compared regulation of outward na - ca exchange currents by ca and ba . a and b , shows current traces obtained from a single patch at different concentrations of regulatory ca or ba , respectively . ateach concentration indicated , regulatory ca or ba was present before and during the application of 100 mm na to activate the outward current . note that ba was considerably less effective at activating na - ca exchange compared to ca . for example , virtually no current is observed at 3 m ba whereas this level of ca leads to near maximal currents for ca . in addition , the progressive loss of i1 inactivation with increasing ca is much less apparent for ba - regulated currents . , c and d , shows typical concentration dependencies for ca and ba regulation , respectively , for outward exchange currents in two separate patches . the concentration ranges examined were selected to determine kd and illustrate differences between ca and ba on steady - state current properties . the complex relationship of regulatory ca with i1 and i2 inactivation leads to a near linear relation for steady state currents up to 10 m ca , followed by a progressive decline as ca begins to compete with cytoplasmic na ( as seen in fig . 5 a ) . ba regulated peak inaca and steady - state inaca exhibited kd 's of 9.3 and 10.3 m , respectively , and i1 inactivation was not dramatically changed ( as seen in fig . we observed similar differences in regulation of outward currents between ca vs. ba in 12 different patches . pooled data from 9 patches is shown in fig . 6 for peak outward currents regulated by ba or ca . current values were normalized to that obtained for peak outward current in the presence of 3 m regulatory ca , allowing direct comparison of all data . first , the affinity of regulatory ba ( kd = 8.7 m ) is 30 times lower than that for ca ( kd = 260 nm ) . second , the efficiency of ba regulation is substantially lower than that observed with ca . even at the highest ba concentrations examined , ba appeared to be much less effective at alleviating na - induced inactivation compared with ca .7 for pooled results from nine patches ( 39 determinations at each concentration ) . as regulatory cawas progressively increased , steady - state current approached the same level as peak current . in contrast , this behavior was not observed when ba served as the regulatory ion . in two patches examined at 1 mm regulatory ba ( not shown ) , a small reduction in peak to steady state ratio was observed . finally , we compared the ability of cai and bai to compete for nai at the intracellular transport site . to accomplish this , outward na - ca exchange currents were examined in excised patches after treatment with 12 mg / ml - chymotrypsin for 12 min . after this treatment , both i1 inactivation and divalent regulatory effects ( i2 inactivation ) were eliminated . thus , competition between nai and divalent cations could be observed by examining outward current with different concentrations of divalents present . divalent vs. nai competition appears as a reduction of outward current due primarily to : ( a ) increasing electroneutral ca - ca or ca - ba exchange , ( b ) simple competition between na and divalent cation occupancy of the transport site , and / or ( c ) the progressive reduction in driving force for the exchange reaction . typical and pooled results ( mean sd , n = 4 ) are shown in fig . outward currents were activated by 100 mm na , and pipette ca was constant at 8 mm . for ca competition , substantial inhibition of outward exchange currentin contrast , the inhibitory effects of ba are greatly reduced and only become evident between 100 and 300 m ba . we examined the ability of ba to substitute for ca on several aspects of na - ca exchange function . we show that na - ba exchange is substantially reduced in the forward direction ( i.e. , nao - bai exchange ) , appears to be reduced in the reverse direction ( nai - bao exchange ) and is considerably less effective as an activator of the exchanger at the high affinity regulatory ca binding site . these alterations in na - ca exchange function are likely to contribute to the failure of cardiac relaxation during superfusion with ba - containing media . for inward current measurements , substantial na - ca exchange currents were observed at ca concentrations of 1 m and above . in contrast , inward currents due to na - ba exchange were barely detectable even at 100 and 300 m ba ( fig .3 ) . as both na - ca and na - ba currents were measured in the same patches , our results indicate that na - ba exchange is orders of magnitude less effective than na - ca exchange . our data indicate that both the affinity for transport and the efficiency of transport are greatly reduced for na - ba exchange . for example , less inward current was observed at 300 m ba than was produced by 3 m ca . comparatively , with equal concentrations of ca and ba ( e.g. , 100 m ) , inward na - ca exchange current exceeded na - ba exchange by nearly 300-fold . a kd for ba - activation of inward na - ba exchange was not determined as higher concentrations of ba ( e.g. , 1 mm ) invariably led to the appearance of a small outward current . although the induction of this unidentified outward current may partially mask inward currents at lower ba concentrations ( e.g. , 100300 m ) , it seems unlikely that we have grossly under - estimated na - ba exchange . one possibility is that the outward current represents an endogenous ca - activated cl conductance in oocyte membranes . despite using cl - free pipette and perfusing solution , residual cl from the sealing solutionhowever , if present , inward na - ca exchange currents would also be underestimated , presumably by a similar or greater amount . in addition , we observed this pattern of large na - ca vs. small na - ba exchange currents during several long recordings ( 10 min ) in single patches . over this time course , nearly complete run - down of the ca - activated cl conductance occurs due to diffusion of cl from the pipette tip and genuine current rundown . both forward andreverse transport modes of na - ca exchange are regulated by cytoplasmic ca ( matsuoka et al . , 1995 ) . therefore , the possibility exists that reduced inward na - ba exchange is a consequence of reduced exchanger activation by ba . however , the large differences we observed between inward na - ca and na - ba exchange currents can not be attributed to the failure of ba to activate the exchanger . as shown in figs . 5 and 6 , 300 m ba is sufficient to activate 60 % of the current obtainable with ca activation . therefore , even though ba activation is less effective than ca , substantial activation of inward na - ba exchange currents would be expected at the concentrations examined . thus , alterations of vmax and / or the apparent kd for transport appear to be causal for reduced inward na - ba exchange . the results obtained from patches after deregulation by - chymotrypsin ( fig .8 ) showed relatively weak competition between ba and na , supporting the idea of lower affinity at the intracellular transport site . it is of interest to compare our results with those obtained from other experimental systems . for example , in cardiac sarcolemmal vesicles , vmax is reduced by 21-fold and the km is 2.4-fold larger when ba is substituted for ca ( tibbits and philipson , 1983 ) . as vesicular uptake is now considered to be mediated almost exclusively by inside - out oriented vesicles ( li et al . , 1991 ) , our results show a similar or greater reduction in transport capacity and a much larger shift in affinity for na - ba exchange . as an example , a 100 pa inward current for na - ca exchange would result in a comparatively small na - ba exchange current ( i.e. , 5 pa ) . however , at ba concentrations 30 m and below , inward currents were never observed . this may be due to our inability to reliably measure currents less than a few picoamps . in cho cells expressing the bovine cardiac na - ca exchanger , extracellularna - dependent ba efflux could be measured , consistent with forward na - ba exchange . however , a reduction in ba concentration due to forward na - ba exchange was not observed in these same cells based on fura - 2 measurements ( condrescu et al . , 1997 ) . the reasons for these discrepancies remain unknown but may reflect loss of resolution by the various techniques . outward na - ba exchange currents appear to be considerably smaller than those observed using ca as the transported cation . however , since we can not measure outward na - ca and na - ba exchange currents in the same patch , this comparison is strictly qualitative . notwithstanding this limitation , comparison with other published data shows that ba substitution for ca can eliminate or greatly diminish currents associated with the exchanger based on whole cell measurements in guinea pig ( kimura et al . , 1987 ) and rabbit ventricular cells ( shimoni and giles , 1987 ) . in contrast , na - ba exchange activity could be readily measured in cho cells expressing the cardiac exchanger using either ba or fura - 2 measurements under conditions analogous to our outward exchange measurements ( chernaya et al . exchange activity was also regulated by cytosolic ca in this preparation ( chernaya et al . one surprising result from the present study is the marked effects of temperature on the appearance of outward na - ba exchange currents ( fig . , the small outward currents are regulated by cai ( i2 ) but do not exhibit nai - dependent ( i1 ) inactivation . substantially greater currents are observed at 37c , with near normal i1 and i2 regulation . this condition or a greatly reduced affinity for extracellular ba would reduce the fraction of exchangers with intracellularly oriented ion binding sites and consequently would alleviate i1 inactivation . such behavior is analogous to lowering extracellular ca which reduces i1 inactivation ( hilgemann et al . , 1992a ) . this strong temperature dependence must also be considered when comparing results from other studies examining na - ba exchange . finally , we examined the ability of ba to substitute for ca as an activator of the exchanger at the high affinity regulatory ca binding site . second , the efficiency of ba activation is considerably less than that observed with ca over the concentration range examined . at 300 m regulatory ba , maximal outward na - ca exchange currents are only 60 % of those observed for regulatory ca . third , unlike ca , ba does not appear to strongly influence i1 inactivation . raising cytoplasmicca progressively alleviates i1 inactivation ( hilgemann et al . , 1992a ) whereas differences in the profile of ba regulated currents are unremarkable . this feature may prove useful in future studies of the mechanism ( s ) of i1 and i2 regulation . in conclusion , we have characterized the effects of substituting ba for ca on inward and outward exchange currents and on regulatory properties of the cloned canine cardiac na - ca exchanger , ncx1 . by all accounts , the transport and regulatory consequences of this substitution should severely impair the ability of the exchange mechanism to maintain ionic homeostasis . other contributory factors include the reduction or absence of sr ba uptake ( palade , 1987 ; chernaya et al . , 1996 ) and prolonged depolarization due to effects on l - type ca channels ( lee et al . , 1985 ) and k channels ( imoto et al . , 1987 ) . however , while ba substitution alters numerous other homeostatic processes , the demonstrated changes in na - ca exchange function alone would appear sufficient to prevent cardiac relaxation . the underlying rationale and different experimental conditions used in the present study are shown . for outward current measurements , extracellular solutions ( pipette ) contained 8 mm ca or ba , and currents were activated by switching from li - based to na - based intracellular ( bath ) solutions . for inward current measurements , extracellular ( pipette ) solutions contained 100 mm na and currents were activated by switching to intracellular solutions with various concentrations of either ca or ba . the effects of replacing 1 mm extracellular ca with 1 mm ba on electrically stimulated shortening for a canine ventricular myocyte are shown . upon substituting ba for ca , restoration of extracellular ca leads to near full recovery of resting length and shortening . ( a ) illustrates typical inward currents activated by the application of cytoplasmic ca or ba . pooled results from three to nine patches ( normalized to the current value obtained at 3 m cai in nine patches ) ( means se ) are shown in b. the effects of different concentrations of regulatory ca or ba on outward na - ca exchange currents are shown for a single patch in a and b. the pipette solution contained 8 mm ca . the different concentrations of regulatory ca ( a ) or ba ( b ) were present before and during the application of 100 mm na to activate the current . typical concentration dependencies of peak and steady - state ( ss ) outward currents are shown for regulation by ca ( c ) and ba ( d ) from two separate patches . note the difference in concentration range between these graphs . typical outward na - ba ( a and b ) and na - ca ( c and d ) exchange currents examined at 30c ( left ) and 37c ( right ) . the pipette solution contained 8 mm ba or ca and currents were activated by the application of 100 mm na at the indicated concentrations of regulatory cai . data were obtained by making measurements at 30c followed by increasing bath temperature and repeating measurements at 37c ( 57 min later ) . regulation of outward na - ca exchange currents by ba and ca ( inset ) . pooled results ( mean sd ) from three to nine determinations in nine separate patches . currents were normalized to the value of current obtained at 3 m regulatory cai ( in all 9 patches ) . the relationship between peak and steady - state outward na - ca exchange currents regulated by cai ( filled squares ) and bai ( open squares ) is shown for pooled results from three to nine patches ( mean sd ) . for cai regulation , steady - state current approaches peak current levels reflecting the progressive reduction in i1 inactivation . the pipette contained 8 mm ca and currents were activated by the application of 100 mm na . both i1 and i2 regulation are absent after deregulation and the inhibitory effects of different concentrations of ca and ba are evident . pooled results from four patches ( mean sd ) are shown in b. currents were normalized to the value of current obtained in the absence of regulatory divalent cations .\noutput:\n" }, { "from": "agent", "value": "cardiac muscle fails to relax upon replacement of extracellular ca2 + with ba2 + . among the manifold consequences of this intervention , one major possibility is that na + - ba2 + exchange is inadequate to support normal relaxation . this could occur due to reduced transport rates of na + - ba2 + exchange and / or by failure of ba2 + to activate the exchanger molecule at the high affinity regulatory ca2 + binding site . in this study , we examined transport and regulatory properties for na + - ca2 + and na + - ba2 + exchange . inward and outward na + - ca2 + or na + - ba2 + exchange currents were examined at 30c in giant membrane patches excised from xenopus oocytes expressing the cloned cardiac na + - ca2 + exchanger , ncx1 . when excised patches were exposed to either cytoplasmic ca2 + or ba2 + , robust inward na + - ca2 + exchange currents were observed , whereas na + - ba2 + currents were absent or barely detectable . similarly , outward currents were greatly reduced when pipette solutions contained ba2 + rather than ca2 + . however , when solution temperature was elevated from 30c to 37c , a substantial increase in outward na + - ba2 + exchange currents was observed , but not so for inward currents . we also compared the relative abilities of ca2 + and ba2 + to activate outward na + - ca2 + exchange currents at the high affinity regulatory ca2 + binding site . while ba2 + was capable of activating the exchanger , it did so with a much lower affinity ( kd 10 m ) compared with ca2 + ( kd 0.3 m ) . moreover , the efficiency of ba2 + regulation of na + - ca2 + exchange is also diminished relative to ca2 + , supporting 60 % of maximal currents obtainable with ca2 + . ba2 + is also much less effective at alleviating na + i - induced inactivation of ncx1 . these results indicate that the reduced ability of ncx1 to adequately exchange na + and ba2 + contributes to failure of the relaxation process in cardiac muscle ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: it is estimated that in 47 % of the reported injuries in the united states eye injury registry , the mechanism of injury increased the risk for an ocular foreign body ,1 however , the presence of a leech as an ocular foreign body was seldom reported . herein , we report the youngest case of conjunctival leech infestation in english literature , which was removed carefully without long - term complication . a 2 - year - old girl was brought to our outpatient clinic with a complaint of irritable crying after being taken to a stream in hualien 1 day previous , where she played in the water . there was no history of trauma to the eye or any other chronic eye disorders . upon examination , slit - lamp examination showed conjunctival injection with a moving dark black brown foreign body partly attached in the lower conjunctiva near the limbus , resembling uveal prolapse . it was then identified as a live leech grasping the bulbar conjunctiva ( figure 1 ) . after applying topical anesthetics , the leech was extracted under microscope with forceps , and it measured 1 cm in length ( figure 2 ) . the patient began using topical antibiotic and corticosteroid agents afterward . by 1 week after extraction , the patient had no obvious symptoms or signs , except for a mild congestion and patchy subconjunctival hemorrhage . there was no evidence of scleral perforation , corneal injury , uveal prolapse , or uveitis . therapeutic use of leeches has been documented over the past 2,500 years . before the medical and pharmacological advances that followed world war ii , bloodletting by leeches was even reported to be an effective way of treating acute congestive glaucoma .2 in modern plastic surgery , they have been used as decongestants for draining periorbital and scrotal hematomas .3,4 in a hospital emergency setting , there have been cases of ocular leech infestation described in publication , eg , a 32 - year - old man in people s republic of china ,5 a 4 - year - old girl in ethiopia ,6 a 67 - year - old man in iran ,7 a 66 - year - old woman in australia ,7 a 38 - year - old woman in japan ,8 a 28 - year - old man in the uk ,9 a 4 - year - old girl in germany ,10 and a 7 - year - old boy in turkey .11 herein , we report the youngest case of conjunctival leech infestation in english literature . in previous literature , five ocular leeches were removed directly with forceps after instillation of local anesthetic .5,8,1012 other preparing methods before leech removal included irrigation with normal saline in combination with injection of suxamethonium into the worm ,6 application of 3 % hypertonic saline drops ,7 or even direct application of cooking salt to the leech .9 none of the articles reported long - term complications . the method of extraction we used involved instilling topical anesthetic drops and removing the leech with forceps using precaution to ensure that the leech s suckers and midbody were detached from the eyeball completely . we advocate that leech removal with forceps after instillation of local anesthetic is a safe method and should be attempted first . in refractory cases when the leech is firmly attached , additional preparing methods could be used , taking possible undesired eye irritation into consideration . although most human leech infestations have been found by otolaryngologists in the nasopharynx , ocular leech infestation should be considered in the differential diagnosis of patients presenting with ocular complaints , especially in those with a history of swimming or any type of exposure to water in streams and lakes . with proper management , it is feasible to preserve optimal ocular function , minimize morbidity , and reduce discomfort in the patient .\noutput:\n" }, { "from": "agent", "value": "this case report describes a female toddler with manifestations of ocular leech infestation . a 2 - year - old girl was brought to our outpatient clinic with a complaint of irritable crying after being taken to a stream in hualien 1 day previous , where she played in the water . the parents noticed that she rubbed her right eye a lot . upon examination , the girl had good fix and follow in either eye . slit - lamp examination showed conjunctival injection with a moving dark black brown foreign body partly attached in the lower conjunctiva . after applying topical anesthetics , the leech , measuring 1 cm in length , was extracted under a microscope . the patient began using topical antibiotic and corticosteroid agents . by 1 week after extraction , the patient had no obvious symptoms or signs , except for a limited subconjunctival hemorrhage , and no corneal / scleral involvement was observed ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: bicuspid aortic valve ( bav ) is the most frequent congenital cardiac lesion and is found in 0.9 to 2.0 % of the general population ( 1 ) . the congenitally bicuspid aortic valve may have normal function throughout life , or may develop stenosis or regurgitation with or without infection ( 2 ) . case reports of spontaneous aortic thrombosis in the neonate or adult in association with a bicuspid aortic valve are rare , but reported , most of uncertain origin ( 3 ) . the commonest clinical manifestation of antiphospholipid syndrome is with thrombosis . thrombosis in the venous circulation is the most common , but may also occur in the arterial and microvascular compartments . a 51 year old gentleman was referred from coronary care to our unit as an emergency with thrombosis of the aortic valve and ascending aorta . he had been unwell for a two week period prior to admission complaining of generalised malaise and an episode of temporary visual loss in his right eye . his past medical history revealed a mixed picture of arterial and venous thrombosis including a right femoropopliteal bypass for thrombus at the age of 15 , a deep vein thrombosis ( dvt ) in his left leg at the age of 49 and a further embolic event in his left hand . he had been commenced on warfarin at the time of his dvt however this had been stopped 8 weeks before his admission so that he could be investigated at a local haematology clinic . on transfer he was haemodynamically stable in sinus rhythm and clinical examination was essentially normal except for the presence of a soft systolic ejection murmur . transthoracic echocardiography undertaken in coronary care revealed a mobile thrombus , 4.4 x 1.8 cm , attached to the right coronary cusp of the aortic valve , which appeared thickened and calcified . he was taken to theatre as an emergency . a pre - operative transoesophageal echocardiogram ( toe ) confirmed the presence of thrombus on the aortic valve extending into the ascending aorta ( fig 1 ) . after median sternotomy and initiation of cardiopulmonary bypass the ascending aorta was clamped at the level of the innominate artery . a calcified bicuspid aortic valve was excised and replaced with a 27 - mm ats open pivot heart valve . no organisms were seen on gram staining of the thrombus however following advice from the microbiological team empirical therapy with vancomycin and gentamicin was initiated . he made an uneventful postoperative recovery and was commenced on intravenous heparin after surgery until he was adequately anticoagulated with warfarin and aspirin . transoesophageal echocardiogram depicting thrombus in the ascending aorta he was subsequently readmitted with pyrexia , general malaise , lethargy , anorexia , dizziness and flushing . repeated culture results were negative and echocardiography of the prosthetic valve showed good function and no evidence of vegetations . despite this it was decided to treat mr x as a culture negative endocarditis , with a six week course of intravenous vancomycin and gentamicin . since discharge he has remained well . haematological investigations taken prior to admission , whilst he was off warfarin , revealed a normal activated partial thromboplastin time and antithrombin concentration . the cardiolipin antibody ( igg and igm ) were within normal range , however lupus anticoagulant antibodies were positive and considered significant particularly in view of the correlation with his clinical picture . spontaneous thrombosis of the ascending aorta is a rare and usually fatal event . in most casesour patient was found to have both a congenital bicuspid aortic valve and elevated lupus anticoagulant antibodies . antiphospholipid syndrome is diagnosed by the presence of antiphospholipid antibody , typically identification of lupus anticoagulant singly or in combination with anticardiolipin antibody ( 4 ) . in this casethrombosis of the bicuspid aortic valve occurred when his warfarin was discontinued for haematological investigations despite 3 previous thrombo - embolic events . lupus anticoagulant comprises a subgroup of antiphospholipid antibodies that disrupt the actions of the prothrombinase complex ( factors xa , va and prothrombin in combination on phospholipid membranes ) . antiphospholipid antibodies behave as acquired inhibitors of anticoagulation , prolonging phospholipid - dependant coagulation tests ( 5 ) . the activated partial thromboplastin time ( aptt ) this report illustrates the significance of testing for prothrombotic disorders in at risk individuals , to prevent similar scenarios perhaps with the early institution of anticoagulant therapy .\noutput:\n" }, { "from": "agent", "value": "we present the case of a 51 - year - old man who was admitted as an emergency with spontaneous thrombosis of the aortic valve and ascending aorta . at operation he was found to have a congenitally bicuspid aortic valve and subsequent investigation revealed primary antiphospholipid syndrome . he underwent successful removal of the thrombus combined with mechanical replacement of the aortic valve ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the alternate congestion - decongestion response of the erectile tissue of nasal turbinate and septum of two nostrils leads to altered unilateral nasal resistance . thus , the air flow through one nostril is greater than next at any given point of time which later switches to another . the nasal cycle which lasts for 25 min to 23 h is closely related to the ultradian rhythm of cerebral dominance that lasts for 1.53 h. the dominance of nasal cycle is inversely correlated to the alternating dominance in the cerebral hemispheres ; this is regulated by a common mechanism mediated through the autonomic nervous system . electroencephalogram ( eeg ) studies have shown that integrated eeg amplitudes are greater over the cerebral hemisphere contralateral to the dominant nostril . this rhythm of cerebral dominance plays an important role in cognitive performance , memory processes , mood , and behavior . slow yogic breathings through a particular nostril have been shown to be effective in improving cardio - respiratory functions , autonomic imbalances , and psychological stress . studies have observed that left nostril yoga breathing ( lnyb ) enhanced performance in the right hemisphere dominant tasks such as spatial memory scores and right nostril yoga breathing ( rnyb ) improved left hemisphere dominant tasks such as letter - cancellation and verbal memory scores . an ancient yogic treatise in samskrit called shivaswarodaya describes that breathing through a particular nostril affects cognitive activities and emotions of an individual . study by telles et al . showed that right nostril breathing facilitates the left hemisphere activity through a significant reduction in p300 evoked potential latency . the neuroelectric events that underlie p300 generation arise from the interaction between frontal lobe , hippocampal , and temporoparietal function . thus , researches on uninostril yoga breathing increasingly point towards its activating effect on contralateral brain hemispheres ( especially the frontals ) in terms of : ( a ) enhancement of cognitive task performances and ( b ) greater integrated eeg amplitudes . functional near - infrared spectroscopy ( fnirs ) is a noninvasive optical method that can measure the real time change in oxygenated hemoglobin ( oxyhb ) , deoxygenated hemoglobin ( deoxyhb ) , and their sum that is , total hemoglobin ( totalhb ) or blood volume in different brain regions including bilateral prefrontal cortices ( pfcs ) . though the spatial resolution of the fnirs device is coarse , its temporal resolution is excellent and fnirs results are physiologically comparable to fmri results . a recent study used fnirs to study the effect of yoga breathing technique called kapalabhati ( kb ) on blood flow changes in pfcs of 18 healthy individuals and 18 schizophrenia patients . there was a significant increase in bilateral prefrontal oxyhb ( in mol / l ) in healthy subjects during the practice of kb . thus , in order to understand the mechanism through which the nasal cycle relates to ultradian rhythm of cerebral dominance , present study was planned to understand the effect of yoga breathing through a particular nostril on oxygenation and blood flow changes in bilateral prefrontal cortices in healthy individuals using fnirs . thirty - two male subjects with ages ranging between 18 and 35 years ( group mean standard deviation [ sd ] , 23.754.14 years ) and average education of 15.782.88 ( mean sd ) years were included in the study . sex differences have been documented in structure , function , and chemistry of the brain , and different phases of menstrual cycle have been shown to influence the cerebral blood flow , hence the study included only male participants . they had an experience of practicing the three yoga breathing techniques that are , rnyb , lnyb and breathe awareness ( ba ) ranging between 3 and 36 months ( group mean sd , 12.58.6 months ) . all of them had completed a residential training course in yoga which was for 1 - month . in addition to this , all the subjects included in the study were given week long training in the breathing practices assessed in the present study for 30 min each day for a week before starting the study . all subjects were checked for their health using general health questionnaire ( ghq ) and those with ghq score 7 were excluded . they were all right handed dominant based on their response to the edinburgh handedness inventory . also , none of them was taking medication and they did not use any other wellness strategy . the variables to be recorded and the study design were described to the subjects after which their signed consent to participate in the study was obtained . demographic data of the subjects each subject performed single intervention on each day at the same time , empty stomach , but the intervention was randomized using slips numbered from 1 to 3 . recorded audio - tape of instructions was played during the time of the experiment for rnyb , lnyb , and ba , respectively . the inhalation and exhalation ratio was 2:3 , the duration of inhalation was 6 s and exhalation was 9 s. therefore , the breathing time was 15 s for a single breath , approximately 4 breaths in a minute and 80 breaths in the total duration of 10 min . each session lasted for 15 min where the first 5 min was for baseline recording ( pre ) than any one of yogic breathing was performed for 10 min . the intervention of rnyb , lnyb , and ba was practiced for 10 min continuously without any interval . the oxy - hemoglobin ( oxyhb ) and deoxy - hemoglobin ( deoxyhb ) concentration were assessed over the left and right hemisphere . it has 28 questions with four different sub scales to assess the physical fitness , anxiety and insomnia , social dysfunction , and depression . the questioner has acceptable psychometrics and has intimae consistency and reliability with cronbach 's alpha of 0.85 and validity of 0.76 . , u.s.a . ) is a continuous wave device which measures changes in attenuation at 2 wavelengths ( 730 and 850 nm , 15 nm ) , sampling at 25 khz and allows for the differentiation of two dynamic absorbers ( oxyhb and deoxyhb ) . it has 4 light emitting and 10 detector probes with 16 channels that can be measured quasi simultaneously . the optodes were affixed to a probe set with an inter - optode distance of 2.5 cm covering an area of 6 cm 18 cm . the recording was made in a dark sound attenuated cabin . for horizontal fixation , the lower edge of the probe setsample size was calculated using two - tailed g power ( calculated sample size = 32 ; effect size 1.05 , alpha = 0.05 , power = 0.80 ) . the waveforms of oxyhb and deoxyhb changes in bilateral pfc were acquired from all the subjects in all 16 channels , and the data was averaged according to the task condition ( pre , during and post ) . the average of the oxyhb , deoxyhb , and totalhb levels on both right ( channels 18 ) and left side ( channels 916 ) of the brain was taken . thereby , one mean value of each condition ( pre and during ) for each side of the brain ( right and left ) was obtained for each participant . the data were analyzed by the statistician using statistical package for social sciences version 10.0 ( ibm india private limited ) . wilk 's test was used to check the normality of the data . as the data was found to be normally distributed , paired samples t - testwas used to measure the changes in oxyhb , deoxyhb , and totalhb levels , respectively , during rnyb , lnyb , and ba practices from the baseline ( pre ) levels in all the subjects and independent samples t - test was used for between group comparisons . thirty - two male subjects with ages ranging between 18 and 35 years ( group mean standard deviation [ sd ] , 23.754.14 years ) and average education of 15.782.88 ( mean sd ) years were included in the study . sex differences have been documented in structure , function , and chemistry of the brain , and different phases of menstrual cycle have been shown to influence the cerebral blood flow , hence the study included only male participants . they had an experience of practicing the three yoga breathing techniques that are , rnyb , lnyb and breathe awareness ( ba ) ranging between 3 and 36 months ( group mean sd , 12.58.6 months ) . all of them had completed a residential training course in yoga which was for 1 - month . in addition to this , all the subjects included in the study were given week long training in the breathing practices assessed in the present study for 30 min each day for a week before starting the study . all subjects were checked for their health using general health questionnaire ( ghq ) and those with ghq score 7 were excluded . they were all right handed dominant based on their response to the edinburgh handedness inventory . also , none of them was taking medication and they did not use any other wellness strategy . the variables to be recorded and the study design were described to the subjects after which their signed consent to participate in the study was obtained . each subject performed single intervention on each day at the same time , empty stomach , but the intervention was randomized using slips numbered from 1 to 3 . recorded audio - tape of instructions was played during the time of the experiment for rnyb , lnyb , and ba , respectively . the inhalation and exhalation ratio was 2:3 , the duration of inhalation was 6 s and exhalation was 9 s. therefore , the breathing time was 15 s for a single breath , approximately 4 breaths in a minute and 80 breaths in the total duration of 10 min . each session lasted for 15 min where the first 5 min was for baseline recording ( pre ) than any one of yogic breathing was performed for 10 min . the intervention of rnyb , lnyb , and ba was practiced for 10 min continuously without any interval . the oxy - hemoglobin ( oxyhb ) and deoxy - hemoglobin ( deoxyhb ) concentration were assessed over the left and right hemisphere . it has 28 questions with four different sub scales to assess the physical fitness , anxiety and insomnia , social dysfunction , and depression . the questioner has acceptable psychometrics and has intimae consistency and reliability with cronbach 's alpha of 0.85 and validity of 0.76 . the system ( fnir100 - ack - w , biopac systems , inc . , u.s.a . ) is a continuous wave device which measures changes in attenuation at 2 wavelengths ( 730 and 850 nm , 15 nm ) , sampling at 25 khz and allows for the differentiation of two dynamic absorbers ( oxyhb and deoxyhb ) . it has 4 light emitting and 10 detector probes with 16 channels that can be measured quasi simultaneously . the optodes were affixed to a probe set with an inter - optode distance of 2.5 cm covering an area of 6 cm 18 cm . the recording was made in a dark sound attenuated cabin . for horizontal fixation , the lower edge of the probe setsample size was calculated using two - tailed g power ( calculated sample size = 32 ; effect size 1.05 , alpha = 0.05 , power = 0.80 ) . the waveforms of oxyhb and deoxyhb changes in bilateral pfc were acquired from all the subjects in all 16 channels , and the data was averaged according to the task condition ( pre , during and post ) . the average of the oxyhb , deoxyhb , and totalhb levels on both right ( channels 18 ) and left side ( channels 916 ) of the brain was taken . thereby , one mean value of each condition ( pre and during ) for each side of the brain ( right and left ) was obtained for each participant . the data were analyzed by the statistician using statistical package for social sciences version 10.0 ( ibm india private limited ) . wilk 's test was used to check the normality of the data . as the data was found to be normally distributed , paired samples t - testwas used to measure the changes in oxyhb , deoxyhb , and totalhb levels , respectively , during rnyb , lnyb , and ba practices from the baseline ( pre ) levels in all the subjects and independent samples t - test was used for between group comparisons . within group comparisons [ table 3 and figure 1 ] revealed that during rnyb oxyhb levels increased significantly in the left pfc as compared to the baseline ( p = 0.026 ) , whereas no significant change was observed in the right hemisphere ( p = 0.654 ) . during lnyb , we observed a trend towards significance for a reduction in oxyhb in the right hemisphere ( p = 0.057 ) . in the left pfc , there was no significant change in oxyhb levels as compared to the baseline ( p = 0.854 ) . the control intervention ba did not show any significant changes in the levels of oxyhb in bilateral pfc ( left pfc : [ p = 0.145 ] ; right pfc [ p = 0.061 ] ) . comparison within the group before and during rnyb , lnyb and ba groups for changes in oxy - hb , deoxy - hb , total - hb changes in oxygenated hemoglobin levels before and during right nostril yoga breathing , left nostril yoga breathing and breath awareness in left and right hemispheres . oxyhb = oxygenated hemoglobin ; rnyb = right nostril yoga breathing ; lnyb = left nostril yoga breathing ; ba = breath awareness ; pfc = prefrontal cortex for oxyhb levels , comparison between rnyb and ba showed that oxyhb increased significantly in the left pfc during rnyb as compared to ba [ p = 0.012 , table 4 ] ; with no significant difference between them in right pfc [ p = 0.972 , table 4 ] . similarly , the comparison between the oxyhb levels during rnyb and lnyb revealed a significant increase in oxyhb in left pfc during rnyb [ p = 0.024 , table 5 ] as compared to lnyb , with no such difference in right pfc [ p = 0.589 , table 5 ] . no significant differences were observed between oxyhb levels during lnyb and ba in both the pfc [ table 5 ] . comparison between rnyb and ba groups for changes in oxy - hb , deoxy - hb , total - hb during the intervention comparison between rnyb and lnyb groups for changes in oxy - hb , deoxy - hb , total - hb during the intervention during rnyb , we did not observe any significant change in deoxyhb levels in the left as well as right pfc , respectively , as compared to the baseline [ left pfc ( p = 0.289 ) ; right pfc ( p = 0.443 ) ; table 3 and figure 2 ] . similar results were seen during lnyb as well ( left pfc : [ p = 0.359 ; table 3 ] ; right pfc : [ p = 0.808 ; table 3 ] ) . practice of ba also revealed no significant changes during the practice in both the hemispheres but after the practice of ba , there was a significant reduction in deoxyhb in the left pfc [ p = 0.023 , table 3 ] . changes in deoxygenated hemoglobin levels before and during right nostril yoga breathing , left nostril yoga breathing and breath awareness in left and right hemispheres . oxyhb = oxygenated hemoglobin ; rnyb = right nostril yoga breathing ; lnyb = left nostril yoga breathing ; ba = breath awareness ; pfc = prefrontal cortex comparison between deoxyhb levels during rnyb and ba , rnyb and lnyb , or lnyb and ba did not show any significant differences in both the hemispheres , respectively [ table 4 ] . though within group comparison of totalhb levels did not show significant change from the baseline during all the three interventions in both the hemispheres , respectively [ table 3 and figure 3 ] , between group comparisons revealed a significant increase in blood volume in the left pfc during rnyb as compared to ba [ p = 0.017 , table 4 ] . a significant increase in blood volume was seen during rnyb as compared to lnyb as well [ p = 0.034 , table 5 ] . other between the group comparisons for change in blood volume did not reveal any significant change on both the pfc [ table 5 ] . changes in total hemoglobin levels before and during right nostril yoga breathing and left nostril yoga breathing and breath awareness in left and right hemispheres . oxyhb = oxygenated hemoglobin ; rnyb = right nostril yoga breathing ; lnyb = left nostril yoga breathing ; ba = breath awareness ; pfc = prefrontal cortexwithin group comparisons [ table 3 and figure 1 ] revealed that during rnyb oxyhb levels increased significantly in the left pfc as compared to the baseline ( p = 0.026 ) , whereas no significant change was observed in the right hemisphere ( p = 0.654 ) . during lnyb , we observed a trend towards significance for a reduction in oxyhb in the right hemisphere ( p = 0.057 ) . in the left pfc , there was no significant change in oxyhb levels as compared to the baseline ( p = 0.854 ) . the control intervention ba did not show any significant changes in the levels of oxyhb in bilateral pfc ( left pfc : [ p = 0.145 ] ; right pfc [ p = 0.061 ] ) . comparison within the group before and during rnyb , lnyb and ba groups for changes in oxy - hb , deoxy - hb , total - hb changes in oxygenated hemoglobin levels before and during right nostril yoga breathing , left nostril yoga breathing and breath awareness in left and right hemispheres . oxyhb = oxygenated hemoglobin ; rnyb = right nostril yoga breathing ; lnyb = left nostril yoga breathing ; ba = breath awareness ; pfc = prefrontal cortex for oxyhb levels , comparison between rnyb and ba showed that oxyhb increased significantly in the left pfc during rnyb as compared to ba [ p = 0.012 , table 4 ] ; with no significant difference between them in right pfc [ p = 0.972 , table 4 ] . similarly , the comparison between the oxyhb levels during rnyb and lnyb revealed a significant increase in oxyhb in left pfc during rnyb [ p = 0.024 , table 5 ] as compared to lnyb , with no such difference in right pfc [ p = 0.589 , table 5 ] . no significant differences were observed between oxyhb levels during lnyb and ba in both the pfc [ table 5 ] . comparison between rnyb and ba groups for changes in oxy - hb , deoxy - hb , total - hb during the intervention comparison between rnyb and lnyb groups for changes in oxy - hb , deoxy - hb , total - hb during the interventionduring rnyb , we did not observe any significant change in deoxyhb levels in the left as well as right pfc , respectively , as compared to the baseline [ left pfc ( p = 0.289 ) ; right pfc ( p = 0.443 ) ; table 3 and figure 2 ] . similar results were seen during lnyb as well ( left pfc : [ p = 0.359 ; table 3 ] ; right pfc : [ p = 0.808 ; table 3 ] ) . practice of ba also revealed no significant changes during the practice in both the hemispheres but after the practice of ba , there was a significant reduction in deoxyhb in the left pfc [ p = 0.023 , table 3 ] . changes in deoxygenated hemoglobin levels before and during right nostril yoga breathing , left nostril yoga breathing and breath awareness in left and right hemispheres . oxyhb = oxygenated hemoglobin ; rnyb = right nostril yoga breathing ; lnyb = left nostril yoga breathing ; ba = breath awareness ; pfc = prefrontal cortex comparison between deoxyhb levels during rnyb and ba , rnyb and lnyb , or lnyb and ba did not show any significant differences in both the hemispheres , respectively [ table 4 ] . though within group comparison of totalhb levels did not show significant change from the baseline during all the three interventions in both the hemispheres , respectively [ table 3 and figure 3 ] , between group comparisons revealed a significant increase in blood volume in the left pfc during rnyb as compared to ba [ p = 0.017 , table 4 ] . a significant increase in blood volume was seen during rnyb as compared to lnyb as well [ p = 0.034 , table 5 ] . other between the group comparisons for change in blood volume did not reveal any significant change on both the pfc [ table 5 ] . changes in total hemoglobin levels before and during right nostril yoga breathing and left nostril yoga breathing and breath awareness in left and right hemispheres . oxyhb = oxygenated hemoglobin ; rnyb = right nostril yoga breathing ; lnyb = left nostril yoga breathing ; ba = breath awareness ; pfc = prefrontal cortexthe present study was planned to see the effects of yoga breathing through a particular nostril on the hemodynamic changes in the bilateral pfc on 32 healthy male volunteers . we found that rnyb lead to a significant increase in the level of oxyhb and totalhb in the left pfc in comparison to ba or lnyb , also , there was a trend toward significant reduction in oxyhb in right pfc during lnyb and ba , respectively . increase in totalhb and oxyhb and a reciprocal decrease in deoxyhb are expected to be observed in activated areas of the brain in nirs measurements which indicates an increase in the blood flow , though researchers have found activation of a brain region when there is : ( 1 ) no change in totalhb alongside an increase in oxyhb and a reciprocal decrease in deoxyhb and ( 2 ) an increase or no change in deoxyhb accompanying increases in totalhb and oxyhb . oxyhb is considered as the most sensitive indicator of changes in regional cerebral blood flow in nirs measurements . we found an increase in both oxyhb and totalhb with no change in deoxyhb in the left pfc during rnyb . thus , the present study suggests activation or increase in the blood flow in the left pfc during rnyb and trend towards deactivation of right pfc during lnyb and ba , respectively . these results support the relationship between nasal cycle and ultradian rhythm of cerebral dominance and point toward change in the blood flow and oxygenation in contralateral brain regions as one of the mechanisms underlying this relationship . present study also explains : ( 1 ) better performance in the left hemisphere dominant tasks such as verbal memory scores and letter - cancellation task and ( 2 ) increased integrated eeg amplitudes and reduced p300 latency in left hemisphere observed immediately after rnyb respectively . we also observed a trend toward the significant decrease in oxyhb [ p = 0.053 ; table 3 and figure 1 ] along with no change in deoxyhb or totalhb in right pfc during lnyb . but studies have observed the better performances in right hemisphere dominant tasks and higher integrated eeg amplitudes in the right hemisphere after lnyb . thus , why we did not get activating effects on right hemisphere following lnyb or in contrast why our results show a deactivating or relaxing trend is difficult to explain and more detailed studies to understand the underlying mechanisms are needed in future . hereone important aspect is the traditional ancient yogic view on uninostril yogic breathing where lnyb also known as chandra anulomaviloma is believed to produce the calming and relaxing effect on the body in contrast to rnyb or surya anulomaviloma which is more activating and energizing . previously , similar diverging effects of rnyb and lnyb have been observed on autonomic nervous system , where rnyb lead to higher sympathetic activity but lnyb , on the other hand , brought parasympathetic dominance . the exact mechanism through which uninostril breathing influences cerebral blood flow is not known . pfc receives serotonergic input from dorsal raphe nucleus of the brainstem , as well as noradrenergic input from another brainstem nucleus , the locus coeruleus ( lc ) . a large number of studies have shown that these two neurotransmitter systems ( serotonin and nordrenaline ) modulate the functional properties of the pfc in both humans and animal models . studies have revealed that breathing through a particular nostril can alter metabolism and autonomic activites . the mechanical receptors in the nasal mucosa are activated with airflow into the nostrils , and this signal is unilaterally transmitted to the hypothalamus thereby altering the autonomic functions mediated via hypthalamo - pituitary - adrenal ( hpa ) axis . telles et al . found that regular practice of rnyb for a month leads to a significant increase of 37 % in baseline oxygen consumption . the authors attributed this increase in metabolism to increased sympathetic discharge mediated by increased output of adrenaline from the adrenal medulla . interestingly , lc has been identified as an upstream component of circuitry providing for dorsal medial pfc modulation of emotional stress - induced ( hpa ) activation . thus , uninostril yoga breathing may influence pfc through hpa - lc mediated noradrenaline release . another neurotransmitter which may play an important role in mediating pfc activation is serotonin . in order to understand the neuro - physiological mechanisms involved in zen meditation , another study used 24 - channel near - infrared spectroscopy during a 20 - min session of abdominal ( tanden ) breathing in 15 healthy volunteers . they found a significant increase in the level of oxyhb in anterior pfc during tanden breathing , accompanied by a reduction in feeling of negative mood compared to the baseline . they also observed changes in eeg such as increased alpha band activity and decreased theta band activity during tanden breathing and eeg changes were correlated with a significant increase in whole blood serotonin ( serotonin ) levels . thus , the author concluded that tanden breathing lead to the activation of the anterior pfc and serotonin system . this may be responsible for the improvement of negative mood and eeg signal changes observed during tanden breathing . another study assessed three primary lines of evidence that comprised of the effects of serotonin and noradrenaline on impulsivity , cognitive flexibility , and working memory and found supporting evidence toward the activating effect of serotonin and deactivating effect of noradrenaline on pfc . improvement in mood and eeg changes have been observed with rnyb , as these changes are correlated with serotonin level as well and serotonin has an activating effect on pfc , it appears probable that rnyb may be mediating its pfc activating effect via increased serotonin release from the dorsal raphe nucleus in the brainstem . now the question arises , what makes rnyb specifically engage the dorsal raphe nucleus pathway ? it is well known that right and lnyb have diverging effects on the autonomic nervous system , where rnyb causes sympathetic activation and lnyb leads to parasympathetic dominance . rnyb stimulates the paraventricular nucleus and may selectively increase corticotrophin releasing hormone ( crh ) and cortisol by modulation of hpa axis . crh is the stress neurotransmitter which plays an important role in the activation of the central sympathetic and serotonergic systems and release of serotonin from dorsal raphe nucleus has been shown to be mediated by the release of crh . thus , it is hypothesized that rnyb causes prefrontal activation through hpa - crh - dorsal raphe nucleus mediated serotonin release . lnyb , on the other hand , leads to parasympathetic dominance by suppressing the activation of the paraventricular nucleus and thereby decreasing crh and cortisol secretion . it is known that neural connections exist between the crh neurons in the paraventricular nucleus of the hypothalamus and noradrenergic neurons in lc . also , increased parasympathetic response ( as observed after lnyb ) could result in a decrease in both heart rate and respiration that may lead to the stimulation of lc by the paragigantocellular nucleus . thus , two breathing techniques may follow different pathways to cause the activation or deactivation of contralateral hemispheres [ figure 4 ] . a hypothetical mechanism can be postulated to explain the activating and deactivating effects of rnyb and lnyb as observed in our study : this involves hpa - lc mediated noradrenaline release to cause pfc deactivation and hpa - crh - dorsal raphe nucleus mediated serotonin release to cause pfc activation [ figure 4 ] . crh = corticotrophin releasing hormone ; pfc = prefrontal cortex ; rnyb = right nostril yoga breathing ; lnyb = left nostril yoga breathing present study has several limitations . a randomized controlled design would have been better , but this could not be achieved in the present study due to limited subject availability . the main objective of present study was to understand the mechanism through which uninostril yoga breathing affects cognition . thus , this preliminary study was planned to see the effect during the breathing process on pfc activation . in future , we plan to assess the post - breathing effects as well to find out the duration for which the effect lasts after the breathing technique . future studies should also use other comprehensive imaging techniques such as fmri to confirm these findings and should observe the effect of uninostril breathings on other brain areas as well . effect of uninostril yoga breathing on neuro - chemicals should also be assessed in future studies to understand the mechanism behind activation or deactivation of pfcs . future studies should also apply and observe the effects of uninostril yoga breathing on individuals with various psychopathologies where lateralized cerebral dysfunctions are prominent , viz . , attention deficit hyperactivity disorder , alzheimer 's disease , depression , obsessive compulsive disorder etc . yoga breathing through a particular nostril was found to have an effect on contralateral frontal hemodynamics . this may be the probable mechanism behind the cognitive changes induced by uninostril yoga breathing .\noutput:\n" }, { "from": "agent", "value": "objectives : to measure the effect of the right and left nostril yoga breathing on frontal hemodynamic responses in 32 right handed healthy male subjects within the age range of 1835 years ( 23.75 4.14 years ) . materials and methods : each subject practiced right nostril yoga breathing ( rnyb ) , left nostril yoga breathing ( lnyb ) or breath awareness ( ba ) ( as control ) for 10 min at the same time of the day for three consecutive days , respectively . the sequence of intervention was assigned randomly . the frontal hemodynamic response in terms of changes in the oxygenated hemoglobin ( oxyhb ) , deoxygenated hemoglobin ( deoxyhb ) , and total hemoglobin ( totalhb or blood volume ) concentration was tapped for 5 min before ( pre ) and 10 min during the breathing practices using a 16 channel functional near - infrared system ( fnir100 - ack - w , biopac systems , inc . , u.s.a . ) . average of the eight channels on each side ( right and left frontals ) was obtained for the two sessions ( pre and during ) . data was analyzed using spss version 10.0 through paired and independent samples t - test.results : within group comparison showed that during rnyb , oxyhb levels increased significantly in the left prefrontal cortex ( pfc ) as compared to the baseline ( p = 0.026 ) . lnyb showed a trend towards significance for reduction in oxyhb in the right hemisphere ( p = 0.057 ) . whereas ba caused significant reduction in deoxyhb ( p = 0.023 ) in the left hemisphere . between groups comparison revealed that oxyhb and blood volume in the left pfc increased significantly during rnyb as compared to ba ( oxyhb : p = 0.012 ; totalhb : p = 0.017 ) and lnyb ( oxyhb : p = 0.024 ; totalhb : p = 0.034 ) . conclusion : rnyb increased oxygenation and blood volume in the left pfc as compared to ba and lnyb . this supports the relationship between nasal cycle and ultradian rhythm of cerebral dominance and suggests a possible application of uninostril yoga breathing in the management of psychopathological states which show lateralized cerebral dysfunctions ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: stem cells represent the building blocks of our bodies , functioning as the natural units of embryonic generation during development , and adult regeneration following tissue damage . they are defined by two distinct characteristics : the ability to maintain themselves through cell division , sometimes after long periods of inactivity ( self - renewal ) , and the ability to give rise to more specialized cell types ( differentiation ) . based on the stage in development they are derived from , stem cells are broadly classified as embryonic , umbilical cord , and adult stem cells . potency of stem cells decreases during development from totipotent stem cells at the morula stage , capable of differentiating into all embryonic and extraembryonic tissues , to pluripotent stem cells at the blastocyst stage , forming all embryonic tissues , and to multi - or uni - potent adult stem cells , forming tissues within their germ layer ( figure 1 ) . modern understanding of stem cell biology dates back to 1960s , when multipotent hematopoietic and stromal stem cells residing in the bone marrow were identified . from then on , a number of works have reported the isolation of stem cells from adult tissues . adult stem cells , also called somatic stem cells , prompt tissue homeostasis throughout life and ensure tissue regeneration following damage . they reside in specific anatomic locations ( stem cell niches ) and are regulated by a combination of cellular , molecular , and physical signals . numerous types of adult stem cells have been identified , including hematopoietic , mesenchymal , endothelial , intestinal , and neuronal stem cells , each displaying different properties and potency . mesenchymal stem cells , which have been isolated from a range of adult tissues including bone marrow , periosteum , fat , skeletal muscle , and synovial fluid , as well as from the cord blood , umbilical cord , and placenta , have been extensively explored as a source of cells for biomedical applications , owing to their broad regenerative potential , paracrine regulatory effects , and strong immunomodulatory activity . notably , cell populations isolated from different tissues exhibit phenotypic similarities , as well as specific differences in gene expression profiles and biosynthetic properties . importantly , adult stem can be harvested and reimplanted in the same patient , therefore circumventing the immunological problems associated with allogeneic cell transplantation . however , adult stem cells exhibit limited proliferation potential and progressive loss of functionality upon in vitro expansion , and an age - associated decline in cellular fitness , which limit their use for generating large amounts of functional cells for experimental and clinical applications . on the other hand , human embryonic stem cells ( hescs ) , which have been first derived from early embryos in 1998 , are characterized by virtually unlimited proliferation potential and ability to give rise to all tissues constituting the human body , thus holding a high potential for biomedical research and clinical applications as an allogeneic cell source . however , the broader differentiation potential also presents a challenge in directing / controlling the cell fate , and a higher risk of tumor formation after transplantation of hesc - derived tissue progenitors compared to adult stem cells . the ethical controversies involving isolation of hesc and the need for an autologous pluripotent stem cell source have fueled intense investigations into cellular reprogramming , leading to the generation of induced pluripotent stem cells ( ips ) in 2006 ( figure 1 ) . more recently , the new techniques of cellular reprogramming have also been adapted for transdifferentiation the ability of cells to switch from one specialized cell type to another directly , without reversal into a less specialized cell ( figure 1 ) . we are now at a point when our growing understanding of the stem cell regenerative potential , and the development of new technologies offer unprecedented possibilities to conduct biomedical research and to translate the findings into new treatments . in the current paper , we will present the state of the art in human pluripotent stem cells and transdifferentiation research , and discuss some of the biomedical applications that this emerging technology is expected to empower . thomson and colleagues were the first to derive hesc lines from the inner cell mass of human blastocysts generated during in vitro fertilization procedures . derivation from morula stage embryos , from developmentally arrested ( poor quality ) embryos , and from single blastomeres has also been reported , although with lower efficiencies . between 650 % of normal embryosgive rise to new hesc lines , whereas only up to 3 % success has been reported with poor quality embryos . chen and colleagues systematically explored the timing of inner cell mass isolation and found that isolation on day 6 postfertilization results in the highest hesc derivation efficiency ( ~ 50 % ) , about 10-fold increased compared to isolation on day 5 , and about 5-fold increased compared to hesc derivation from intact blastocysts . hesc typically grow in compact colonies on feeder layers of murine embryonic fibroblasts or human cells , which produce the extracellular matrix for cell attachment and condition the culture medium with paracrine factors . protein substrates ( e.g. matrigel , laminin , vitronectin ) and synthetic matrices can also be used for cell derivation and / or culture , providing a more reproducible culture system . hesc culture media were initially supplemented with fetal bovine serum of selected lots , or serum replacement , and with growth factors ( i.e. , basic fibroblast growth factor ) which activate the intracellular signaling networks maintaining pluripotency . in 2006 , ludwig and colleagues developed a defined medium for feeder - free derivation and culture of hesc , accomplishing one of the critical steps to standardize cell production and banking . however , hesc cultivation and passaging are conducted manually , using enzymes ( collagenase iv , dispase , trypsin ) or mechanical dissociation of colonies . survival of hesc as single cells or small aggregates at passaging and after freezing - thawing cycles has been extremely low , until the discovery that application of a selective rho - associated kinase ( rock ) inhibitor , y - 27632 markedly diminishes dissociation - induced apoptosis . further investigations are aimed at automating and scaling up hesc production , such as expansion and differentiation in three - dimensional carriers in suspension culture bioreactors . hescs are commonly characterized by probing the expression of pluripotency markers , including transcription factors ( oct4 , sox2 , nanog ) , surface antigens ( stage specific antigens ssea - 4 , ssea - 3 , proteoglycans tra - 1 - 60 , tra - 1 - 81 ) , and enzymes ( alkaline phosphatase and telomerase ) . pluripotency is confirmed by testing the formation of teratomas containing tissues of all three germ layers after injection into immunocompromised mice . in addition , genetic status and microbiological status are screened to assess quality of the cultures . the described hesc culture environment has allowed extensive ( potentially unlimited ) expansion of undifferentiated cells , while maintaining a normal euploid karyotype . however , several studies showed that hesc cultivation can lead to accumulation of genomic abnormalities , including amplifications and deletions of whole chromosomes or large genomic regions , amplification of certain gene regions ( i.e. , myc oncogene ) , changes in single nucleotide polymorphism , mutations in mitochondrial genome , and aberrant methylation profiles . many of these alterations were observed in late passages , and are likely to provide a growth advantage to the cells . in the future , it will be important to evaluate how specific genomic changes might affect the differentiated progeny of hesc , and to regularly monitor the genomic status of hesc applying high - resolution techniques . first indications that nuclei of somatic cells can be reprogrammed to generate all germ layers of an adult animal date back to 1958 , when gurdon and colleagues cloned mature fertile xenopus laevis from cultured intestinal cells of tadpoles . it took until 1997 to clone the first mammalian , dolly the sheep , by transferring the nucleus of an epithelial cell into enucleated oocyte . reports of successful cloning of mice , cats , dogs , and other animals by somatic cell nuclear transfer followed . recently , it was shown that human somatic cell nuclei can be reprogrammed when intact oocytes are used as the recipient cells , resulting in the first triploid pluripotent cell lines . meanwhile , a groundbreaking discovery that has transformed the field came from an alternative approach in 2006/2007 , when takahashi and colleagues reprogrammed first mouse and then human skin fibroblasts to aninduced pluripotent state by forced expression of four transcription factors : oct4 , sox2 , klf4 , c - myc , delivered by retroviruses . understanding of esc biology was essential for the generation of induced pluripotent stem cells ( ips ) , guiding the selection of transcription factors and culture conditions . improvements of the reprogramming methods followed rapidly , including the use of alternative nonintegrating vectors , reprogramming by recombinant proteins , using only two factors for reprogramming , and replacement of transcription factors with small molecules . in 2010 , warren and colleagues reported on cellular reprogramming using modified rna , avoiding genetic manipulation , and increasing the efficiency of the process . whereas optimization of techniques is still ongoing , generation of hips lines in a safe way opens the possibility for their use in replacement therapies . many of the culture protocols developed for hesc have been successfully adapted to hips , which resemble hesc in their morphology , feeder dependence , surface marker expression , and in vivo teratoma formation capacity . however , it remains an open question how similar are various hesc and hips lines . a study by the international stem cell initiative characterizing 59 hesc lines from 17 laboratories showed similarities in the expression patterns of most hesc markers , as well as differences in expression patterns of some lineage markers and imprinted genes . variable efficiencies to form specific lineages , such as cardiac , neuronal , and pancreatic in vitro , were also observed . in hips , the problem of variability resulting from different genetic backgrounds and culture conditions is compounded by the differences in reprogramming protocols , which involve major transcriptional and epigenetic shifts . perhaps not surprisingly , studies showed larger heterogeneity of hips compared to hesc on a single - cell level , distinct gene expression and methylation signatures , epigenetic memory of somatic cell origin , and differences in the yield and properties of differentiated progeny , such as early senescence of ips - derived cells . there have also been reports of similarities between cohorts of hesc and hips , such at the study of boulting and colleagues , who have found a similar range of efficiencies for motor neuron differentiation between hesc and hips lines . bock and colleagues have approached the problem by establishing genome - wide reference maps for dna methylation and gene expression of 20 hesc and 12 hips lines , and combined these with assaying in vitro differentiation propensity and evaluating 500 lineage - specific transcripts . the assays were combined in a scorecard for a quick and comprehensive characterization of pluripotent cell lines . their results suggest that hesc and hips should be regarded as two partially overlapping groups , with inherent variability among both hesc and hips lines . some studies have indicated that hips retain certain epigenetic memory from the parent cells , and it is largely unclear to what extent the origin of the reprogrammed cells could affect their safety and function . ideally , the source cells would be easily accessible with minimal risk procedures for the patients ( i.e. , blood sample ) , available in large quantities , and allow relatively high reprogramming efficiency and fast hips derivation process . the elucidation of the molecular and cellular events occurring during embryogenesis is of paramount importance to understand the key pathways regulating cell differentiation and tissue formation under normal and pathological conditions . historically , early development was studied in experimental animals , with mouse being the most popular due to its defined genetics and reproductive ability . strong conservation of genes and signaling pathways regulating development between the species has justified the use of animal models as research platform . mouse studies led to identification of several genes and signaling pathways , including wnt , nodal and bmp pathways , which display specific spatiotemporal expression profiles during embryogenesis and play an important role in germ layer specification and tissue formation ( reviewed by tam and loebel ) . subsequent studies in mesc cultures revealed that the same pathways are involved in the regulation of germ layer development in vitro . despite the similarities observed , there are also differences between mouse and human development , including the timing and profile of expression of control genes , as well as the onset and patterning of tissue formation . in addition , discrepancies exist between mesc and hesc , which differ in morphology , cell surface markers , responsiveness to specific factors ( including the leukemia inhibitory factor signaling pathway ) , and pluripotent state . noteworthy , recent studies demonstrated that hesc display a closer similarity with mouse epiblast stem cells ( episc ) , which are derived from postimplantation embryos , suggesting that mouse episc might be a closer equivalent for comparative developmental studies between the two species . today , the ability to culture human pluripotent stem cells and to apply developmentally relevant inductive signals offers an unprecedented possibility to establish human models of embryonic development in vitro . early lineage specification is recapitulated when esc are induced to form three - dimensional cell aggregates embryoid bodies ( ebs ) . in order to direct differentiation toward specific cell lineages , ebsare stimulated with specific growth factors and signaling molecules in tightly controlled concentrations and temporal sequences . typical factors currently used to promote human ebs differentiation include egf , fgf , ra , bmp - 4 for ectodermal - mesodermal induction , tgf - and activin - a for mesodermal induction , and a set of small molecules for endoderm specification . examples of specific lineages derived from hesc using directed differentiation approach include functional motor neurons , human cardiovascular progenitors , pancreatic endoderm , insulin - secreting - cells , hepatocytes , and others . importantly , cells exhibited functionality following in vivo implantation , such as improvement in cardiac function in rodent models of myocardial infarction and development of glucose - responsive endocrine cells from implanted pancreatic endoderm . similarly , stepwise induction protocols have been successfully used for differentiation of ips lines toward different specialized cell types , although the authors often report differences in differentiation efficiency and properties of differentiated progeny . factors such as size of ebs and variability of initial hesc colonies have also been shown to affect differentiation outcomes . for some lineages , differentiation has been achieved in monolayer culture , thereby simplifying the protocols and avoiding the variability associated with eb cultures . frequently , a combination of ebs and monolayer culture is used , utilizing the effects of three - dimensional environment on cell differentiation , and accessibility of monolayer culture for subsequent cell characterization . hesc and hips technologies allow the generation of novel in vitro models to study the underlying mechanisms of disease development , and establish platforms for the screening of new drugs to prevent or reverse disease progression . in one of the first examples , digiorgio and colleagueshave shown that motor neurons derived from hesc are sensitive to toxic effects of glial cells that carry a mutation in sod1 gene , causing amyotrophic lateral sclerosis ( als ) , a fatal neurodegenerative disease . to study the familial forms of the disease , the group has established hips lines from patients with als and showndevelopment of models to study inherited and degenerative disorders , including alzheimer 's disease , parkinson 's disease , schizophrenia , diabetes , gaucher 's disease , and muscular dystrophy is ongoing and expected to significantly affect our understanding of a variety of medical conditions . creation of disease - specific hips is especially valuable when the underlying mechanisms of the disease are not well understood , and the affected cells are not available from the patients , for example in neurodegenerative diseases or cardiac conditions . generation of hesc / hips libraries from specific patient populations and healthy individuals also allows the development of screening platforms to evaluate toxicity and safety of existing and new drugs . during recent years , a considerable number of drugs were withdrawn from the market due to unforeseen cardiotoxic side effects , and cardiotoxicity is one of the major reasons for late - stage attrition of drug candidates . another serious complication is drug - induced liver injury , which is among the most frequent reasons for withdrawal of approved drugs from the market . the early detection of fatal side effects of new drugs could prevent the continuation of a useless and cost - intensive developing process . also , exclusion of compounds proving false negative in suboptimal test systems could be prevented by improving detection of potential toxicity . currently , negative effects are not detected during in vitro and preclinical studies , due to the limited functional capacity and genetic diversity of cellular models used , and due to the interspecies differences between experimental animals and humans in pharmacotoxicological effects . the potential usefulness of hesc - derived cardiac cells for safe pharmacology was shown recently , where cells were reactive to several drugs in a manner that resembles mature cardiomyocytes . in addition , there has been progress in the establishment of protocols for the generation of hepatocyte - like cells from hesc and hips . with respect to evaluating hepatotoxicity using these cells , it will be important to establish the degree of their similarity to primary cells , as well as to identify specific assays to evaluate the functionality of the cells and to detect the drug - induced liver injury in vitro . a large number of medical conditions are associated with loss or malfunction of tissues and organs , and result in patient distress , disability , and death . treatments for these patients currently rely on the transplantation from living and deceased donors , or implantation of medical devices that are limited in their functionality and availability . the ability of stem cells to self - renew and differentiate into specialized cells offers great possibilities in the field of regenerative medicine , both for the ex vivo construction of tissue substitutes ( tissue engineering ) and for transplantation of healthy , potentially genetically - corrected cells ( cell therapy ) . in tissue engineering , stem cellsare combined with biomaterial scaffolds , which act as a functional template for regeneration and tissue maturation under appropriate culture conditions . to date , adult stem cells have largely been used for experimental and clinical tissue engineering applications . however , adult stem cells display limited proliferation and differentiation potential , progressive loss of functionality upon in vitro expansion , and age - associated decline in cellular fitness . in contrast , pluripotent stem cells allow the generation of an unlimited supply of reparative cells ( which are patient - matched in the case of hips ) . to avoid the risk of teratoma formation following in vivo implantation , hesc and hips are induced into lineage - specific progenitors , which display differentiation potential restricted within the germ layer . in one example , our group and others have derived mesodermal progenitors with similarity to adult mesenchymal stem cells in the expression of surface markers , global gene expression profile , and potential to differentiate into osteogenic , chondrogenic , and adipogenic lineage . hesc - mesenchymal progenitors have displayed excellent potential for formation of bone - like tissue when seeded in three - dimensional scaffolds and cultured in dynamic culture systems , suggesting they could be a promising cell source for regeneration of the skeletal system . in some studies , in vivo transplantation of hesc - mesenchymal progenitors showed restricted developmental potential of the cells , as teratoma formation was not observed . in addition , hesc - mesenchymal progenitors injection improved the outcome of ischemic hindlimb injuries . in light of the variability detected between hesc and hips lines , the current challenges lay in the development of robust protocols that will allow effective and reproducible differentiation of various hips lines . in addition , therapeutic applications of hesc and hips derivatives will critically depend on the development of stringent protocols for selection and / or purification of well - defined , stable tissue progenitors , that will demonstrate limited developmental potential within the selected lineage . advances in the hesc field have already resulted in first clinical trials using hesc - derived cells . in 2010 , geron corporation started a phase i clinical trial to evaluate the safety of hesc - derived neural progenitor cells administration in patients with neurologically complete subacute spinal cord injuries ( http://clinicaltrials.gov/ , number nct01217008 ) . unfortunately the trial has been stopped in 2011 due to financial difficulties of the company . currently , advanced cell technology has two ongoing prospective clinical trials ( phases i / ii ) to evaluate the effects of subretinal injection of hesc - derived retinal pigment epithelium cells in patients with dry age - related macular degeneration and patients with stargardt 's macular dystrophy ( http://clinicaltrials.gov/ , no . preliminary studies indicated measurable improvements in the vision of two nearly blind patients that lasted four months following the treatment . a similar clinical trial for treatment of age - related macular degeneration with hesc - derived retinal pigment epithelium cellsis expected to start in the uk in 2012 by the london project to cure blindness ( http://www.thelondonproject.org/ ) . in addition to tissue replacement , stem cells represent a valuable tool in cell therapy for the correction of genetic diseases . in one of the recent studies , deyle et al . reported the disruption of the allele carrying the dominant mutation in the type i collagen genes causing osteogenesis imperfecta , using a combination of gene - targeting and ips technology . mesenchymal stem cells derived from the bone of patients affected by the disease were gene targeted to disrupt the mutant alleles causing the disease , converted to hips , expanded in vitro , and then induced to differentiate toward the osteogenic lineage . following in vivo implantation on ceramic scaffolds , gene - targeted osteogenic cells were able to form bone tissue in experimental animals . correction of genetic mutations was reported for other diseases , including 1 - antitrypsin deficiency and x - linked chronic granulomatous disease , using the zinc finger nuclease technology , which holds great potential for efficient and precise gene manipulation at the desired genomic locations . in summary , stem cell technology , along with the accurate genetic manipulation of hips , opens new possibilities for the generation of clinically relevant cells for autologous cell - based therapies . our growing understanding of the stem cell biology and the development of specific cell lineages has allowed the generation of multiple specialized cell types from stem cells , and the identification of distinct developmental stages that are governed by genetic and epigenetic regulatory networks . in parallel , an alternative approach is being investigated , in which one somatic cell type could be directly converted transdifferentiated into another somatic cell type . this way , abundant adult cells , such as dermal fibroblasts or adipocytes , could be used to produce other therapeutically important cells , such as neurons , cardiomyocytes or pancreatic beta cells . natural transdifferentiation involves a stepwise dedifferentiation of the primary cell to an intermediate cell type , that can then differentiate into the new lineage . in contrast , experimentally induced transdifferentiation involves a direct conversion through a simultaneous downregulation of one genetic programme and a concomitant upregulation of the new genetic programme . in one of the first experiments , muscle - specific genes were induced in pigmented epithelium , nerve , fat , liver , and fibroblast cells by forced expression of myod , a master regulator of muscle differentiation . however , it was not clear until 2008 how the procedure could be applied more generally to other cell types . following the ips reprogramming experiments , zhou and colleagues found that reexpressing a combination of 3 transcription factors , tested from a list of 20 key developmental regulators , can turn pancreatic exocrine cells into pancreatic beta - like cells in adult mice . using a similar approach , vierbuchen and colleagues showed that a combination of 3 factors with important roles in neural development converts mouse embryonic and postnatal fibroblasts into functional neurons in vitro . in a later study , it was shown that the same factors work in converting terminally differentiated hepatocytes into neurons , thereby demonstrating the possibility to reprogram cells between different germ layers . interestingly , the resulting neurons silenced the donor cell transcriptional program , suggesting a binary lineage switch rather than an induction of hybrid cell phenotypes . however , a small but detectable epigenetic memory of the donor cells remained in the induced neurons . current examples of experimentally induced transdifferentiation rely on the ectopic expression of master regulator genes , which are essential for lineage specification during development and can direct the establishment of a new epigenetic state when expressed in the host cell . to achieve a complete phenotypic switch between the two mature cells andgenerate functional cells for potential clinical applications , the activation of a new epigenetic state in the host cells must be associated with full deactivation of the original epigenetic state . this might be more cumbersome to achieve between more distantly related cells owing to their larger epigenetic differences , resulting in relatively inaccessible chromosomal regions . possible strategies to convert more distant cell types could involve the use of chemicals that loosen the chromatin structure and favor epigenetic rearrangements . in addition , reduction of factors that support the original epigenetic state of the mature host cells , and the use of factors that promote the reentry into cell cycle could facilitate the transdifferentiation . taken together , transdifferentiation studies underline the importance of specific factors in lineage specification , and overturn the long - believed notion of stable and irreversible lineage commitment events . with further development and optimization , transdifferentiation protocols could offer a shortcut to production of differentiated cells for biomedical research and clinical applications , potentially avoiding the extensive cell proliferation required for hips derivation and differentiation . in addition , transdifferentiation opens the possibility to convert different cell types directly in vivo to drive tissue repair and regeneration in situ , an approach that would be impossible using ips technology due to the teratoma - forming ability of pluripotent stem cells . on the other hand , direct conversion between terminally differentiated cells , which are characterized by limited proliferative potential , may not be suitable for experimental and clinical applications where large amounts of cells are needed , and in situations where disease conditions result from genetic mutations . hitherto , only a few instructive factor combinations have been reported to directly convert mature cell types , and it is likely that these will depend on the selected target and final cell types . as with the ips , a number of questions regarding the transdifferentiated cell stability , functionality , and safety need to be addressed , and a deeper understanding of the reprogramming process is needed before transdifferentiation can be translated into a therapeutic setting . advances in pluripotent stem cell biology and transdifferentiation have generated great enthusiasm in the scientific community over the last years , and are expected to affect numerous biomedical applications . hesc and hips allow the study and modeling of human development and tissue formation under diverse experimental conditions , and therefore represent an excellent platform for understanding human diseases and developing innovative therapeutic solutions . in parallel , development of transdifferentiation technology offers new insights into adult cell plasticity and could lead to expedited protocols for differentiated cell production . in the context of regenerative medicine , hesc and hipsoffer the possibility to generate an unlimited number of functional cells for reconstructive and reparative therapies . creation of hips libraries is underway , and will expedite both safety pharmacology studies , as well as development of novel therapies . approval of the first hesc - based clinical trials in the usa is encouraging for the field , and signifies the potential of pluripotent stem cells to cure the most devastating diseases of our time . however , there is a lot of work to be done to fully determine the clinical potential , efficacy , and safety of hesc and hips - based treatments . as with other medical breakthroughs , it is only via scrupulous scientific investigation that the true potential of human pluripotent stem cells may be realized .\noutput:\n" }, { "from": "agent", "value": "stem cells divide by asymmetric division and display different degrees of potency , or ability to differentiate into various specialized cell types . owing to their unique regenerative capacity , stem cells have generated great enthusiasm worldwide and represent an invaluable tool with unprecedented potential for biomedical research and therapeutic applications . stem cells play a central role in the understanding of molecular mechanisms regulating tissue development and regeneration in normal and pathological conditions and open large possibilities for the discovery of innovative pharmaceuticals to treat the most devastating diseases of our time . not least , their intrinsic characteristics allow the engineering of functional tissues for replacement therapies that promise to revolutionize the medical practice in the near future . in this paper , the authors present the characteristics of pluripotent stem cells and new developments of transdifferentiation technologies and explore some of the biomedical applications that this emerging technology is expected to empower ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: pseudoaneurysms of the thoracic aorta are caused by the transmural disruption of the thoracic wall and the leak contained by the surrounding mediastinal structures . one of these surgeries that can lead to the ascending aorta false aneurysms is the bentall procedure . the pseudoaneurysm of the ascending aorta is an unusual complication in cardiac surgery , with high incidence rates of morbidity and mortality . we herein underline the possibility of the formation of the ascending aorta pseudoaneurysm and right atrial ( ra ) fistula , leading to right - sided heart failure following a previous bentall procedure . a 44 - year - old woman presented with exertional dyspnea , which had increased in the preceding two months , and edema of the lower extremities . she had a medical history of acute aortic dissection ( type a ) and the bentall procedure and aortic arch revision two years before . after the bentall procedure , she had no early postoperative complications . however , on the 8th postoperative day , she developed fever ( oral temperature = 39 c ) . transesophageal echocardiography ( tee ) and chest computed tomographic ( ct ) scan were performed for the second time in order to work up mediastinitis and endocarditis , both of which were ruled out . there was a wound infection at the site of the axillary cannulation ; and due to positive blood culture with pseudomonas and leukocytosis with left shift , antibiotics such as tazocin , vancomycin , and amikacin were started . nearly after 10 days , she was discharged with no fever or any other complications . during her follow - up , she had no complaints or complications . during her second admission , the patient s vital signs were stable . physical examination revealed 4 edema of the lower extremities , ascites , and holosystolic murmur in the left lower sternal border . chest x - ray demonstrated cardiomegaly , hyperemia in the lungs , right - sided pleural effusion , and enlarged shadow of the ascending aorta . preoperative echocardiography revealed a large pulsatile echo - free space ( 7 cm ) , surrounding the tube graft of the ascending aorta , and a small connection between this echo - free space and the tube graft just at the site of the right coronary artery implantation with a small orifice ( 2.5 mm ) , mostly suggestive of a pseudoaneurysm . furthermore , there was a continuous flow between this echo - free space and the ra with a small connection ( 3 mm ) , indicative of the fistulization of the pseudoaneurysm to the ra ( figures 1 and 2 ) . contrast study with the injection of agitated saline showed the rapid filling of the ra , followed by the large pseudoaneurysm . other echocardiographic studies illustrated a normal left ventricular size with mild systolic dysfunction ( left ventricular ejection fraction = 45 % ) . intraoperative echocardiography before surgical repair : the short - axis view of the aortic tube graft in the ascending aorta with a large pseudoaneurysm surrounding the tube graft . the estimated diameter of the pseudoaneurysm is about 7 cm , compared with the 2.75 cm diameter of the tube graft intraoperative echocardiography before surgical repair : the off - axis view of transesophageal echocardiography demonstrates the color flow of the pseudoaneurysm fistulizing to the right atrium with a continuous flow via a small orifice , estimated to about 6 mm in size ( arrow ) multi - slice ct scan was also conducted , and the results showed a large pseudoaneurysm of the ascending aorta around the tube graft , 10578 mm in diameter , with a compression effect on the superior vena cava ( svc ) . the most probable origin of the pseudoaneurysm was the right lateral side of the prosthetic valve . an intimal flap from old dissections in the aortic arch extended to the proximal part of the left common carotid artery . there was moderate abdominal ascites and right pleural effusion ( 700cc ) . under general anesthesia and after heparinization ( 3 mg / kg ) , peripheral cannulation , encompassing the right axillary artery and the femoral vein , after median sternotomy and decortication , the svc was cannulated and the ascending aorta , which was surrounded by the large pseudoaneurysm , was relieved . therefore , the patient was cooled down to 28 c and the flow of the pump was decreased . the wall of the pseudoaneurysm was opened longitudinally , and the defects related to the right coronary artery anastomosis to the composite of the graft were controlled by the surgeon s finger . the ascending aorta was clamped , and cardiac arrest was performed with the use of a cardioplegic solution via the anterograde and retrograde methods . a small part of the anastomosis was opened from the peripheral part of the right coronary ostium , and the blood was directed into the pseudoaneurysm through the said defect . the pseudoaneurysm space beside the ra appendage was directed into the ra with a diameter of 5 mm at the orifice and , as a result , one indirect aorta - ra fistula was formed , which resulted in a left - to - right shunt . the patient was weaned off from cpb easily , and intraoperative tee revealed the perfect result of the surgery ( figure 3 ) . postoperative echocardiographic study showed the disappearance of the large echo - free space , normal function of the tube graft of the ascending aorta , no leakage from the proximal or the distal part of the tube graft , and no abnormal space around it . intraoperative echocardiography after surgical repair : the long - axis view of the aorta ( tube graft with a bileaflet mechanical aortic prosthesis ) with normal functioning and no evidence of residual pseudoaneurysm or leakage from the tube graft av , aortic valve lv , left ventriclemost patients tend to develop pseudoaneurysms in the ascending aorta after previous cardiac and aortic operations . the potential sites for the pseudoaneurysm formation are aortic and coronary ostial suture lines , aortotomy site , aortic cannulation site , proximal or distal aortic suture lines , aortic vent site , and cardioplegic needle puncture site . suture line tension and persistent bleeding into the space between the graft and the wrapped aortic wall seem to be the most important mechanisms of the pseudoaneurysm formation . in order to assess the complexity of an aortic aneurysm , ct scan and two - dimensional echocardiography are complementary techniques . in our patient , the aortic pseudoaneurysm was formed due to a previous bentall procedure ; and given the location of the pseudoaneurysm , suture line tension was the likely culprit . the aneurysm - atrium fistula had led to right - sided heart failure , which is very rare and unusual . pseudoaneurysms can be life - threatening , and their concurrence with ra fistulization , although rare , constitutes a very serious complication . accordingly , we would recommend that pseudoaneurysms and fistulizations be taken into account in patients with right - sided heart failure and a history of the bentall procedure . pseudoaneurysms can be life - threatening , and their combination with right atrial fistulization , albeit rare , constitutes a very serious complication . it is , therefore advisable that pseudoaneurysms and fistulizations be taken into consideration in patients with right - sided heart failure and a history of the bentall procedure .\noutput:\n" }, { "from": "agent", "value": "abstractpseudoaneurysms of the ascending aorta , which are rare and life - threatening complications in cardiovascular surgeries , can be caused by the bentall procedure . we describe a 44 - year - old woman , who had a medical history of acute aortic dissection ( type a ) and the bentall procedure and was admitted because of exertional dyspnea , edema of the lower extremities , ascites , and holosystolic murmur in the left lower sternal border . preoperative echocardiography revealed a pseudoaneurysm of the ascending aorta and fistulization of the pseudoaneurysm to the right atrium . multi - slice computed tomographic scan also showed a large pseudoaneurysm of the ascending aorta around the tube graft . the patient underwent surgery , during which the pseudoaneurysm was resected , the ostium of the right coronary artery was reimplanted , and the orifice of the right atrial fistula was sutured . intraoperative transesophageal echocardiography revealed the perfect result of the surgery . the patient was discharged uneventfully ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: in the last 2 decades , the use of excimer laser phototherapeutic keratectomy ( ptk ) has become an accepted modality for the treatment of several anterior corneal irregularities , including persistent epithelial defects and superficial opacities of the cornea .1,2 epithelial basement membrane dystrophy ( ebmd ) is commonly treated with ptk at our institution . ebmd , also known as map - dot - fingerprint , anterior basement membrane , or cogan s microcystic epithelial dystrophy , is a common dystrophy , with 2 % of the population estimated to be affected . ebmd stems from an inherent dysfunction in the basal epithelial cells resulting in the secretion of abnormal basement membrane that extends into the epithelium as well as the accumulation of fibrillogranular material both between bowman s layer and basement membrane and within the epithelium .3 it is characterized by epithelial microcysts , map - like configurations , and fingerprint lines as a result of irregular and redundant basement membrane proliferation . approximately 10 % of ebmd patients experience symptoms of either pain from recurrent corneal erosions or decreased vision secondary to corneal surface irregularity .3,4 treatment for symptomatic ebmd begins with topical lubricants , hypertonic solutions , and bandage soft contact lenses , while medically refractory cases are recommended for surgical treatments such as stromal puncture with a needle or neodymium : yag laser and epithelial debridement .5,6 in cases of ebmd , epithelial debridement with diamond - dusted burr polishing or ptk ablation to the level of bowman s membrane has shown to be effective .711 to the authors knowledge , the present study is the largest series of ebmd eyes treated with ptk to date . we present the long - term outcomes of ptk , our preferred technique , performed on a cohort of patients who had failed conservative management for ebmd . we hypothesize that those patients with a favorable early posttreatment course continue to benefit from treatment in the long term . a search of medical records to identify all patients who had undergone ptk for ebmd between september 2000 and september 2015 at the byers eye institute was performed . the benefits and risks of ptk were discussed with all patients , and written informed consent was obtained . ethical approval for this retrospective study was granted by the institutional review board of stanford university medical center and was conducted in strict adherence to health insurance portability and accountability act of 1996 and the tenets of the declaration of helsinki . patients were included in the study if they had failed conservative treatment for ebmd . ebmd patients presented with symptomatic recurrent corneal erosions , irritation , or visual symptoms with morphological slit - lamp findings of ebmd . patients were considered to have recurrent erosions if they had painful episodes at night or on awakening in conjunction with slit - lamp findings of epithelial irregularity . eyes were considered to have morphological slit - lamp findings of ebmd if microcysts , maps , dots , or fingerprint changes were seen on slit - lamp examination . the amo visx star excimer laser ( 193 nm wavelength , 160 mj / cm fluence ; abbott medical optics inc , santa ana , ca , usa ) was used for all ptk treatments with a repetition rate of 2 hz . the central cornea was treated using a 6.0 - mm spherical treatment zone wit5 m ( 1520 pulses ) of tissue removal . the peripheral cornea was treated using a spherical 3 - mm zone in a donut - like pattern using the joystick and head movement to apply the treatment . postoperative management included a bandage contact lens used along with fluorometholone ( fml ) 1 % twice a day and moxifloxacin or ciprofloxacin four times a day until the bandage contact lens was removed . patients were continued on muro 128 for at least 1 month and longer as needed . the patient s corrected distance visual acuity ( cdva ) , symptoms , corneal findings with special attention to corneal haze and ebmd features , history of recent erosions , and manifest refraction were recorded . the presence of recurrent erosions , visual complaints or irritation with characteristic ebmd morphological features anywhere on the cornea 3 months after successful ptk , and reepithelialization were criteria for recurrence . postoperative cdva to preoperative cdva was compared with paired , 2 - tailed t - test for normally distributed data and with wilcoxon signed - rank test for non - normally distributed data as determined by the shapiropostoperative cdva and duration of time to recurrence between subgroups were compared with 2 - variable t - test for normally distributed data and with wilcoxon rank - sum test for non - normally distributed data as determined by the shapirothe correlation of cdva stability with time was estimated by calculating the pearson product - moment correlation coefficient . the cumulative probability of recurrence of ebmd - related symptomsstatistical analysis was performed using stata ( statacorp lp , college station , tx , usa ) and excel ( microsoft corporation , redmond , wa , usa ) . a search of medical records to identify all patients who had undergone ptk for ebmd between september 2000 and september 2015 at the byers eye institute was performed . the benefits and risks of ptk were discussed with all patients , and written informed consent was obtained . ethical approval for this retrospective study was granted by the institutional review board of stanford university medical center and was conducted in strict adherence to health insurance portability and accountability act of 1996 and the tenets of the declaration of helsinki . patients were included in the study if they had failed conservative treatment for ebmd . ebmd patients presented with symptomatic recurrent corneal erosions , irritation , or visual symptoms with morphological slit - lamp findings of ebmd . patients were considered to have recurrent erosions if they had painful episodes at night or on awakening in conjunction with slit - lamp findings of epithelial irregularity . eyes were considered to have morphological slit - lamp findings of ebmd if microcysts , maps , dots , or fingerprint changes were seen on slit - lamp examination . the amo visx star excimer laser ( 193 nm wavelength , 160 mj / cm fluence ; abbott medical optics inc , santa ana , ca , usa ) was used for all ptk treatments with a repetition rate of 2 hz . the central cornea was treated using a 6.0 - mm spherical treatment zone wit5 m ( 1520 pulses ) of tissue removal . the peripheral cornea was treated using a spherical 3 - mm zone in a donut - like pattern using the joystick and head movement to apply the treatment . postoperative management included a bandage contact lens used along with fluorometholone ( fml ) 1 % twice a day and moxifloxacin or ciprofloxacin four times a day until the bandage contact lens was removed . patients were continued on muro 128 for at least 1 month and longer as needed . the patient s corrected distance visual acuity ( cdva ) , symptoms , corneal findings with special attention to corneal haze and ebmd features , history of recent erosions , and manifest refraction were recorded . the presence of recurrent erosions , visual complaints or irritation with characteristic ebmd morphological features anywhere on the cornea 3 months after successful ptk , and reepithelialization were criteria for recurrence . postoperative cdva to preoperative cdva was compared with paired , 2 - tailed t - test for normally distributed data and with wilcoxon signed - rank test for non - normally distributed data as determined by the shapiro wilk test . postoperative cdva and duration of time to recurrence between subgroups were compared with 2 - variable t - test for normally distributed data and with wilcoxon rank - sum test for non - normally distributed data as determined by the shapiro wilk test . the correlation of cdva stability with time was estimated by calculating the pearson product - moment correlation coefficient . the cumulative probability of recurrence of ebmd - related symptoms was determined using the kaplan meier method . statistical analysis was performed using stata ( statacorp lp , college station , tx , usa ) and excel ( microsoft corporation , redmond , wa , usa ) . all patients had complete ophthalmologic examination including cdva and slit - lamp biomicroscopy before surgery . of the 58 eyes , 29 ( 50 % ) had recurrent erosions ; 30 ( 52 % ) had visual symptoms , including glare , photophobia , blur , or image distortion ; and 4 ( 7 % ) had a combination of erosions and visual symptoms . patients were followed up for a minimum of 3 months postoperatively , with a range of follow - up from 3 to 170 months . a total of 32 eyes had at least 1 year of follow - up , and a total of 11 eyes had at least 5 years of follow - up . for patients presenting with symptoms of visual disturbances , the average visual acuity preoperatively was ~ 20/32 ( log - mar 0.24 sd 0.21 ) . the mean final postoperative cdva wa20 / 25 ( logmar 0.07 sd 0.12 ; p 0.0001 ; table 1 and figure 1a ) . of the 30 eyes in this cohort , 14 ( 46.7 % ) gained 2 lines of visual acuity , 8 ( 26.7 % ) gained 1 line , 7 ( 23.3 % ) had the same cdva , and 1 ( 3.3 % ) lost 2 lines of visual acuity compared to preoperative measurement . cdva gains were stable with no significant trend toward improving or worsening cdva with longer follow - up ( figure 2a ) . for patients presenting with symptoms of pain from recurrent erosions , the mean final postoperative cdva was ~ 20/20 ( logmar 0.05 sd 0.16 ; p = 0.0785 ; figure 1b ) . of the 29 eyes in this cohort , 5 ( 17.2 % ) gained 2 lines of visual acuity , 8 ( 27.6 % ) had the same cdva , 6 ( 20.7 % ) lost 1 line , and 1 ( 3.4 % ) lost 2 lines of visual acuity compared to preoperative measurement . cdva gains were stable with no significant trend toward improving or worsening cdva with longer follow - up ( figure 2b ) . there was no statistically significant difference in postoperative cdva between the 2 groups of patients . however , patients presenting with symptoms of visual disturbances did have worse preoperative cdva compared to patients presenting with recurrent erosions ( logmar 0.24 vs 0.05 , p = 0.01 ) and also experienced a greater improvement in cdva postoperatively ( 0.17 vs 0.07 , p = 0.01 ) . both groups of patients had similar rates of significant loss of visual acuity ( 2 lines ; 3.3 % vs 3.4 % , p = 0.98 ) . for patients presenting with symptoms of visual disturbances , there was no statistically significant difference in preoperative versus postoperative manifest refraction spherical equivalent ( + 0.25 dsimilarly , for patients presenting with symptoms of pain from recurrent erosions , there was no statistically significant difference in preoperative versus postoperative manifest refraction spherical equivalent ( + 0.26 d sd 1.44 , p = 0.63 ) . for patients presenting with symptoms of visual disturbances ,26 out of 30 eyes ( 86.7 % ) experienced initial resolution of symptoms following ptk . of these 26 eyes , 6 eyes ( 23.1 % ) experienced a recurrence of symptoms at an average follow - up time of 37.7 months postoperatively ( range 4105 months , sd 42.8 ) . among these eyes , 3 ( 50 % ) had recurrence of visual disturbances within the first year postoperatively , 5 ( 83.3 % ) had improved cdva compared to preoperative values , and 1 ( 16.7 % ) had unchanged cdva compared to preoperative values . a total of 6 out of 30 eyes ( 20.0 % ) demonstrated morphologic recurrence of ebmd findings on postoperative slit - lamp examination . however , there was no significant difference in mean cdva between eyes with and without morphologic recurrence ( p = 0.7734 ) , and none of these eyes underwent a repeat treatment with ptk . the probability of being recurrence free from visual disturbances at 5 years postoperatively for eyes that had an initial treatment response to ptk was estimated at 83.0 % ( 95 % confidence interval [ ci ] 68.7 % 97.0 % ) by the kaplan meier analysis ( figure 3a ) . for patients presenting with symptoms of pain from recurrent erosions ,23 out of 29 eyes ( 79.3 % ) experienced initial resolution of symptoms following ptk . of these 23 eyes , 3 eyes ( 13.0 % ) experienced a recurrence of symptoms at an average follow - up time of 9.7 months postoperatively ( range 811 months , sd 1.5 ) . all 3 of these eyes had recurrence of painful erosions within the first year postoperatively . a total of 5 out of 29 eyes ( 17.2 % ) demonstrated morphologic recurrence of ebmd findings on postoperative slit - lamp examination . of these , only 1 eye ( 20 % ) reported symptomatic recurrence of painful erosions . of the 6 eyes that did not respond initially to ptk , 2 eyes underwent repeat ptk , with 1 of these eyes reporting improved but persistent symptoms at the final follow - up and 1 eye reporting no further symptoms at the final follow - up . of the 3 eyes experiencingrecurrence of painful erosions , 1 underwent repeat ptk with no further symptoms at the final follow - up . the probability of being recurrence free for symptomatic erosions at 5 years postoperatively for eyes that had an initial treatment response to ptk was estimated at 88.0 % ( 95 % ci 65.3 % 96.6 % ) by the kaplanwhen comparing between the 2 groups , there were no statistically significant differences in rates of primary treatment response , rates of symptomatic recurrence , or time to recurrence . postoperatively all corneas reepithelialized within 14 days and 91 % within 7 days , and no infections occurred . for patients presenting with symptoms of visual disturbances , the 1 eye ( 3.3 % ) with reduced cdva postoperatively had a final cdva of 20/50 ( logmar 0.4 ) and was noted to have corneal edema and stromal haze that had not been present preoperatively . for patients presenting with symptoms of recurrent erosions , the 7 eyes ( 24 % ) with reduced cdva postoperativelyof these eyes , 4 had no new ocular findings and clear corneas at the final slit - lamp examination and a mean final cdva of 20/25 ( logmar 0.1 sd 0.08 ) . the remaining 3 eyes had either guttata , stromal edema , or dots on the final slit - lamp examination , and a mean final cdva of ~ 20/50 ( logmar 0.43 sd 0.12 ) . of the 58 eyes examined , 9 eyes ( 15.5 % ) showed new or progressed evidence of stromal haze or corneal opacity after ptk . there was no statistically significant difference in postoperative cdva between eyes with and without new or progressed stromal haze or corneal opacity . among eyes with new or progressed stromal haze , only 1 ( 11.1 % ) demonstrated reduced cdva by 2 lines , with 5 ( 55.6 % ) showing improved cdva and 3 ( 33.3 % ) showing no change in cdva . all patients had complete ophthalmologic examination including cdva and slit - lamp biomicroscopy before surgery . of the 58 eyes , 29 ( 50 % ) had recurrent erosions ; 30 ( 52 % ) had visual symptoms , including glare , photophobia , blur , or image distortion ; and 4 ( 7 % ) had a combination of erosions and visual symptoms . patients were followed up for a minimum of 3 months postoperatively , with a range of follow - up from 3 to 170 months . a total of 32 eyes had at least 1 year of follow - up , and a total of 11 eyes had at least 5 years of follow - up . for patients presenting with symptoms of visual disturbances , the average visual acuity preoperatively was ~ 20/32 ( log - mar 0.24 sd 0.21 ) . the mean final postoperative cdva wa20 / 25 ( logmar 0.07 sd 0.12 ; p 0.0001 ; table 1 and figure 1a ) . of the 30 eyes in this cohort , 14 ( 46.7 % ) gained 2 lines of visual acuity , 8 ( 26.7 % ) gained 1 line , 7 ( 23.3 % ) had the same cdva , and 1 ( 3.3 % ) lost 2 lines of visual acuity compared to preoperative measurement . cdva gains were stable with no significant trend toward improving or worsening cdva with longer follow - up ( figure 2a ) . for patients presenting with symptoms of pain from recurrent erosions , the mean final postoperative cdva was ~ 20/20 ( logmar 0.05 sd 0.16 ; p = 0.0785 ; figure 1b ) . of the 29 eyes in this cohort , 5 ( 17.2 % ) gained 2 lines of visual acuity , 8 ( 27.6 % ) had the same cdva , 6 ( 20.7 % ) lost 1 line , and 1 ( 3.4 % ) lost 2 lines of visual acuity compared to preoperative measurement . cdva gains were stable with no significant trend toward improving or worsening cdva with longer follow - up ( figure 2b ) . there was no statistically significant difference in postoperative cdva between the 2 groups of patients . however , patients presenting with symptoms of visual disturbances did have worse preoperative cdva compared to patients presenting with recurrent erosions ( logmar 0.24 vs 0.05 , p = 0.01 ) and also experienced a greater improvement in cdva postoperatively ( 0.17 vs 0.07 , p = 0.01 ) . both groups of patients had similar rates of significant loss of visual acuity ( 2 lines ; 3.3 % vs 3.4 % , p = 0.98 ) . for patients presenting with symptoms of visual disturbances , there was no statistically significant difference in preoperative versus postoperative manifest refraction spherical equivalent ( + 0.25 d sd 1.82 , p = 0.65 ) . similarly , for patients presenting with symptoms of pain from recurrent erosions , there was no statistically significant difference in preoperative versus postoperative manifest refraction spherical equivalent ( + 0.26 d sd 1.44 , p = 0.63 ) . for patients presenting with symptoms of visual disturbances , 26 out of 30 eyes ( 86.7 % ) experienced initial resolution of symptoms following ptk . of these 26 eyes , 6 eyes ( 23.1 % ) experienced a recurrence of symptoms at an average follow - up time of 37.7 months postoperatively ( range 4105 months , sd 42.8 ) . among these eyes , 3 ( 50 % ) had recurrence of visual disturbances within the first year postoperatively , 5 ( 83.3 % ) had improved cdva compared to preoperative values , and 1 ( 16.7 % ) had unchanged cdva compared to preoperative values . a total of 6 out of 30 eyes ( 20.0 % ) demonstrated morphologic recurrence of ebmd findings on postoperative slit - lamp examination . however , there was no significant difference in mean cdva between eyes with and without morphologic recurrence ( p = 0.7734 ) , and none of these eyes underwent a repeat treatment with ptk . the probability of being recurrence free from visual disturbances at 5 years postoperatively for eyes that had an initial treatment response to ptk was estimated at 83.0 % ( 95 % confidence interval [ ci ] 68.7 % 97.0 % ) by the kaplan meier analysis ( figure 3a ) . for patients presenting with symptoms of pain from recurrent erosions ,23 out of 29 eyes ( 79.3 % ) experienced initial resolution of symptoms following ptk . of these 23 eyes , 3 eyes ( 13.0 % ) experienced a recurrence of symptoms at an average follow - up time of 9.7 months postoperatively ( range 811 months , sd 1.5 ) . all 3 of these eyes had recurrence of painful erosions within the first year postoperatively . a total of 5 out of 29 eyes ( 17.2 % ) demonstrated morphologic recurrence of ebmd findings on postoperative slit - lamp examination . of these , only 1 eye ( 20 % ) reported symptomatic recurrence of painful erosions . of the 6 eyes that did not respond initially to ptk , 2 eyes underwent repeat ptk , with 1 of these eyes reporting improved but persistent symptoms at the final follow - up and 1 eye reporting no further symptoms at the final follow - up . of the 3 eyes experiencingrecurrence of painful erosions , 1 underwent repeat ptk with no further symptoms at the final follow - up . the probability of being recurrence free for symptomatic erosions at 5 years postoperatively for eyes that had an initial treatment response to ptk was estimated at 88.0 % ( 95 % ci 65.3 % 96.6 % ) by the kaplan meier analysis ( figure 3b ) . when comparing between the 2 groups , there were no statistically significant differences in rates of primary treatment response , rates of symptomatic recurrence , or time to recurrence . postoperatively all corneas reepithelialized within 14 days and 91 % within 7 days , and no infections occurred . for patients presenting with symptoms of visual disturbances , the 1 eye ( 3.3 % ) with reduced cdva postoperatively had a final cdva of 20/50 ( logmar 0.4 ) and was noted to have corneal edema and stromal haze that had not been present preoperatively . for patients presenting with symptoms of recurrent erosions , the 7 eyes ( 24 % ) with reduced cdva postoperativelyof these eyes , 4 had no new ocular findings and clear corneas at the final slit - lamp examination and a mean final cdva of 20/25 ( logmar 0.1 sd 0.08 ) . the remaining 3 eyes had either guttata , stromal edema , or dots on the final slit - lamp examination , and a mean final cdva of ~ 20/50 ( logmar 0.43 sd 0.12 ) . of the 58 eyes examined , 9 eyes ( 15.5 % ) showed new or progressed evidence of stromal haze or corneal opacity after ptk . there was no statistically significant difference in postoperative cdva between eyes with and without new or progressed stromal haze or corneal opacity . among eyes with new or progressed stromal haze , only 1 ( 11.1 % ) demonstrated reduced cdva by 2 lines , with 5 ( 55.6 % ) showing improved cdva and 3 ( 33.3 % ) showing no change in cdva . our study of 58 ptk - treated eyes with ebmd is , to our knowledge , the largest series described thus far for ebmd treated with ptk . the results of our study support previous findings that ptk is effective in treating both the recurrent erosions and visual disturbances that result from ebmd .2,8,1214 moreover , this study has demonstrated that improvement in visual acuity and epithelial integrity is stable in long - term follow - up . in comparing outcomes between these 2 groups , we found similar rates of primary treatment response , with the majority of patients responding to treatment and the majority of responders having sustained relief from symptoms on long - term follow - up . although recurrence of erosions tended to present earlier than recurrence of visual disturbances , there was no statistically significant difference in time to recurrence between the 2 groups . overall , we found ptk for ebmd to be a safe procedure with similarly low complication rates between the 2 groups . the only significant difference in the complication rate between the 2 groups was the greater proportion of patients with reduced postoperative cdva in patients presenting with recurrent erosions . we hypothesize that this is related to the better preoperative cdva for this group at baseline and thus higher probability of worse cdva on repeat testing with expected fluctuations in performance . in support of this hypothesis , there was no significant difference in postoperative cdva between the 2 groups of patients . other commonly practiced methods of surgically treating ebmd include epithelial debridement alone or epithelial debridement with anterior stromal puncture or diamond - dusted burr polishing of bowman s layer . itty et al15 reported a study of 74 eyes treated with epithelial debridement with and without anterior stromal puncture . although both eyes with visual disturbances and painful erosions were included , there was no separate analysis performed for these 2 groups . they found that at an average 33 months follow - up , there was a 24 % morphologic recurrence rate that projected to 44.7 % by 5 years . we found a similar rate of morphologic recurrence at the final follow - up ( 20.0 % for patients with visual disturbances and 17.2 % for patients with painful erosions ) , but many of these patients did not experience recurrent symptoms . although our study had a larger proportion of patients with worse postoperative cdva , this was seen primarily in our patients with painful erosions , which comprised only 18 % of eyes in the study by itty et al , while comprising 49.2 % of our study population . aldave et al16 found that the use of epithelial debridement and diamond - dusted burr polishing of bowman s layer for recurrent corneal erosions and visually significant epithelial irregularity associated with ebmd and corneal trauma resulted in improved visual acuity and resolved recurrent erosions at an average 18.9 months follow - up in 96 % of 25 eyes , which compared favorably to our primary treatment response rate of 79.3 % for recurrent erosions . they found that 12/47 ( 25.5 % ) eyes developed new mild central subepithelial haze but that this haze was not associated with decreased vision . this was similar to our rate of new corneal haze postoperatively ( 15.5 % ) . in a follow - up study by the same group , epithelial debridement and diamond - dusted burr polishingwere found to result in no recurrent erosions in 95 % of 37 eyes with a mean of 33.2 months of follow - up .17 in all 22 eyes treated for visual disturbances with 3 months of follow - up , there was no morphologic recurrence of ebmd and recurrence of symptomatic visual disturbance . soong et al18 evaluated the use of diamond - dusted burr polishing of bowman s layer in the setting of recurrent erosions due to both ebmd and no corneal dystrophy . over an average follow - up of 12.3 months , they found a 6 % rate of recurrent erosions and concluded that diamond - dusted burr polishing was a safe and less costly alternative to ptk for the treatment of recurrent erosions due to ebmd . sridhar et al12 compared the outcomes of ptk versus diamond - dusted burr polishing of bowman s layer specifically for recurrent erosions in ebmd . in 15 eyes , bowman s membrane was ablated with ptk , and 27 eyes underwent diamond - dusted burr to polish bowman s membrane in the area of the epithelial defect . they reported a higher incidence of corneal haze in the ptk group compared to that in the diamond burr group , 5 eyes ( 35.7 % ) compared to 7 eyes ( 25.9 % ) , respectively . a higher rate of recurrent erosions was reported in the ptk group than in the diamond burr group , 4 eyes ( 26.7 % ) compared to 3 eyes ( 11.1 % ) , respectively . visual acuity outcomes were slightly better in the ptk group than those in the diamond burr group . they found no statistical difference between the groups in terms of visual outcome , corneal haze , or recurrence . our series reports a lower rate of corneal haze , ( 15.5 % ) , with no statistical difference in cdva between the groups with and without new corneal haze . we report a lower recurrence rate for erosions ( 13.0 % ) but a larger proportion of eyes with reduced visual acuity ( 24.1 % ) . notably , sridhar et al did not explicitly report their primary treatment response rate , whereas our recurrence rate for erosions is specifically for patients who experienced a primary treatment response . previous studies reporting on the outcomes of ptk for ebmd show similar results in visual improvement with differences in the recurrence rate that may be accounted for by differences in the population and type of recurrence . their technique was similar , and of 17 eyes with longstanding visual reduction , 14 ( 82.4 % ) had increased visual acuity by 2 lines at a mean follow - up interval of 30 months . no morphologic recurrence was seen in the treatment zone of any of the 24 eyes , with 1 eye out of 10 experiencing recurrence of recurrent corneal erosions .2,8 pogorelov et al11 reported similar results using a similar technique demonstrating no recurrences of erosions in 15 eyes following ptk at a mean follow - up of 4.8 years . in 12 cases of ebmd , dinh et al13 found a 42 % recurrence rate of any type such as recurrent erosions or decreased vision plus slit - lamp morphological findings within the first year . germundsson et al14 reported a 46 % total recurrence rate and 13 % symptomatic recurrence rate for either visual disturbances or erosions in 51 eyes at an average 43 months of follow - up . future studies assessing efficacy of treatment for ebmd may benefit from prospective data collection to avoid these limitations . our results have demonstrated that both visual disturbances and painful erosions associated with ebmd can be expected to respond to ptk in the majority of cases , and for those cases that show a treatment response , relief from symptoms is maintained over long - term follow - up . prior studies have shown good efficacy and safety for less costly alternatives , including epithelial debridement , anterior stromal micro - puncture , and diamond - dusted burr polishing . thus , despite the positive outcomes we report here for ptk in treating ebmd , ophthalmologists may want to consider initial treatment with more cost - effective treatment modalities prior to ptk . ebmd is a heterogenous group of dystrophies leading to the classic ebmd changes .3,19 ptk may not correct the underlying pathology in some forms of ebmd , perhaps leading to a subgroup of patients with either no primary treatment response or early recurrence after ptk . more detailed studies exploring the clinical molecular correlations behind ebmd are needed to better understand and predict both treatment response and recurrence . in the meantime , the results of this study may better inform ophthalmologists and their patients regarding the likelihood of treatment response , recurrence , and complications for ptk in the setting of ebmd .\noutput:\n" }, { "from": "agent", "value": "purposethe purpose of this study was to evaluate the long - term efficacy of phototherapeutic keratectomy ( ptk ) in treating epithelial basement membrane dystrophy ( ebmd ) . methodspreoperative and postoperative records were reviewed for 58 eyes of 51 patients with > 3 months follow - up ( range 3170 months ) treated for ebmd with ptk after failure of conservative medical treatment at byers eye institute of stanford university . symptoms , clinical findings , and corrected distance visual acuity ( cdva ) were assessed . the primary outcome measure was symptomatic recurrence as measured by erosions or visual complaints > 3 months after successful ptk.resultsfor eyes with visual disturbances ( n = 30 ) , preoperative cdva wa20 / 32 ( 0.24 log - mar , sd 0.21 ) and postoperative cdva was ~ 20/25 ( 0.07 logmar , sd 0.12 ; p < 0.0001 ) . twenty - six eyes ( 86.7 % ) responded to treatment , with symptomatic recurrence in 6 eyes ( 23.1 % ) at an average of 37.7 months ( sd 42.8 ) . for eyes with painful erosions ( n = 29 ) , preoperative cdva was ~ 20/25 ( 0.12 , sd 0.19 ) and postoperative cdva was ~ 20/20 ( 0.05 . sd 0.16 ; p = 0.0785 ) . twenty - three eyes ( 79.3 % ) responded to treatment , with symptomatic recurrence in 3 eyes ( 13.0 % ) at an average of 9.7 months ( sd 1.5 ) . the probability of being recurrence free after a successful treatment for visual disturbances and erosions at 5 years postoperatively was estimated at 83.0 % ( 95 % confidence interval 68.7 % 97.0 % ) and 88.0 % ( 95 % confidence interval 65.3 % 96.6 % ) , respectively.conclusionthe majority of visual disturbances and painful erosions associated with ebmd respond to ptk . for those with a treatment response , symptomatic relief is maintained over long - term follow - up ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: according to a recently released ' the korean diabetes research report 2012 ' by korean diabetes association , one out of ten adults has diabetes disease , two out of ten have the impaired fasting glucose which is stage of diabetes , and three out of ten adults are threatened by high blood glucose . in addition , the aging society proceeds quickly , thereby the number of diabetes patients are predicted about 6 million in 2050 , approximately a 2-fold increase compared to the current number of diabetes patients . also , the incidence of acute and chronic complications associated with diabetes is expected to increase . especially diabetic nephropathy occurs more frequently among the patients suffered from diabetes for a long time . also , it is a complication that has a large impact on patient 's quality of life . a balanced diet was recommended for diabetes mellitus patient as a key component of diet therapy . on the other hand , food intake increases burden to kidney function in diabetic nephropathy patients . therefore , the patient who proceeded to diabetic nephropathy needs nutrition education to properly manage the disease and to increase the quality of life . . diabetic nephropathy occurs in 20 % to 40 % of patients with diabetes , and is a most likely causes of end - stage renal disease reported worldwide . continuous microalbuminuria ( 30 - 299 mg / day ) appears in the early stages of diabetic nephropathy with type 1 diabetes , and it is an indicator of nephropathy onset and the development of cardiovascular disease . a patient who had a progression from microalbuminuria to macroalbuminuria ( 300 mg / day ) has a high risk of developing end - stage renal disease in few years . according to a recent study , the deterioration of renal function could be delayed by proactive management at the initial diagnosis point , therefore , it is important to implement a personalized diet customized to individuals as soon as possible . in this case report , the nutrition education for one patient with diabetic nephropathy is discussed . the patient was a 52 - year - old woman who was diagnosed with type 2 diabetes mellitus approximately 6 years ago . the patient had been taking oral hypoglycemic agents ( glimepiride ) and insulin ( glargine 18 - 20 iu before breakfast and 4 iu before bed ) to control blood glucose level . the patient 's 2 hrs postprandial blood level was normally maintained between 280 - 300 mg / dl , however , the level increased to 300 - 400 mg / dl , in recent 2 - 3 weeks and the patient was hospitalized to control high glucose level . in addition to that , the patient had been receiving medical treatment for hypertension and dyslipidemia , and regular blood tests and urine tests were performed to monitor significant changes . the patient had been diagnosed with renal failure and proteinuria one year ago , and at the time of this hospitalization , the patient was diagnosed with stage 4 chronic kidney disease , and was consulted for nutrition education of diabetic nephropathy . the patient 's height and weight were 158 cm and 81.4 kg , respectively , percent of ideal body weight was 155.5 % , indicating she was severely obese . the patient preferred a salty soup and stew , and the actual amount of intake exceeded the recommendation . when eating out once a week , the patient often ate a hamburger or a noodle meal . the patient 's diet history was analyzed by the 24 - hr recall method using can pro 3.0 software ( the korean nutrition society , seoul , south korea ) ( table 2 ) . the patient consumed approximately 1,840 kcal / d with a protein intake of 67.5 g , and the energy ratio from carbohydrate , protein , and fat was 61.7 % : 14.4 % : 23.9 % , respectively . the patient did not take any nutritional supplements , and did not drink alcohol , or smoke . the patient 's physical activity was rated to mild level of a homemaker ; she participated in weight training or bowling for 2 hrs ( 3 times a week ) . - energy : 1,600 kcal ( 30 kcal / kg x 52.4 kg ideal body weight [ ibw ] ) - protein : 40 g / d ( 0.8 g / kg 52.4 kg [ ibw ] ) - potassium : 2,000 mg / d this patient revealed problematic dietary habits including excessive carbohydrate intake , excessive protein intake , and excessive potassium intake ( table 3 ) . after analysing etiology , lack of knowledge and absence of education experience were selected as main causes . therefore nutrition education for diabetic nephropathythe nutritional problems of \" excessive carbohydrate intake \" and \" excessive protein intake \" were managed by establishing adequate nutrition through a diet comprising 1,600 kcal of energy , and below 60 percent of energy from carbohydrate and 40 g of protein per day . food models and a food exchange list were configured to provide nutritional training for the proper dietary intake . the association of carbohydrate intake and blood glucose control was discussed in relation to the nutritional problem of \" excessive carbohydrate intake \" . also , recommended amount of rice intake was 2/3 - 3/4 bowls ( 2.3 exchanges ) , which is reduced from one bowl ( 3 exchanges ) a meal . usually , it was necessary to take a proper amount of fat for preventing malnutrition and lack of caloric intake arise when protein and carbohydrates were restricted . however the patient had dyslipidemia and limited intake of animal fat was recommended . in addition , the patient was provided with information on the importance of eating the low - salt diet and tips for how to eat the low - salt diet easily .1 ) apply of spicy and sour flavor seasoning like pepper or vinegar , instead of salt or fermented soybean paste .2 ) limit the intake of high - salt - containing foods , such as kimchi , and other salted and pickled foods , 3 ) consume side dishes during meals without the addition of salt , 4 ) grilled food rather than boiled was recommended and use the food 's own flavor effectively when cooking , 5 ) when salting , focus on one kind of food . the patient was instructed to limit their intake of high potassium - containing foods ( grains , potatoes , sweet potatoes , corn , soybean , green vegetables , nuts , tomatoes , kiwi , banana , melon etc . ) . to reduce potassium intake , the intake of raw vegetables was recommended . it was also recommended to remove the shell before cooking , to use leaves rather than stem and to boil vegetables in water 4 - 5 times of their volumes . the results of nutrition education after 3 months are shown in table 4 - 6 . the patient 's diet history during last 3 months was analyzed by the 24 - hr recall method using can pro 3.0 software ( the korean nutrition society , seoul , south korea ) . the patient consumed approximately 1,300 kcal / d with a protein intake of 37.6 g , and the energy supply from carbohydrate , protein , and fat was 71.3 % , 11.6 % , and 17.1 % , respectively . after receiving the nutrition education for three months , the patient 's energy intake was reduced by 500 kcal compared to three months ago . this article is a case report of a patient with chronic kidney disease caused by diabetic nephropathy . because this patient had never received any nutrition education , the patient 's food and nutrition related knowledges was poor . as a result , the patient had problems including excessive intakes of carbohydrate , protein , and potassium , which was problematic for disease management . to solve this problem , three months after the education , the patient 's blood profile data was collected from electronic medical records ( emr ) , and the patient 's dietary intake data was collected through direct interviews . after intervention , carbohydrate intake did not conform exactly to recommendation , but protein intake and limitation of high - potassium foods were fairly well complied . excessive carbohydrate intake should be avoided as far as possible owing to its blood glucose control issues . to slow the progression of kidney complications , protein intake should be limited to 0.8 - 1 g / kg ibw / d for those with microalbuminuria , and should be limited to 0.8 g / kg ibw / d for those with macroalbuminuria , and should be limited to 0.6 - 0.8 g / kg ibw / d for those with end - stage renal disease . adequate fat intake is necessary to prevent malnutrition , because a lack of caloric intake can induce the restricted protein and carbohydrate intake . dyslipidemia is one of the most common complication in patients with diabetic nephropathy and is correlated with disease progression . this patient needs to be screened for microalbuminuria to prevent the progression of diabetic nephropathy , and dyslipidemia should be treated to reduce cardiovascular mortality . the consumption of oils with saturated fatty acids and meat should be limited , and stir - fried vegetables and vegetable oil should be consumed in moderation . for strict blood pressure control , potassium is involved in the contraction and relaxation of muscles in the human body and is an essential electrolyte . however , when kidney function decreases , excess potassium can not be easily excreted and is accumulated in the body , creating a burden . therefore , potassium intake should be limited in chronic kidney disease or in the case of hyperkalemia . therefore , the intake of coarse grains and vegetables should be limited , and should be soaked in water for more than 2 hours , and then blanched in boiling water before cooking . phosphorus in combination with calcium is found in bones and teeth . in reduced renal function , the amount of phosphorus that is emitted through the kidneys decreases and the blood levels of phosphorus increase . therefore , drug therapy is required in chronic kidney disease stages and the intake of foods that contain high levels of phosphorus should be reduced . a diabetic diet entails consumption of a healthy and balanced diet . whereas a chronic kidney disease or diabetic nephropathy diet should be designed to delay the progression of kidney disease , uremia due to renal dysfunction , hypertension , edema , hyperkalemia , hyperlipidemia and to control blood glucose along with the regulation of sodium , protein , and potassium levels . thus compared to the diabetic diet , the diabetic nephropathy diet is a little more complicated and restrictive . however , a personalized diet plan and continuous monitoring are required in diabetic nephropathy patien according to the patient 's stage of disease .\noutput:\n" }, { "from": "agent", "value": "in recent years , several studies have reported that the prevalence of diabetes mellitus is increasing every year , and also the acute and chronic complications accompanying this disease are increasing . diabetic nephropathy is one of chronic complications of diabetes mellitus , and food intake which is burden to kidney function should be limited . at the same time , diet restriction could deteriorate quality of life of patient with diabetic nephropathy . according to the results of previous studies , the aggressive management is important for delaying of the progression to diabetic nephropathy . also , the implementation of a personalized diet customized to individuals is an effective tool for preservation of kidney function . this is a case report of a patient with diabetic nephropathy who was introduced to a proper diet through nutrition education to prevent malnutrition , uremia and to maintain blood glucose levels ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: although the basic principles of resuscitation were described by versalius more than 500 years ago , the practice of cardiopulmonary resuscitation in its modern form only starts 50 years ago . despite advances in the understanding and practices of airway management , ventilatory support , external cardiac compression and drug therapy the outcome of patients undergoing cardiopulmonary resuscitation remained poor . patients may have spontaneous circulation restored and admitted to the intensive care unit , but then developed complications related to ischaemic insult to the brain as well as to the rest of the body . the term post - resuscitation disease was coined by the russian resuscitologist vladimir a. negovsky in 1972 to describe the constellation of pathological processes caused by ischaemia and reperfusion associated with cardiac arrest and the subsequent resuscitation . this is more recently renamed post - cardiac arrest syndrome because \" the term resuscitation is now used more broadly to include treatment of various shock states in which circulation has not ceased ... ( and ) the term postresuscitation implies that the act of resuscitation has ended ... \" 4 key components contribute to the development of this syndrome : 1 ) post - cardiac arrest brain injury ; 2 ) post - cardiac arrest myocardial dysfunction ; 3 ) systemic ischaemia / reperfusion response ; and 4 ) persistent precipitating pathology . there is evidence to support that proper management in the post - resuscitation phase can improve outcome of these patients and therapeutic hypothermia is one important component of such management . to avoid confusion , there is a need to define terminology used in relation to manipulation of body temperature : hypothermia is defined as core body temperature of less then 36 regardless of the cause.induced hypothermia is defined as an intentional reduction of a patient 's core temperature below 36 . therapeutic hypothermia is defined as controlled induced hypothermia ; i.e. induced hypothermia with the potentially deleterious effects such a shivering , being controlled or suppressed.controlled or therapeutic normothermia is defined as bringing down core temperature in a patient with fever , and maintaining temperature within a range of 36 - 37.5 , with the potentially deleterious effects such a shivering , being controlled or suppressed . hypothermia is defined as core body temperature of less then 36 regardless of the cause . induced hypothermia is defined as an intentional reduction of a patient 's core temperature below 36 . therapeutic hypothermia is defined as controlled induced hypothermia ; i.e. induced hypothermia with the potentially deleterious effects such a shivering , being controlled or suppressed . controlled ortherapeutic normothermia is defined as bringing down core temperature in a patient with fever , and maintaining temperature within a range of 36 - 37.5 , with the potentially deleterious effects such a shivering , being controlled or suppressed . the degree of therapeutic hypothermia can mild ( 34.0 - 35.9 ) , moderate ( 32.0 - 33.9 ) , moderately deep ( 30.0 - 31.9 ) or deep ( early studies showed that induced hypothermia improved outcome in cardiac arrest patients . although both studies were small ( 12 patients had induced hypothermia in each study ) case series . however , further progress was hindered by 1 ) lack of understanding of the underlying pathophysiology , 2 ) lack of reliable methods to control body temperature , and 3 ) lack of intensive care facilities to manage possible complications . the early hypothesis that beneficial effect of hypothermia was due to reduction of metabolism leads to the adoption of more profound cooling ( around 30 ) . the result was serious complications which can not be handled effectively without the support of intensive care , which was then only at its infancy . further studies in the recent decades showed that the mechanism of cerebral protection by hypothermia is more complicated and neurological outcome can be improved by mild to moderate degree of hypothermia . two studies published in 2002 provided the evidence basis that hypothermia can improve neurological outcome . coupled with advances in technology in hypothermia and intensive care in general , the study population of both the study by bernard et al . and the haca study group are patients suffering from out - of - hospital ventricular fibrillations . there is evidence that cooling patients with presenting rhythms other than vf or vt following out - of - hospital arrests does no harm : 2 retrospective cohort studies found that the outcomes for patients presenting with pea / systole did not differ from those observed among the group presenting with vf or vt . there is little published evidence to support the use of therapeutic hypothermia following in - hospital cardiac arrest . an analysis of patients entered into arrich and erchacars group found that 13 % of procedures were performed post in - hospital cardiac arrest .43 % of these were cooled and although the initiation of hypothermia was faster than that for the out - of - hospital arrests , there was no difference in outcome between the patients treated with hypothermia and those with normothermia . the haca in - hospital multi - center trial is currently investigating whether therapeutic hypothermia is beneficial for patients following in - hospital cardiac arrest . in both the haca and bernard studies , patients who are hypotensive ( map 60 mmhg or sbp 90 mmhg despite adrenaline infusion ) were excluded . the underlying reason being the possible deleterious effect of hypothermia on cardiovascular function and coagulation . however , there are several publications suggesting that post - cardiac arrest patients in cardiogenic shock could actually also benefit from moderate therapeutic hypothermia . reduction in platelet count and platelet dysfunction is noted when body temperature is dropped to 35 ; and when temperature is below 33 , synthesis and kinetics of clotting enzymes and plasminogen activator inhibitors are also affected . however , it was found in a recent study which assessed the risk and severity of bleeding during simultaneous use of mild hypothermia and thrombolysis that bleeding risks were similar to historical controls treated with thrombolytics alone , although there was a trend toward more red blood cell units being required to reach target hematocrit in hypothermic patients who developed bleeding complications and needed transfusions . . the procedures of therapeutic hypothermia can be divided into 4 phases : induction , maintenance , de - cooling ( or rewarming ) and normothermia . this is the initial phase during which the patient 's body temperature is lowered to the target of 32 - 34 . continuous core temperature measurement should be started before induction of therapeutic hypothermia to ensure that the patient 's body temperature is within the target range and to avoid overshoot . this is preferably achieved by bladder , rectal , central venous , or oesophageal measurement . however , it should be noticed that bladder temperature may poorly reflect core temperature if the patient is oliguric , and other monitoring sites are preferred . this phase is associated with many possible complications most of which can be minimized by rapid cooling . rapid cooling can be achieved by rapid bolus administration of 30 to 40 ml / kg cold ( 4 ) isotonic resuscitation fluid over 1 hour . despite theoretical problems this methodwhen core temperature drops to 32 , metabolic rate decreases to 50 - 65 % of normal . the issue of how to interpret arterial blood gases in hypothermic patients ( alpha - stat versus ph - stat ) is a topic of some controversy and readers are referred to review articles for detailed discussion . hypothermia can lead to hypokalaemia , hypophosphataemia and hypomagnesaemia as a result of intracellular shift as well as urinary loss because of tubular dysfunction . it is particularly important to monitor and replace potassium in order to avoid arrhythmia . on the other hand , it is the result of increased fat metabolism , leading to an increase in the levels of glycerol , free fatty acids , ketonic acids , and lactate . hyperglycaemia due to reduction of insulin secretion and insulin resistance should be controlled by close monitoring and insulin therapy . the main sources of relevant data come from patients with hypothermia induced during cardiac surgery . cardiac output decreased along with the heart rate ; however , the hypothermia - induced decrease in metabolic rate usually equaled or exceeded the decrease in cardiac output , so that the balance between supply and demand remained constant or improved . however , the actual cardiac output is also affected by the volume status and effect of sedation . systolic function of myocardium may actually be improved during mild to moderate hypothermia but diastolic function is usually impaired . it is important to note that the effect of hypothermia on myocardial contractility is strongly dependent on heart rate . if the heart rate is allowed to decrease along with the temperature , myocardial contractility as measured by systolic function usually increases , although there may be a mild degree of diastolic dysfunction . however , if the heart rate is artificially increased through administration of chronotropic drugs or a pacing wire , myocardial contractility decreases significantly . this phenomenon has been demonstrated in animal studies and also in patients undergoing cardiothoracic surgery . thus , the effect of hypothermia on myocardial function strongly depends on whether the heart rate is allowed to decrease [ 20 - 22 ] . maintaining euvolemia is one important aspect of management during therapeutic hypothermia and one challenge is cold induced diuresis . the underlying mechanisms leading to cold - induced diuresis include increased venous return caused by constriction of peripheral vessels ( particularly in the skin ) due to hypothermia - induced increases in plasma noradrenaline levels and activation of the sympathetic nerve system , activation of atrial natriuretic peptide , decreased levels of antidiuretic hormone and renal antidiuretic hormone receptor levels , and tubular dysfunction . if uncorrected , diuresis can cause hypotension as well as electrolyte depletion and increase in blood viscosity . the risk for hypovolemia increases significantly if the patient is simultaneously treated with diuretic agents such as mannitol . however , hypotension can be quite easily prevented by avoiding or promptly correcting hypovolemia , and by avoiding excessive stimulation of heart rate . while profound hypothermia of 28 is associated with severe arrhythmia , mild to moderate hypothermia could stabilize membranes . study in normal human showed that the threshold for vasoconstriction is about 36.5 and that for shivering is 35.5 . the threshold is slightly higher in female but the difference is 0.5 . shivering of postoperative patients may lead to increased risk of morbid cardiac events especially in older patients with heart disease : the result of increased rate of metabolism and oxygen consumption , leading to excess work of breathing and tachycardia . however , the situation may be different in sedated patients . while hypothermia in an awake patient causes tachycardia , inducing hypothermia intentionally in sedated patientsshivering will increase oxygen consumption , but as the patient is on mechanical ventilation , there will be no increase in the work of breathing . nevertheless , it is important to prevent or aggressively treat shivering because it significantly complicates hypothermia induction , and leads to an undesirable increase in metabolic rate and oxygen consumption . shivering may be controlled by one and more of the following methods : 1 ) drugs lowering shivering threshold , e.g. acetaminophen ( paracetamol ) , aspirin , and nonsteroidal antiinflammatory drugs ; 2 ) drugs suppressing shivering response paralyzing agents , sedatives , opiates , and others ; and / or 3 ) skin counterwarming . drugs lowering shivering threshold are not quite effective in general . of the drugs which suppress shivering , it was found that there is significant variation in sedation protocols amongst the 68 icus included in the selected studies . midazolam ( 5 mg / h to 0.3 mg / kg / h ) being most commonly used , followed by propofol ( up to 6 mg / kg / h ) . a quarter of icus do not use any analgesic , the rest use either fentanyl ( 0.5 - 10 mcg / kg / h ) or morphine . use of neuromuscular blocking agents , however , is associated with several disadvantages some of which can be reduced by adequate sedation : 1 ) attempts of the brain to generate a shivering response will not cease ; 2 ) they can mask seizure ; 3 ) they lack of vasodilating effect of sedatives ; and 4 ) their use is associated with development of critical illness polyneuromyopathy . the importance of adequate sedation and suppression of hypothermia - induced stress responses is underscored by observations from animal experiments suggesting that some or all of hypothermia 's neuroprotective effects can be lost if cooling is used in non - sedated animals . it was found that 4 increase in skin temperature could \" compensate \" for 1 drop in core temperature to prevent a shivering response . some areas of the body ( hands , feet and face ) have a higher concentration of \" temperature sensors \" and warming of those areas could have a greater effect on suppressing shivering . by reducing shivering , counterwarming can reduce metabolic rate and oxygen consumption of hypothermic patients . during this phase , the goal is to maintain core temperature at 32 - 34 for 12 - 24 hours . the patient is usually more stable during this phase with fewer disturbances in their haemodynamic , volume or electrolyte status , as well as less shivering . however , the patient is subjected to other hazards including changes in pharmacokinetics , nosocomial infections and bedsores . conventionally , patients are maintained cool by surface cooling through exposure , placing ice packs to the neck , groins and axillae , and / or spraying with water . rubber cooling blankets can also be used but should be placed over the patient . placing those blankets under the patient can lead to skin damage due to vasoconstriction in already pressurized areas . although widely available and inexpensive , conventional surface cooling is difficult to control as there is no internal feedback mechanism . these may be classified as non - invasive surface cooling devices such as hydrogel - coated water circulating pads or water - circulating wrapping garments , and invasive core cooling devices using intravascular catheters . a problem with surface cooling is that 40 - 90 % the patient 's surface area needs to be covered and carries a risk of skin lesions . but they can be started immediately using nurse - driven protocols without direct physician intervention . core - cooling methods , on the other hand , are highly reliable once the catheter is in place , with a cooling rate of 2.0 - 4.5 / hour . however , insertion of catheter is required and it can lead to complications such as thrombosis and infection . even short duration of hypothermia during perioperative period for intracranial aneurysm increase the risk of postoperative bacteraemia . a study has shown that 3 days of prophylaxis with ampicillin - sulbactam can reduce early onset nosocomial pneumonia but not the incidence of late - onset nosocomial pneumonia . after 12 - 24 hours of cooling , patient can be allowed to warm up slowly . the goal should be 0.2 - 0.33 per hour until the patient is 36.5 - 37.0 . more rapid warming must be prevented to avoid electrolyte disturbance due to transcellular shift , hypoglycaemia due to increased insulin sensitivity , as well as aggravated brain destruction . this can be prevented by slow rewarming , allowing the kidneys to excrete the excess potassium . however , this should not be a reason to accept hypokalaemia in the induction or maintenance phase . for patients with renal dysfunction , renal replacement therapythis may be the result of nosocomial infection or part of the post - cardiac arrest syndrome . furthermore , cerebrovascular reactivity may be impaired following hypothermia treatment and thus increase the potential harmful effects of fever even more . there was a case report in which a post - cardiac arrest patient who initially improved after rewarming deteriorated after development of fever and subsequently died . it is recommended that patients should be maintained normothermic after decooling until 72 hours have elapsed since restoration of spontaneous circulation . current evidence supports that induction of therapeutic hypothermia in selected patients after cardiac arrest can improve neurological outcome . lack of familiarity and lack of a concrete protocol are the most important amongst the list of perceived barriers . it is hoped that by summarizing the current state of knowledge on the subject and highlighting issues on clinical management will enable more patients to benefit from the therapy .\noutput:\n" }, { "from": "agent", "value": "pioneer works on therapeutic hypothermia ( th ) half a century ago already showed promising results but clinical application was limited by a lack of understanding of the underlying pathophysiology , lack of reliable method for temperature control and lack of intensive care facilities to deal with possible complications . more recently , 2 studies in 2002 supported the application of moderate th ( 32.0 - 34.0 ) in post - cardiac arrest patients . although the studies included only patients suffering from out - of - hospital vf , many icus world - wide are applying the therapy to all post - cardiac arrest patients irrespective of site or presenting rhythm . while primary coagulopathy and cardiogenic shock are usually stated as relative contraindications , evidences are accumulating to support the application of th in patients with cardiogenic shock . th can be divided into 4 phases : induction , maintenance , de - cooling and normothermia . induction is usually achieved by infusion of cold isotonic fluid . the precautions included avoidance of over - cooling , hypokalaemia , hyperglycaemia , and shivering . th can be maintained by many different methods , varying in their level of invasiveness , cost and effectiveness . issues including changes in pharmacokinetics and haemodynamics , and susceptibility to infection need to the addressed . the optimal duration of maintenance is unknown but the usual practice is 12 - 24 hours . de - cooling and rewarming is especially challenging because complications can be serious if temperature rise by more than 1 every 3 - 5 hours . life - theatening hyperkalaemia can occur especially if patient suffers from renal insufficiency . fever is a frequent complication either due to infection or post - cardiac arrest syndrome but patient must be kept normothermic for 72 hours ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: first , patients show considerable variations in their responses to treatment and in rates of recurrence . management might best be optimized by involving active monitoring by the patients themselves , by arranging for suitably spaced self - tests of vision . ideally , such tests not only should alert caregivers to deterioration of results but should also provide measures of rates and magnitudes of change to aid priority assignments . there is a long tradition of recommending self - testing by means of plain amsler metamorphopsia grids . acuity tests are easier to evaluate but require both rigorous control over test conditions and outside assistance to check responses for accuracy . these limitations apply equally to clinical charts and to the multitude of look - alikes that are available on internet websites and as software applications or apps for tablets and mobile phones . further , acuity tests exhibit considerable intersession variability and some patients report pronounced short - term variations of vision . those that rely on dedicated hardware , for example , microperimeters , preferential hyperacuity perimeters , and adaptometers , may be too expensive to find widespread use among patients . electronic tablets and so - called smartphones , on the other hand , are readily available to many patients and could serve as useful platforms for novel , dedicated self - tests for macula edema . for maximum utility , such tests should be fairly tolerant to environmental variables like test distance , they should be doable without outside assistance , and they should be capable of transmitting results for remote monitoring . additional desirable properties include small or no demands on fixation stability and the use of ever - new test target combinations , to prevent false gains from memorization . a recently described shape discrimination test , the myvisiontrack , appears to meet the above demands . using a forced - choice test paradigm , set up for advanced remote monitoring , the test has been shown to be capable of discriminating groups of subjects with different stages of age - related macula degeneration ( amd ) . the present study explored the utility of another type of test , namely , a test that employs receptive field - size dots or rarebits . rarebit testing was devised with the specific aim of uncovering low degrees of neurovisual damage , where conventional tests often fail . the rarebit name refers to the test target 's information content , which is minuscule compared with the information overload contained in conventional test targets . normal eyes are expected to see essentially all rarebit probes , in central and peripheral vision alike . conversely , eyes that have suffered losses of receptive fields or damage to their upstream connections will miss some probes , in relation to the severity of damage . several studies of various aspects of rarebit testing have reported good sensitivity and specificity for a variety of retinal and visual pathway lesions , good reproducibility , and good acceptance by tested subjects . a new presentation format , namely , segmented digits , may have a better potential . a normal eye needs no more than three rarebits to recognize a segment , even if briefly flashed , whereas eyes that have lost receptive fields need larger numbers . , the multiple rarebit test principle has been shown to perform significantly better than conventional clinical tests in a variety of conditions , including macula edema . here , we describe a new multiple rarebit test version in the form of a smartphone / tablet application named the multibit test ( mbt ) . we present longitudinal observations from a small series of patients being monitored for amd with choroidal neovascularization ( cnv ) . test performance was evaluated on an individual basis , by contrasting trends among observed mbt results with objective features documented during independently scheduled clinical examinations . the aims of this first pilot study were to obtain a general impression of test performance and to secure the information needed to plan a long - term , large - scale multicenter study . patients were recruited from the amd / cnv treatment programme of the retina unit at the sahlgrenska university hospital , a tertiary - care center . exclusion criteria were the bilateral presence of currently inactive lesions judged to run a small risk of recurrence , the presence of additional , non - maculopathic causes of visual loss , and inability to participate in conventional acuity testing . those who had the same type of lesions in both eyes ( active or inactive ) provided results from the least involved eye only whereas those who had different types of lesions provided results from both eyes . a total of 36 eyes qualified for study . examination intervals were decided on an individual basis , depending on the response to any previous antineovascular treatment and on current disease activity as judged from biomicroscopy , ocular coherence tomography ( oct ) , and retinal angiography . lesions showing edema and / or leakage were judged active , otherwise inactive . currently active lesions were usually treated within a few days of examination , using ranibizumab in accordance with the manufacturer 's recommendations ( novartis , basel ) . all controls were examined once only , in the same way as the patients , excluding angiography . to avoid intereye dependencies , the mbt was developed by author lars frisn for iphone and ipod touch tablets with high - resolution retina screens ( apple , cupertino , ca ) . the latter type of device was used here because of its lower price and lower operating costs . at a laptop viewing distance ( 0.5 m ) , each screen pixel subtended 0.5 or about 80 % of that of a foveal cone . the full screen subtended 10.05.7 . screen brightness was forced ( in software ) to 80 % of maximum . surround illumination was outside investigator control as actual tests were performed in home settings but patients were instructed to seek total darkness . segmented digits were generated in the manner previously described for the digitstep test , the personal computer precursor to the app . the test digits subtended 4050 , equivalent to 0.1 decimal ( 20/200 snellen ) optotypes . they were built up by single - pixel rarebits in a segmented format as exemplified in figure 1 . numbers of rarebits per segment ( rps ) were preset at 3 , 4 , 5 , 6 , and 7 in test level 1 and 8 , 10 , 16 , 30 , and 60 in test level 2 . in the interest of saving on test time and maximizing tested areas , pair members were selected at random and presented in a left - to - right sequence in randomly selected screen locations . the digits were presented for 150 ms each , with a 150 ms blank interval in between , that is , briefly enough to frustrate refixation . digit pairs were separated by a time interval of 4 seconds , providing ample time for response . a complete mbt test comprised 3 presentations of the 5 rps settings contained in the user - selected test level . the verbal responses were automatically recorded in an internal audio file . once all 15 digit pairs had been shown , , the same sequence of 15 digit pairs was displayed in an easily read format and the audio file was played back . scoring was performed by comparing the digits actually shown with the recorded responses , pair by pair , and tapping appropriately labelled buttons . the percentage of correct responses was calculated automatically at the end of the test and displayed as the test score . test duration was about 2 min , not counting the time needed for scoring results . mbt devices were provided on loan to the study participants . following careful instructions , identification of the appropriate test level , and supervised training , participants were asked to perform monocular self - tests under constant conditions at home , in total darkness , at least twice a week , using their reading glasses , with occlusion of the nontested eye . those who had access to a wireless local area network and were willing to take on emailing of test results were instructed accordingly . otherwise , participants were asked to bring their test devices to their scheduled clinical appointments , where downloading of stored results took place . visual acuity was assessed at all clinic visits using a transilluminated early treatment diabetic retinopathy study ( etdrs ) acuity chart ( precision vision , la salle , il ) , using full ametropia correction . each correctly read test letter provided a score of 1 , for a maximum of 100 . test scores were evaluated on an individual basis and were contrasted with outcomes of clinical examinations performed at independently scheduled intervals . the main outcome measures , concordance between clinical ratings and vision test outcomes , the analytical tool ( medcalc software v 12.7.7.0 , ostend , belgium ) also provided estimated specificity at fixed sensitivity levels as well as estimated sensitivity at fixed specificity levels , with bootstrapped ( 1,000 iterations ) confidence intervals . at the time of entry into the study , the 28 patients had a mean age of 767 ( sd ) years . figure 2 presents overviews of etdrs and mbt results at entry , revealing a wide range of visual deficits . the patients returned for renewed clinical evaluations at mean intervals of 63 days . at each follow - up , results were compared with those of the nearest preceding visit . in all , 144 intervisit intervals or epochs were available for analysis . twenty - six epochs were clinically judged to exhibit impairment , 50 epochs were judged to exhibit improvement , and 68 epochs were judged stable . decisions as to active treatment were based solely on the results of the clinical examinations . the patients made a total of 1203 mbt self - tests during periods averaging 39 weeks in length . being closely monitored and treated as needed , most patients showed less dramatic changes , as exemplified in figure 4 . in the figure , with mbt , impairments could often be discerned in advance of the preplanned clinical follow - up dates . following treatment of active disease ( in the plots symbolized by open diamonds ) , mbt scores could be seen to improve , and variation could be seen to decrease , but scores remained consistently subnormal . epochs showing trends of decreasing scores , or increasing variation , or both , were rated worse . the outcomes of the clinical examinations , which included biomicroscopy and scrutiny of oct parameters and maps , were summarized in the same manner . figure 5 illustrates the concordance of clinical and etdrs results in ( a ) and clinical and mbt results in ( b ) . , kappa equals 1 in case of perfect agreement whereas kappa 0 indicates chance agreement . for etdrs , kappa equaled 0.03 ( 95 % confidence interval ( ci ) 0.090.15 ) and for mbt 0.41 ( ci 0.290.53 ) . notably , the etdrs confidence interval includes 0 whereas the mbt interval neither includes 0 nor overlaps the etdrs interval . mbt sensitivity and specificity were illuminated by roc analysis of entry - point data , when all subjects were nave to the test task . at the 95 % specificity level , sensitivity was estimated to be 80 % ( ci 6091 ) , at the criterion level 90 . conversely , at the 95 % sensitivity level , specificity was estimated to be 70 % ( ci 4590 ) , at the criterion level 96 . like its personal computer based predecessor , the mbt app exhibited good sensitivity and specificity in cross - sectional analysis of the entry - point data . the concordance is gratifying in view of the impossibility to control external factors in real - life self - testing situations . uncontrolled factors include ametropia correction , viewing distance , background illumination , and various types of environmental distractors . in spite of the uncontrolled external - factor conditions of the present studythe present finding of limited utility of the etdrs test was not unexpected as acuity tests have long been known to be quite tolerant to various forms of visual system injury . plausible explanations relate to an overload of information in both space and time and memorization effects . furthermore , acuity tests target function in a restricted retinal area only , in and close by the fixation point ( or the preferred locus of fixation ) . such a narrow focus may be misleading in conditions like amd , where the disease process is neither confined to the point of fixation nor uniformly distributed throughout the involved area . the mbt bypasses these limitations by minimizing information and employing an extensive test area ( 10.05.7 ) . furthermore , by employing random positioning of targets within the test area , the mbt does not demand a stable fixation . turning to longitudinal aspects of self - testing in amd , the so - called home study demonstrated a significantly better outcome for patients who were monitored with preferential hyperacuity perimetry at home compared to patients under routine clinical care . the present report demonstrates the possibility to capture gradual changes of scores and score variability with changes in disease activity in individual cases ( figures 3 and 4 ) . plain eye - balling of serial results often allowed recognition of deterioration in advance of independent physician estimates of optimum clinical examination intervals . plain eye - balling also allowed confident rejection of occasional out - of - line scores . this limitation is attributable to the combination of a lack of a theoretical model and a paucity of appropriate analytical tools . empirical modelling is currently in progress but must be tested against a new data set before its utility can be assessed . collection of new and larger data sets is one of the goals of a large - scale , multicenter study that is currently being planned . meanwhile , it is worthy of note that the authors made independent visual evaluations of the result plots . their evaluations agreed in 141 out of the 144 epochs and only 3 were in need of arbitration . another important aspect of agreement concerns that of test results vis - - vis clinical ratings . for the etdrs test , agreement was close to chance level , with a kappa statistic not meaningfully different from 0 ( see also figure 5 ) . forthe mbt , the kappa statistic did differ from 0 but it did not approach 1 , that is , perfect agreement . there is little consensus as to interpretation of intermediate kappa values except that they indicate less - than - perfect agreement . as to the root cause of imperfect agreement , both mbtthe clinical ratings depended heavily on oct results and therefore may appear to be highly reliable . however , ocular coherence tomography has its own limitations . furthermore , the clinical ratings actually constitute subjective summaries of a host of subjective impressions and objective measurements of various morphological features . stable clinical grade may be particularly challenging in the presence of active disease . against this background , it is of little surprise that exclusion of the clinically stable subgroup caused the mbt kappa to rise from 0.41 ( ci 0.290.53 ) to 0.57 ( ci 0.390.75 ) . the study participants were asked to perform at least two tests per week but actual frequencies varied not only between patients but also over time ( figures 3 and 4 ) . nevertheless , a recommendation of twice - weekly testing may strike a constructive compromise between useful diagnostic detail and reasonable demands on patients . some subjects encountered occasional problems with electronic transmission of results within wireless local area networks . while acceptable for this first pilot study , large - scale usage requires a more robust and more elaborate arrangement . a sophisticated framework can provide additional functions , including reminding patients about missed examinations and actively alerting caregivers to deteriorating test results . the mbt has two inherent limitations , both of which apply to the extremes of the measuring range . at the high rps end , there is a limit to the number of rarebits that can be contained within the space allotted to the test digits . therefore , the test may be difficult to apply in cases with advanced visual loss , with optotype acuities worse than approximately 0.2 decimal ( 20/100 snellen , 50 etdrs , 0.7 logmar ) . although it is possible to allot more space to the test digits , there is a trade - off effect in that the perception of dot - defined symbols of large angular subtense may be dominated by dots rather than symbol gestalts . another type of limitation applies to the low rps end , where minute changes of vision may hide in between the two lowest scale steps ( 3 and 4 rps ) . the mbt appears to meet the need for a powerful tool for self - testing of neovascular age - related macula degeneration . the test merits closer study in larger - scale trials and also with other types of macula conditions .\noutput:\n" }, { "from": "agent", "value": "purpose . there is a need for efficient self - tests of vision in patients with neovascular age - related macula degeneration . a new tablet / smartphone application aiming to meet this need is described and its performance is assessed in a longitudinal pilot study . materials and methods . the new multibit test ( mbt ) employs segmented digits defined by rarebits , that is , receptive field - size bright dots briefly presented against a dark background . the number of rarebits per digit segment was varied in a cyclic fashion , in preset steps . there were no fixation demands . twenty - eight patients with neovascular amd of varying severity were monitored for an average of 30 weeks . test scores were evaluated on an individual basis , by contrasting observed trends with the clinical status recorded at independently scheduled clinical examinations . results . serial plots of mbt results revealed gradual improvement after successful antineovascular treatment . recurrences were signalled by gradual deteriorations of results . test results remained stable during clinically stable time intervals . mbt results agreed well with clinical assessments whereas an acuity test performed at chance level . the mbt was well accepted by all subjects . conclusions . the mbt appears to have a good potential for effective self - testing of vision in amd and merits large - scale studies . exploration of mbt performance with other forms of macula conditions may be worthwhile ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: although diabetes is highly prevalent worldwide , its presence among american indians and alaska natives ( ai / ans ) is particularly alarming . adjusting for age , ai / ans suffer from type 2 diabetes mellitus at rates greater than two times those of non - hispanic whites and exhibit the highest prevalence of this disease of any racial group in the united states . given the sharp increase in incident diabetes among ai / ans over the last 20 years , these circumstances seem unlikely to change without substantial intervention . the special diabetes program for indians diabetes prevention ( sdpi - dp ) demonstration project has been implemented over the past decade to address this problem using a well - established , evidence - based preventive intervention . the sdpi - dp initiative was developed based upon the national institute of diabetes , digestive and kidney disease 's ( niddk ) diabetes prevention program ( dpp ) , which was a large - scale clinical trial that demonstrated that lifestyle interventions ( e.g. , changing diet and exercise habits ) can be effective in delaying or preventing the onset of diabetes in individuals who are at increased risk for developing this disease . the dpp outcomes did not differ significantly for various ethnic groups , including american indians ; however , the dpp was conducted as a highly controlled clinical trial , which did not allow for evaluating the effectiveness of lifestyle interventions in preventing the onset of diabetes in community - based settings with underserved populations . ai / an communities often face a lack of health care resources and a highly mobile population , thereby making it particularly difficult to implement large - scale prevention programs . therefore , the sdpi - dp worked with experts in a variety of ai / an communities to implement cultural adaptations to the original dpp lifestyle curriculum ( e.g. , the use of indigenous foods , drumming during class sessions ) , in order to make the program more relevant to ai / an individuals and more transferrable to a geographically , culturally , and organizationally diverse array of settings in tribal communities . the sdpi - dp demonstration program resulted in reduced diabetes incidence among high risk ai / ans at a rate comparable to the results for ai / ans in the original dpp study . in addition , improvements in weight , blood pressure , and lipid levels were detected following the intervention . however , despite the overall effectiveness with which the intervention was delivered to sdpi - dp participants , several participant characteristics were related to retention in the program ; participants who were younger , were male , had less education , and had lower income were more likely not to complete the core intervention . these initial findings regarding the relationship between sociodemographic factors and retention led program staff to question the potential additional impact of individual - level psychosocial factors on participant engagement , ability to grasp the knowledge conveyed , and mastery of skills related to the behavioral changes associated with the desired outcomes . therefore , it was determined that further analyses were warranted in order to evaluate the extent to which program outcomes were related to individual - level psychosocial characteristics . the observation of a potential impact of psychosocial factors on self - management of medical illnesses is not unique . for example , the influence of depression and anxiety on intervention outcomes for individuals with prediabetes was examined in at least one previous study , and more positive baseline mood was correlated with increased physical activity . specifically , there is evidence that diabetes may increase the likelihood of depressive episodes and that depression may increase the risk of developing diabetes . furthermore , psychological distress in general has also been shown to be associated with many chronic health conditions , including obesity , which is a significant risk factor for the development of type 2 diabetes . other studies have identified increased odds of diabetes among ai / ans with a history of trauma and significant life stressors . conversely , strong coping skills and other positive emotional attributes have been found to enhance metabolic control among those with diabetes . in addition , increased spirituality has been associated with improved self - management among african americans who suffer from diabetes , lower stress and higher quality of life in persons afflicted by chronic illness , and decreased likelihood of developing depression . although the relationship between spirituality and diabetes has not been studied specifically in ai / an populations , previous research has highlighted the importance of religious and spiritual practices for ai / an individuals struggling to overcome other health issues , such as the problematic use of alcohol . additionally , family support has been correlated with increased weight loss in the prevention of diabetes among arab americans . similarly , positive family support was correlated with improved diet in a study of older hispanic adults with diabetes . furthermore , active family nutritional support was linked to improved control of diabetes - related factors ( i.e. , triglycerides , cholesterol , and hba1c ) among navajo tribal members . finally , several psychological and behavioral factors , including increased self - efficacy , were associated with improved weight loss for dpp participants . given this prior body of evidence supporting significant relationships between a variety of psychosocial characteristics and multiple health outcomes , the correlation of psychosocial factors ( psychological distress , trauma exposure , coping skills , spirituality , and family support ) with a key clinical indicator of diabetes risk ( weight ) among ai / ans participating in the sdpi - dp demonstration project was assessed in the present study . resulting insights could suggest enhancements targeting such factors in the core components of sdpi - dp that hold promise for increasing its effectiveness . eligibility criteria for participating in the sdpi - dp demonstration projects were being ai / an ( based on eligibility to receive ihs services ) , being at least 18 years of age , and having either impaired fasting glucose ( ifg ) ( i.e. , a fasting blood glucose ( fbg ) level of 100125 mg / dl and an oral glucose tolerance test ( ogtt ) result 200 mg / dl ) or impaired glucose tolerance ( igt ) ( i.e. , an ogtt result of 140199 mg / dl two hours after a 75 g oral glucose load and an fbg level 126 mg / dl ) . exclusion criteria included a previous diagnosis of diabetes ( not including those who only have had gestational diabetes ) , pregnancy , end - stage renal disease on dialysis , and any condition that would affect successful participation based on provider judgment ( e.g. , cardiac concerns given the physical activity element of the program , severe substance use , and undergoing treatment for cancer ) . participants attended a 16 - session educational curriculum , a series of lifestyle coaching sessions , and community - based exercise programs focused on reducing the risk of developing type 2 diabetes through moderate weight loss , increased physical activity , and healthy eating habits . clinical measurements and participant surveys were obtained at baseline , within 30 days of completing the 16 - session curriculum , and annually thereafter . participants were enrolled at one of 36 tribal , indian health service ( ihs ) or urban indian health care programs serving 80 tribes between 2006 and 2010 . seventy - eight percent of participants were from a rural geographic setting , and 22 % were from an urban area . to be included in the current study , participants minimally completed a baseline clinical assessment and a baseline survey ( n = 3,135 ) . the 193 individuals who completed a baseline clinical assessment but did not complete any participant surveys were excluded from these analyses . these individuals did not differ significantly from those included in the study with regard to age , gender , and baseline weight . the sdpi - dp protocol was approved by the institutional review board of the university of colorado denver and the national ihs institutional review board . when required , grantees obtained approval from other entities overseeing research in their programs ( e.g. , tribal review boards ) . the study sample was 74 % female and had a mean age at baseline of 46.7 years . sixty - three percent of participants attended at least some college courses ; 72 % of participants reported annual household incomes of less than $ 50,000 . sociodemographic variables including participant gender , age , educational status , and annual household income were collected through a survey at baseline . frequency of participants ' experience of various symptoms of depression and anxiety during the previous 30 days was assessed using this scale . item scores ranged from 1 ( none of the time ) to 5 ( all the time ) . participants ' ability to cope with life stressors was measured using the brief resilient coping scale . this 4 - item scale asked participants to rate descriptions of coping reactions ( e.g. , approaching difficult situations in creative ways , focusing on the positive growth that can come from dealing with adversity ) , using a scale ranging from 1 ( does not describe me at all ) to 5 ( describes me exactly ) . a modified 6 - item version of the diabetes family behavior checklist was used to measure participants ' perceptions of positive and negative family support in regard to their efforts to prevent the onset of diabetes . sdpi - dp research staff modified the original checklist slightly by removing items that referred to specific activities for individuals with diabetes ( e.g. , family providing suggestions about taking insulin on time ) that would not have been relevant to a program focusing on diabetes prevention . participants rated how often their family members provided positive support on 4 items ( e.g. , exercising with them ) and negative support on 2 items ( e.g. , criticizing them for not exercising regularly ) . item scores on the six items ranged from 1 ( less than once a month ) to 5 ( at least once a day ) . no items were reverse - scored , as items were phrased in either a positive or negative manner , consistent with the two scored dimensions . two additional psychosocial variables ( trauma experience and spirituality ) were assessed by participant surveys only at baseline . these two particular variables were not collected at follow - up due to the expectation of their high stability across a relatively short period of time . a single dichotomous variable from a posttraumatic stress disorder ( ptsd ) screener captured whether participants had ever experienced a significant traumatic event ( e.g. , being the victim of a violent crime or domestic violence , being in a disaster like a flood or fire , being in combat , being seriously injured in an accident , being sexually assaulted , and witnessing someone else being seriously injured or killed ) . this variable was coded either 0 ( no trauma ) or 1 ( history of trauma ) . spirituality was assessed via a 7 - item scale designed specifically to capture the culturally relevant components of spirituality for ai / ans ; item scores ranged from 1 ( strongly disagree ) to 5 ( strongly agree ) . the items on this scale were developed through consultation with tribal leaders to reflect american indian cultural views of the connectedness of humans to all other physical and transcendental entities . the seven items were as follows : ( 1 ) i am in harmony with all living things , ( 2 ) i feel connected with other people in life , ( 3 ) i follow my tribal path , ( 4 ) when i need to return to balance , i know what to do , ( 5 ) i feel like i am living the right way , ( 6 ) i give to others and receive from them in turn , and ( 7 ) i am a person of integrity . confirmatory factor analyses were conducted at the item level for each psychosocial scale in order to establish measurement invariance across the two time points . subsequently , latent difference scores were created to measure change over time in the outcome variable ( weight ) and applicable psychosocial variables . latent difference scores are not subject to the restrictive assumptions of traditional anova approaches and permit the measurement of change without error by including multiple indicators of each construct at each of two time points . this modeling approach decomposes the data from the second time point into two components : ( 1 ) variance associated with time 1 and ( 2 ) variance associated with the difference from time 1 . therefore , latent difference scores allow for the estimation of baseline variance as well as variance regarding change in a construct over time . following these initial steps , a series of bivariate analyseswere conducted within a structural equation modeling framework , which separately evaluated the relationships between each psychosocial variable and weight . for psychosocial variables that were measured at both baseline and follow - up , three parameters of primary interestwere estimated : ( 1 ) the correlation between the psychosocial characteristic and weight at baseline , ( 2 ) the predictive relationship of the baseline psychosocial characteristics on change in weight , and ( 3 ) the association of change in the psychosocial characteristic with change in weight . for psychosocial variables that were measured only at baseline ( i.e. , trauma and spirituality ) , after evaluating the bivariate relationships , a multivariate model estimated the three parameters described above simultaneously for all psychosocial variables . this model also controlled for baseline sociodemographic characteristics , including gender , age , education , and income . psychosocial variables were eliminated from the multivariate model in a stepwise manner if they reached a p value greater than 0.2 for all three primary parameters , in order to arrive at a final model . biostatisticians have suggested that a p value greater than 0.2 is a reasonable cutoff to eliminate variables that are clearly nonsignificant in regression models . an effect size measure for the final model ( r ) was computed as the proportion of variance of change in weight that was explained by the predictor variables . confirmatory factor analysis and structural equation modelsmacs analyses allow for the inclusion of mean - level information in addition to the covariance structures information of standard structural equation modeling techniques , which is necessary for the interpretation of latent difference scores . macs analyses also provide a particular advantage over ordinary least - squares regression approaches , namely , the fact that the unreliability of instruments / scales is taken into account and that corrections are made for measurement error . when employing structural equation modeling techniques , it is important to assess the degree to which the specified model fits the actual data in order to determine the appropriateness of a particular model . in the present study , the root mean square error of approximation ( rmsea ( 90 % confidence interval ) ; less than .08 is adequate fit and less than .05 is good fit ) , the comparative fit index ( cfi ; greater than .90 is adequate fit and greater than .95 is good fit ) , and the tucker - lewis index ( tli ; greater than .90 is adequate fit and greater than .95 is good fit ) were used as indices of model fit . in all models , full information maximum likelihood ( fiml ) was implemented in all analyses in order to address potential bias and decreased power due to missing data . furthermore , although there was very little variation across programs in class attendance for the participants included in the current study ( 95 % of participants who completed a follow - up assessment had completed at least 14 of the 16 recommended curriculum classes ) , other elements of the program may have varied slightly across sites . therefore , in order to control for the clustering of participants into 36 separate health care programs , standard errors that are robust to nonnormality and nonindependence of observations were computed using a sandwich estimator . descriptive statistics for all clinical and psychosocial variables are presented in table 2 . between baseline and follow - up , a significant decrease of 8.58 lbswas found with regard to average weight ( = 8.58 , p .001 ) . with regard to the change in psychosocial factors , general psychological distress decreased over time ( = 0.14 , p .001 ) , while coping abilities increased ( = 0.07 , p .001 ) . furthermore , positive family support , as perceived by participants , was higher at follow - up ( = 0.27 , p .001 ) , whereas negative family support remained stable ( = 0.03 , p = .28 ) . at baseline , 48 % of sdpi - dp participants reported a lifetime history of at least one significant trauma , and the average level of reported cultural spirituality at baseline was 3.81 ( on a scale from 1 to 5 ) . confirmatory factor analyses of the kessler distress , coping , and family support measures supported invariance of factor loadings and intercepts across the two measurement time points , which indicates that the measures exhibited similar structures and measured the same constructs across time . strong factorial invariance was established for both the kessler distress and coping measures , with all factor loadings and intercepts constrained to be equal across time . partial measurement invariance was established for the family support measure , as one of the intercepts for the positive family support scale was not invariant across time . it is generally acceptable to use measures with partial invariance in further structural models , if at least two indicators ( scale items ) have an invariant factor loading and intercept . in the case of the family support measure , all six items exhibited loading invariance , and all but one item exhibited intercept invariance . it was important to establish that these psychosocial measures had identical or near identical structures at both time points in order to calculate reliable and valid difference scores . bivariate analyses were performed prior to running the multivariate model in order to evaluate the strengths of individual predictor / outcome relationships ( see table 3 ) . all estimates ( = covariance ; = regression coefficient ) are provided in an unstandardized metric in order to allow meaningful interpretation based upon the original scale ranges . all bivariate models exhibited good model fit ( rmsea .05 ; cfi .95 ; tli .95 ) , and several significant correlations were found between psychosocial characteristics and weight at baseline . greater psychological distress at baseline was related to higher baseline weight ( = 2.44 , p .001 ) . in addition , greater negative family support was significantly correlated with higher baseline weight ( = 4.55 , p .001 ) , whereas greater identification with culturally relevant spirituality was associated with lower baseline weight ( = 3.13 , p .001 ) . baseline levels of coping , positive family support , and trauma experience were not significantly related to baseline weight . in addition to investigating the relationships between psychosocial characteristics and weight at baseline , regression analyses were conducted in order to elucidate the predictive relationships between psychosocial variables ( independent variables ) and change in weight from baseline to follow - up ( dependent variable ) . the results of these analyses underscore the importance of psychological distress and family support in predicting weight loss in ai / ans with prediabetes . greater psychological distress at baseline predicted less successful weight loss between baseline and follow - up ( = 1.85 , p .001 ) , and an increase in psychological distress between baseline and follow - up was also significantly related to less successful weight loss ( = 3.23 , p .001 ) . participants who reported an increase in positive family support after the intervention were more successful in losing weight ( = 3.56 , p .001 ) . conversely , higher negative family support at baseline as well as an increase in negative family support after the intervention was significantly associated with less weight loss ( = 1.38 , p = .003 and = 3.13 , p .001 , resp . ) . coping , trauma experience , and cultural spirituality were not significantly related to weight change . after conducting the bivariate analyses , all of the psychosocial variables were included in a single multivariate model . sociodemographic variables ( gender , age , education status , and annual household income ) that have previously been shown to be related to participant engagement and retention in the sdpi - dp program were entered as covariates in the model , in order to determine the effect of the psychosocial factors on weight change above and beyond any potential effect of sociodemographic characteristics . using the stepwise procedure described above , coping and trauma experience were dropped from the final model , as they were neither correlated with baseline weight nor predictive of weight change . results of the final multivariate model are presented in figure 1 , which mirror the results of the bivariate models , with one exception . after controlling for sociodemographic factors and other psychosocial variables , baselinepsychological distress was no longer predictive of weight loss from baseline to follow - up . however , the correlations between psychological distress , negative family support , and cultural spirituality with weight at baseline remained significant . in addition , change in psychological distress , positive family support , and negative family support over the course of the intervention , as well as levels of negative family support at baseline , remained significantly associated with change in weight . overall , the final multivariate model exhibited good model fit ( rmsea = .026 ( .025.028 ) ; cfi = .966 ; tli = .958 ) and accounted for 11 % of the variability in weight change . this proportion of variance explained is not large , but it does represent a medium effect size . the importance of psychosocial characteristics as sources of diabetes risk and resilience has been demonstrated previously among ai / ans . the present study is a critical first step in moving from research focused primarily on individuals with diabetes to examining factors related to successfully preventing incident diabetes among native people at high risk of the disease . although the influence of depression and anxiety on intervention outcomes for prediabetic individuals was examined in at least one previous study , the present study is the first to focus on determining which psychosocial factors successfully predict a specific outcome of a large - scale initiative aimed at preventing the onset of diabetes in the ai / an population . moreover , the statistical approach employed in the current study made it possible to simultaneously examine the relative contributions of the various psychosocial factors to successful health changes in a single model , unlike previous studies that have analyzed psychosocial factors in isolation of one another . specifically , structural equation modeling provides the ability to simultaneously examine the relationships of the psychosocial variables to a key clinical outcome with regard to baseline levels and change over time . as expected , when analyzing such relationships in a bivariate manner , several psychosocial factors were related to baseline levels of weight . higher levels of psychological distress and negative family support were associated with higher weight , whereas greater spirituality was correlated with lower weight . the same pattern of correlations of these three psychosocial variables with weight at baseline also was supported in the multivariate model when controlling for sociodemographic factors . psychosocial factors were also related to the degree of weight change following participants ' completion of the sdpi - dp intervention . greater psychological distress at baseline and increased psychological distress over the course of the intervention both contributed to less weight loss . similarly , greater negative family support at baseline and increased negative family support over the course of the intervention were associated with a smaller reduction in weight . increased positive family support , on the other hand , predicted greater weight loss . controlling for sociodemographic factors within a multivariate model , change in psychological distress , negative family support , and positive family support , as well as baseline levels of negative family support , continued to significantly affect weight reduction . the results of the present study are consistent with prior research on psychological distress as a risk factor with regard to chronic illness and with previous findings regarding the role of positive family support in both reducing the risk of and successfully managing diabetes . the results underscore the importance of regularly assessing the psychosocial status and functioning of ai / ans at high risk of diabetes . prevention programs will be well served by developing the capacity to evaluate and monitor participants ' mental health status , including the presence of depression and anxiety , the nature and extent of their spirituality , and the adequacy of their family support . these personalized assessments , combined with the knowledge of the general effects of psychosocial factors uncovered in the present study , will allow program staff to know which adjunctive interventions may maximize participant benefit with respect to the desired outcomes ( e.g. , weight loss ) . for example , by increasing the focus on mental health components within the core curriculum , one could strengthen participants ' strategies for decreasing depressive and stress - related symptoms , which then may make it more likely that the participants will be more engaged in the intervention and experience more successful weight loss . offering self - management techniques , simple cognitive - behavioral skills , and referral to local support groups or treatment options is a logical extension of the goals , process , and structure of an intensive lifestyle balance intervention . additionally , knowing that a participant has a strong preexisting spiritual focus may be helpful information for program staff who then may be able to use a participant 's connectedness to the natural world as a pathway to increase motivation to engage in a healthier lifestyle . likewise , given the strong relationship between family support and program outcomes , a greater effort should be made to incorporate close family members into various aspects of the prevention program . sdpi - dp demonstration projects have begun to do so , guided by their initial impressions of the potential gains . for example , some programs encourage participants to identify a support person to attend curriculum classes and other program - related activities with the participant . the present study has several limitations , which suggest directions for future research . data specific to the psychosocial characteristics were collected solely by self - report , thereby possibly increasing shared method variance and artificially strengthening the relationships among these variables . future studies may benefit from using a variety of methods to operationalize and assess similar constructs . for example , family support could be measured through multiple informants , including close family members , and levels of depression and anxiety could be assessed through interview - based rating scales . nevertheless , the primary relationships of interest were between self - reported psychosocial characteristics and an objective clinical measure ( weight ) , which were not subject to problems of shared method variance . the relationships between psychosocial factors and program outcomes may wax and wane over a longer follow - up period , or certain interactions may occur over time that are not evident within a relatively short follow - up period . in addition , sdpi - dp participants were more likely to be female , be older , have a higher level of education , and have a higher household income than the general ai / an adult population . though previous research has shown similar trends when comparing clinical populations to the general population , the generalizability of the present findings to individuals with widely differing sociodemographic backgrounds may be limited . for example , it is possible that weight change for males may not be as strongly related to psychological distress or family support as it was for this largely female sample . in addition , individuals with less education and lower household income than the participants in the current study may be more likely to have suffered a greater number of significant traumas . future studies should attempt to enroll individuals with broader sociodemographic characteristics and should include a measure of the number of traumas experienced , which would provide the opportunity to analyze a possible additive effect of repeated trauma upon successful weight loss that was not possible with the dichotomous trauma item used in the present investigation . similarly , although both rural and urban participants were included in the study , the majority of participants lived in rural settings , which may further limit the generalizability of the results . although it would be difficult to extend these results to the mainstream american population without further research , the current findings may also be applicable to other populations that share similar structures and values with ai / an communities ( e.g. , a greater emphasis on extended family support as opposed to individualism ; a spiritual emphasis on connectedness to others and nature ) . furthermore , although a medium effect size for the prediction of weight change within the multivariate model was observed ( 11 % of outcome variability explained ) , additional factors are likely at work and will need to be addressed to more comprehensively improve the effectiveness of such prevention programs . some additional factors may include lack of access to healthy food selections , high levels of family and caregiver stress that make it difficult to follow through with healthy eating and exercise routines , and lack of transportation to attend program classes . moreover , characteristics of the treatment team and health care program in general previously have been shown to be related to participant retention , which in turn predicts program outcomes . therefore , it likely will be critical to incorporate a multifaceted approach to crafting additional components that promise to enhance the intervention . for example , rather than just adding a stand - alone mental health screening module , a program might consider addressing barriers to participation ( e.g. , lack of transportation ) in concert with increasing positive family support and thereby decrease the isolation that can lead to psychological distress . finally , a more precise and comprehensive assessment of mental health status would enable a program to determine the most appropriate approach for decreasing symptoms likely to interfere with participation in the preventive intervention . in light of the relationship between depression and diabetes , referral to a mental health professional is a logical option to be pursued , although other possibilities , such as a group treatment model , should also be considered given the limited numbers of mental health providers within tribal , ihs , and urban indian health care programs . the present study demonstrates the importance of psychosocial factors for maximizing the potential benefits to participants in preventive interventions such as the sdpi - dp demonstration project . the challenge now becomes how to incorporate the lessons learned into the fabric of these programs . augmentation of the current intervention may be achieved either directly by incorporating adjunctive components or indirectly through referral to relevant local resources . the overall goal of these program additions would be to maximize participants ' engagement , their ability to grasp the knowledge conveyed , and their mastery of the skills related to the behavioral changes associated with the desired outcomes .\noutput:\n" }, { "from": "agent", "value": "the association of psychosocial factors ( psychological distress , coping skills , family support , trauma exposure , and spirituality ) with initial weight and weight loss among american indians and alaska natives ( ai / ans ) in a diabetes prevention translational project was investigated . participants ( n = 3,135 ) were confirmed as prediabetic and subsequently enrolled in the special diabetes program for indians diabetes prevention ( sdpi - dp ) demonstration project implemented at 36 indian health care programs . measures were obtained at baseline and after completing a 16 - session educational curriculum focusing on weight loss through behavioral changes . at baseline , psychological distress and negative family support were linked to greater weight , whereas cultural spirituality was correlated with lower weight . furthermore , psychological distress and negative family support predicted less weight loss , and positive family support predicted greater weight loss , over the course of the intervention . these bivariate relationships between psychosocial factors and weight remained statistically significant within a multivariate model , after controlling for sociodemographic characteristics . conversely , coping skills and trauma exposure were not significantly associated with baseline weight or change in weight . these findings demonstrate the influence of psychosocial factors on weight loss in ai / an communities and have substantial implications for incorporating adjunctive intervention components ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: autosomal dominant polycystic kidney disease ( adpkd ) is the most common monogenetic disorder , affecting 1 in 5001000 persons and accounting for 810 % of all cases of end - stage renal failure in western europe . linkage studies have shown that pkd1 on chromosome 16p13 .3 is responsible for adpkd type 1 ( 85 % ) and pkd2 on chromosome 4q2123 for adpkd type 2 ( 15 % ) . despite the relatively high frequency of pkd1 mutant alleles , no individual with homozygous ( pkd1 ) or compound heterozygous ( pkd1 : pkd1bis ) mutations of pkd1 has been described . in the course of ascertaining 400 adpkd families for genetic studies , we identified a white family in which non - consanguinous marriage between affected individuals was documented ( figure 1 ) . we ascertained the complete pedigree structure of the family over three generations and clinically assessed and genotyped all available members with polymorphic markers at pkd1 loci . all available members of the family were screened at least once by abdominal ultrasonography and the diagnosis of adpkd was confirmed according to recognized criteria . two of the affected members of this family ( ii3 and ii5 ) developed end - stage renal disease at 40 and 48 years of age , respectively . they were successfully transplanted with a kidney donated from a cadaver donor at the age of 42 and 49 years , respectively . the proband ( ii6 ) was diagnosed with pkd when she was 31 years old . in contrast , at a similar age she had severe polycystic kidney and liver disease with creatinine clearance of 81 ml / min . individuals iii6 and iii8 were diagnosed with adpkd at ages 7 years and 3 years , respectively . this clinical impression was confirmed by pairwise linkage results , which were consistent with linkage to pkd1 . consistent with linkage results , haplotype inspection showed that the pkd1 haplotype , derived from markers kg8 and cw2 , segregated only with affected individuals and not with definitively unaffected members of this family . the proband ( ii6 ) , who was involved in the non - consanguinous marriage , had a total of four pregnancies ( figure 1 ) . the second and fourth pregnancies resulted in two offspring ( iii6 and iii8 ) who are affected with adpkd . because both these individuals have inherited only one copy of the putative diseased pkd1 haplotype ( paternal ) , they are predicted to be heterozygotes ( pkd1 ) . the first and third pregnancies ( iii5 and iii7 ) were lost at 3 and 4 months of gestation when the proband was 22 and 25 years of age . no apparent cause was identified for either miscarriage , and fetal tissue was not available for further study . according to the proband 's testimony , her parents and the parents of her husband were not relatives and came from different parts of spain . given that adpkd affects 1 in 5001000 live births , bilineal disease is predicted to occur in 1 in 2500001000000 marriages in the general population . a potential consequence of bilineal adpkd is that some of the affected members from these pedigrees may carry two germline mutations . first , in families in which germline mutations of affected parents involve the same polycystic kidney disease gene ( i.e. pkd1 or pkd2 ) , homozygous ( pkd1 or pkd2 ) or compound heterozygous ( pkd1 : pkd1bisor pkd2 : pkd2bis ) mutations are expected in 25 % of offspring . it has previously been reported that in a family with type 1 adpkd , in a marriage between affected consanguinous individuals , there were two live - born heterozygous offspring and two fetuses lost late in pregnancy , suggesting that homozygosity of pkd1 mutations in humans is embryonically lethal . second , in families in which germline mutations of affected parents involve one copy each of pkd1 and pkd2 , trans - heterozygous ( pkd1 : pkd2 ) mutations in both genes are expected in 25 % of offspring . one such family in which trans - heterozygous pkd1 and pkd2 mutations were observed in two affected individuals has been recently reported . the disease associated with the presence of both mutations appears to be more severe than the disease associated with either mutation alone . more recently , a patient with adpkd has been reported who was heterozygous for a de novo pkd1 variant and homozygous for a novel pkd2 mutation . however , the scenario involving compound heterozygous mutations of pkd1 , which is predicted to be more common , has not been described to date . this raises the possibility that homozygous and compound heterozygous mutation combinations may be lethal in humans . mice with heterozygous inactivation of either pkd1 and pkd2 develop focal cysts later in life . in contrast , mice with homozygous inactivation of either pkd1 or pkd2 die , either in utero or perinatally , with massive polycystic kidneys . a major point of interest in our family is whether the miscarriages of our proband might represent mutant pkd1 compound heterozygotes . however , a limitation of our study is that direct dna - based verification was not possible because fetal tissue was not available . based on mendelian segregation , the risk for disease transmission from the non - consanguinous marriage of our proband and her husband to their offspring is 75 % ( i.e. 50 % risk for heterozygotes plus 25 % risk for compound heterozygotes ) . conversely , the risk for maternal age - adjusted fetal loss from an unselected cohort of white pregnancies is 3.5 % . thus , the probability of pkd1 - diseased compound heterozygotes for each of the miscarriages in this family is approximately eightfold greater than the population risk from non - consanguinous marriages . the increased risk for fetal wastage , presumably reflect an increased probability of lethal recessive genes in the offspring . recent studies have suggested that individual cyst formation in adpkd is a cellular recessive two - hit event requiring inactivation of both copies of a pkd gene through germline and somatic mutations within an epithelial cell . a trans - heterozygous variant of the two - hit mechanism , with germline mutation at one polycystin gene coupled with somatic mutation at the other , is supported by observations of somatic pkd1 mutations in kidney cysts of patients with germline pkd2 mutations , and vice versa . since the somatic pkd mutations constitute the rate - limiting step for individual cyst formation , the frequency of such mutationsis predicted to determine both the number of cysts eventually formed and the disease severity . in the individuals with compound heterozygous mutations , all cellsthus , mutant pkd1 compound heterozygosity is expected to be associated with a severe phenotype . the increased disease severity may simply reflect the fact that all the cells in these individuals have two loci that could be involved in the somaticsecond hits . our findings in this family are confirmatory of this possibility since the two offspring who were affected with adpkd type 1 were heterozygous . it is possible that the two fetuses lost in mid - pregnancy were compound heterozygotes . these data provide the most compelling evidence in support of our contention that pkd1 compound heterozygosity may be embryonically lethal . in summary , we report for the first time a clinically proven situation of bilineal inheritance and probably compound heterozygosity in a pkd1 family . based on the arguments presented , our findings suggest that compound heterozygosity of pkd1 mutations in humans may be embryonically lethal .\noutput:\n" }, { "from": "agent", "value": "we report for the first time a family with type 1 adpkd in which the marriage between affected non - consanguinous individuals resulted in two live - born heterozygous offspring and two fetuses lost in mid - pregnancy . given a 25 % chance for mutant compound heterozygosity in the offspring of this family , our findings suggest that compound heterozygosity of pkd1 mutations in humans may be embryonically lethal ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: a 76 - year - old male with 160 cm in height and 58 kg in weight , respectively , was admitted for surgery with known aortic stenosis . preoperative echocardiography exams revealed the followings : aortic valve calcification and severe stenosis , a decreased left ventricular systolic function , trivial tricuspid regurgitation and ejection fraction of 40 - 45 % . in a coronary artery angiography ,1 ) . however , compression of the coronary arteries by major vessels was not revealed . coronary computed tomography ( ct ) the patient was scheduled for aortic valve replacement . at the operating theatre , routine noninvasive and invasive blood pressure monitoring , electrocardiography ( ekg ) , anesthetic induction was done under target - controlled infusion ( tci ) of propofol and remifentanil . tee revealed severe calcified and stenotic aortic valve , trivial tricuspid regurgitation and a good regional wall motion . until the cpb initiation , vital signs were maintained well . at the time of the operation , aortic valve and annuluswere severely calcified and both coronary arteries were originated from the left coronary sinus , but have different ostia . jude medical , minnesota , usa ) and the surgery were done without specific event . during cardiopulmonary bypass weaning , blood pressure and cardiac output were unstable . these situations were repeated for about 30 minutes , and dopamine and norepinephrine infusion were started . the patient was transferred to coronary care unit after surgery , and vital signs were also stable . anomalous origin of the right coronary was considered as the culprit for the difficult weaning process . iabp was removed the next day , and the patient was discharged without any special events . poor ventricle function , regional wall motion abnormalities , or significant unexplained arrhythmias after aortic valve surgery should suspect poor myocardial protection , coronary insufficiency due to mechanical cause , coronary spasm , coronary air / particle emboli , protamin / transfusion reactions , and anomalous coronary artery [ 1 - 4 ] . since the aortic valve has been replaced with a stentless tissue valve , a number of mechanical obstructions in the coronary arteries have been reported . during the surgery , distal suture line , near the coronary artery ostium , teflon pledget , vessel kinking or torsion , after coronary artery reimplantation , obstructs the coronary artery [ 4 - 8 ] . clinically significant air embolism occurs rarely and is usually self - limiting and resolved quickly . particulates emboli , such as a calcified aortic valve , papillary muscle , or aortic vegetation , immediately impair the hemodynamic at the beginning of coronary perfusion and change the ekg . sometimes , hemodynamic fluctuation should be suspected by the coronary artery spasm . intraoperative or postoperative coronary spasms are referable to the coronary artery trauma during manipulation , compression by the drains , electrolytes disturbance or releasing factors [ 9 - 11 ] . sometimes , spasm occurs during the cardiopulmonary bypass weaning , but mostly , resuscitation and intraaortic balloon pumps are needed in the postoperative period . although the right coronary artery was not compressed preoperatively , aortic valve replacement could have made anatomical change to the relationships between anomalous coronary artery and the major vessels . considering the recovery of vital signs postoperatively , blood volume changes in the heart and the major vessels , during the cpb weaning period , could have affected that relationship . the incidences of anomalous origin of the coronary artery is about 0.6 - 2 % and the most common types are the anomalous circumflex origin from the right coronary artery or the right sinus of valsalva . anomalous right coronary origin from the left coronary sinus , anomalous left coronary origin from the right coronary artery , or sinus of valsalva and both coronary arteries from a single ostium were reported . the majorities of these anomalies are benign , but sometimes they result in severe myocardial ischemia , infarction , and sudden death . especially , they are vulnerable to compression , insufficiency and injury during valve surgery . considering that the coronary artery anomaly is accompanied more commonly in patients with aortic valve pathology , anesthesiologists should always be reminded about these complications . in the cases of mechanical obstructionwhen intraoperative coronary artery spasm is expected , intravenous or intracoronary injection of nitrates and calcium antagonists can relieve the spasm , and intracoronary injection of ergonovine can be used as a diagnostic tool . maintenance of high perfusion pressure can quickly resolve the coronary air embolism , but particulates embolus needs a rescue graft , but particulates embolus needs a rescue graft . authors did n't think about the possibilities of compression of the right coronary artery because there was no compression preoperative angiography . excluding other possible causes of unstable vital signs , aberrant coronary artery can be taken into consideration . conclusively , anesthesiologists should always take care for the coronary artery anatomy , even though it is a valve surgery , and especially since they have anomalous origins or pathologies .\noutput:\n" }, { "from": "agent", "value": "we report a case of hemodynamic instability after aortic valve replacement , due to the anomalous origin of the right coronary artery . during the cardiopulmonary bypass weaning process , hemodynamic instability occurred . the cause was not identified at first , and compression of the anomalous right coronary artery was thought to be the culprit , thereafter ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: multimodality management either a combination of surgery followed by adjuvant radiation or radical chemoradiation is the standard of care in locally advanced oral cancers . however , in spite of multimodality management , locally advanced oral cancers have high failure rates . unfortunately , majority of these failures occur in first 1 - 2 years posttreatment completion . however , patients who fail within 1 - month of adjuvant radiotherapy ( rt ) or within 6 months of ctrt ( within 6 months of last dose of platinum ) have a very poor prognosis . metronomic chemotherapy consisting of oral methotrexate and celecoxib has shown promising results in head and neck cancer patients . we recently reported a randomized study which compared metronomic chemotherapy consisting of oral methotrexate and celecoxib with intravenous cisplatin in palliative head and neck cancer patients who had failed post 3 months of curative therapy . metronomic chemotherapy was found to be superior in terms of progression - free survival ( pfs ) and overall survival ( os ) . hence , these patients with early failures are treated with a metronomic combination of celecoxib and oral weekly methotrexate on compassionate grounds when they can not afford cetuximab at our center . this analysis was planned to study the efficacy of metronomic chemotherapy in this group of patients . we hypothesized that if 6 months survival would be 30 % or more , then metronomic chemotherapy should be studied in a randomized phase 2 . this was a retrospective analysis . we maintain a prospective database of patients undergoing palliative chemotherapy in head and neck cancers . biopsy proven squamous cell carcinoma.patients with site of tumor in oral cavity.treated between august 2013 and august 2014 . early failure postmultimodality treatment . early failure was defined as failure ( loco - regional , distant , or both ) either within 1 - month of adjuvant rt or within 6 months of ctrt ( adjuvant or radical ) . recipients of metronomic chemotherapy.ecog ps 0 - 2 . patients with site of tumor in oral cavity . treated between august 2013 and august 2014 . early failure postmultimodality treatment . early failure was defined as failure ( loco - regional , distant , or both ) either within 1 - month of adjuvant rt or within 6 months of ctrt ( adjuvant or radical ) . all of these patients had been seen in the multidisciplinary clinic consisting of surgical oncologist , radiation oncologist , medical oncologist , and radiologist . these patients were deemed unfit for surgery in the view of extensive disease and very short disease - free interval ( dfi ) . these patients were not considered for palliative radiation too , as either they had received radiation before ( n = 84 ) , or the disease was extensive . all of these patients were counseled regarding the poor prognosis and option of cetuximab - based chemotherapy was given . as these patients had logistics issues ( financial ) in procuring cetuximab , they were offered oral metronomic chemotherapy on compassionate grounds . written informed consent was obtained before starting metronomic chemotherapy . these patients had received oral weekly methotrexate 15 mg / m along with oral celecoxib 200 mg po twice daily . the study sample size calculation was done with a type 1 error of 5 % and type 2 error of 20 % . hence , this study had 80 % power and to detect a lower critical limit of survival probability at 6 months of 0.3 , that is , 30 % . it was assumed that the selected samples survival distribution will follow the nonparametric exponential survival distribution . a total of 80 samples are found suitable to carry out this retrospective analysis . on the collection of datathe number of patients was more than the required sample size for such analysis ; however , as a higher sample size would improve the power of the study , we decided to include all the 100 patients . the categorical variables were expressed in frequencies and percentages . the continuous variables in median and interquartile range . the os was calculated from the date of start of chemotherapy till the date of death . in case , if the patient had not died at the last follow - up date , then the respective patient was censored while estimating the os . known prognostic factors ( age , gender , previous rt , previous platinum exposure , and previous event free period ) would be tested for their influence on os . biopsy proven squamous cell carcinoma.patients with site of tumor in oral cavity.treated between august 2013 and august 2014 . early failure postmultimodality treatment . early failure was defined as failure ( loco - regional , distant , or both ) either within 1 - month of adjuvant rt or within 6 months of ctrt ( adjuvant or radical ) . recipients of metronomic chemotherapy.ecog ps 0 - 2 . patients with site of tumor in oral cavity . treated between august 2013 and august 2014 . early failure postmultimodality treatment . early failure was defined as failure ( loco - regional , distant , or both ) either within 1 - month of adjuvant rt or within 6 months of ctrt ( adjuvant or radical ) . all of these patients had been seen in the multidisciplinary clinic consisting of surgical oncologist , radiation oncologist , medical oncologist , and radiologist . these patients were deemed unfit for surgery in the view of extensive disease and very short disease - free interval ( dfi ) . these patients were not considered for palliative radiation too , as either they had received radiation before ( n = 84 ) , or the disease was extensive . all of these patients were counseled regarding the poor prognosis and option of cetuximab - based chemotherapy was given . as these patients had logistics issues ( financial ) in procuring cetuximab , they were offered oral metronomic chemotherapy on compassionate grounds . these patients had received oral weekly methotrexate 15 mg / m along with oral celecoxib 200 mg po twice daily . the study sample size calculation was done with a type 1 error of 5 % and type 2 error of 20 % . hence , this study had 80 % power and to detect a lower critical limit of survival probability at 6 months of 0.3 , that is , 30 % . it was assumed that the selected samples survival distribution will follow the nonparametric exponential survival distribution . a total of 80 samples are found suitable to carry out this retrospective analysis . on the collection of datathe number of patients was more than the required sample size for such analysis ; however , as a higher sample size would improve the power of the study , we decided to include all the 100 patients . the os was calculated from the date of start of chemotherapy till the date of death . in case , if the patient had not died at the last follow - up date , then the respective patient was censored while estimating the os . known prognostic factors ( age , gender , previous rt , previous platinum exposure , and previous event free period ) would be tested for their influence on os . the study sample size calculation was done with a type 1 error of 5 % and type 2 error of 20 % . hence , this study had 80 % power and to detect a lower critical limit of survival probability at 6 months of 0.3 , that is , 30 % . it was assumed that the selected samples survival distribution will follow the nonparametric exponential survival distribution . a total of 80 samples are found suitable to carry out this retrospective analysis . on the collection of datathe number of patients was more than the required sample size for such analysis ; however , as a higher sample size would improve the power of the study , we decided to include all the 100 patients . the categorical variables were expressed in frequencies and percentages . the continuous variables in median and interquartile range . the os was calculated from the date of start of chemotherapy till the date of death . in case , if the patient had not died at the last follow - up date , then the respective patient was censored while estimating the os . known prognostic factors ( age , gender , previous rt , previous platinum exposure , and previous event free period ) would be tested for their influence on os . the median age of the cohort was 45 years ( iqr : 40 - 51.3 years ) . the ecog ps was 0 - 1 in 92 patients and 2 in 8 patients . the subsite of primary was buccal mucosa in 38 patients ( 38 % ) , anterior two - third tongue ( oral tongue ) in 51 patients ( 51 % ) , and alveolus in 11 patients ( 11 % ) . medical comorbidities and hypertension was seen in 14 patients , diabetes mellitus in 10 patients , and ischemic heart disease in 01 patient . habits included oral tobacco consumption in 68 patients ( 68 % ) , smoking in 28 patients ( 28 % ) , and alcohol in 27 patients ( 27 % ) . the baseline median hemoglobin and serum albumin were 11.9 g / dl ( iqr : 10.7 - 13.0 ) and 3.9 g / dl ( 3.6 - 4.3 ) , respectively . forty - seven patients had underwent surgery followed by adjuvant chemoradiation , 29 patients had undergone surgery followed by adjuvant radiation while rest of the 24 patients were planned for neoadjuvant chemotherapy followed by local therapy . in these 24 patients ,16 patients had progressed after nact ; these patients had not received any local treatment . other 8 patients underwent surgery followed by adjuvant chemoradiation post - nact . hence , overall previous radiation and chemotherapy were received by 84 and 71 patients , respectively . previous treatment details the sites of failure were loco - regional in 95 patients ( 95 % ) while 5 patients ( 5 % ) had distant metastasis . the median event free survival ( efs ) post last treatment was 2 months ( iqr : 2 - 4 months ) . details about recurrent stage the median estimated os was 110 days ( 95 % confidence interval [ ci ] : 85 - 134 days ) [ figure 2 ] . the proportion of patients surviving at 6 months was 26.4 % ( 95 % ci : 17.9 - 35.6 ) . the median estimated os was 75 days ( 95 % ci : 41 - 117 days ) in patients with event free period below 3 months while it was 132 days ( 95 % ci : 91 - 149 days ) ( p = 0.41 ) [ figure 3 ] . among the factors tested ( age , sex , and previous treatment details ) numbers at risk are shown at the bottom of the graph kaplan - meier plot showing estimated overall survival according to disease - free interval . disease - free interval range = below3 - failure within 3 months of completing multimodality treatment . disease - free interval range = 3 - 6 : failure after 3 months but within 6 months of completing multimodality treatment numbers at risk are shown at the bottom of the graph influence of different factors on osthe median age of the cohort was 45 years ( iqr : 40 - 51.3 years ) . the ecog ps was 0 - 1 in 92 patients and 2 in 8 patients . the subsite of primary was buccal mucosa in 38 patients ( 38 % ) , anterior two - third tongue ( oral tongue ) in 51 patients ( 51 % ) , and alveolus in 11 patients ( 11 % ) . medical comorbidities and hypertension was seen in 14 patients , diabetes mellitus in 10 patients , and ischemic heart disease in 01 patient . habits included oral tobacco consumption in 68 patients ( 68 % ) , smoking in 28 patients ( 28 % ) , and alcohol in 27 patients ( 27 % ) . the baseline median hemoglobin and serum albumin were 11.9 g / dl ( iqr : 10.7 - 13.0 ) and 3.9 g / dl ( 3.6 - 4.3 ) , respectively . forty - seven patients had underwent surgery followed by adjuvant chemoradiation , 29 patients had undergone surgery followed by adjuvant radiation while rest of the 24 patients were planned for neoadjuvant chemotherapy followed by local therapy . in these 24 patients ,16 patients had progressed after nact ; these patients had not received any local treatment . , overall previous radiation and chemotherapy were received by 84 and 71 patients , respectively . previous treatment details the sites of failure were loco - regional in 95 patients ( 95 % ) while 5 patients ( 5 % ) had distant metastasis . the median event free survival ( efs ) post last treatment was 2 months ( iqr : 2 - 4 months ) . the median estimated os was 110 days ( 95 % confidence interval [ ci ] : 85 - 134 days ) [ figure 2 ] . the proportion of patients surviving at 6 months was 26.4 % ( 95 % ci : 17.9 - 35.6 ) . the median estimated os was 75 days ( 95 % ci : 41 - 117 days ) in patients with event free period below 3 months while it was 132 days ( 95 % ci : 91 - 149 days ) ( p = 0.41 ) [ figure 3 ] . among the factors tested ( age , sex , and previous treatment details ) numbers at risk are shown at the bottom of the graph kaplan - meier plot showing estimated overall survival according to disease - free interval . disease - free interval range = below3 - failure within 3 months of completing multimodality treatment . disease - free interval range = 3 - 6 : failure after 3 months but within 6 months of completing multimodality treatment numbers at risk are shown at the bottom of the graph influence of different factors on osfurther , the results of salvage surgery are impressive if the dfi is 2 years and stage of recurrent tumor is stage i or ii . however , only 16 % of recurrent patients are suitable for salvage surgery , either the dfi is short or the disease is extensive . in our study , we have addressed such patients only . hence , it 's not a surprise that none of these patients was considered for salvage surgery by the multidisciplinary clinic . however , again in the context of early failures as in the present study , re - irradiation is not a feasible option . reirradiation is associated with 2 years os 30 - 40 % in different series ; however , the series are limited to patients who had dfi of more than 1 - year from previous treatment and the tumor volumes were small ( 27 cm ) . the cohort of patients in this study had extensive disease and the maximum dfi was 6 months hence palliative chemotherapy was offered . it started with a small study demonstrating a survival benefit of chemotherapy over patients treated with only supportive measures . over next 30 - 40 years , we have improved survivals modestly by adding targeted therapy to chemotherapy . however , this benefit of targeted therapy , cetuximab was seen in a randomized study done in a selected cohort of patients . likely , platinum - insensitive patients were excluded from this study and are routinely excluded from the treatment defining palliative chemotherapy studies . the definition of this entity has also been variable . in general , patients who receive either cisplatin cumulative dose more than equal to 60 mg / m or carboplatin cumulative dose more than or equal to auc - 4,2 or more cycles of treatment with 4 weeks among them and failure within 6 months of the last dose of platinum are considered as platinum - resistant . figure 1 depicts that 71 patients in our cohort who all had received platinum had failed within 6 months and cumulative doses were far beyond these recommendations . we have also included 29 patients who had failed within 1 - month of surgery and adjuvant rt . these patients were included as these patients have a biological aggressive disease and even these patients are excluded from chemotherapy studies and hence are never addressed . the treatment options in the platinum - resistant and / or early failure patients studied are limited . cetuximab as a single agent seems an appropriate option in this setting . in a study done by vermorken et al . , 117 patients who had progressed on platinum were treated with single - agent cetuximab . the median time to progression and os were 50 days and 178 days , respectively . similar results with a median pfs of 85 days and os of 183 days with single agent cetuximab were reported in platinum refractory patients by baselga et al . combination of cetuximab + cisplatin has shown similar survivals to single agent cetuximab in patients who had progressed within 90 days ( 3 months ) on cisplatin - paclitaxel or cisplatin 5 fu combination . this regimen in retrospective studies has consistently shown to have median os around 10.0 months . however , the cost of cetuximab precludes its use in most of the low and middle - income countries as a routine standard of care ; hence , the search for cheaper alternatives . the mechanism of the action of metronomic is by antiangiogenesis and its effects the endothelial cell of the vasculature supplying the tumor . the endothelial cell is a genotypically stable cell hence it should be unaffected by somatic mutations in the tumor which leads to platinum - resistance . hence , metronomic chemotherapy theoretically should be equally effective in early failures or platinum - resistant patients . metronomic chemotherapy combination of methotrexate and celecoxib , unfortunately , failed to meet its expectation in our study . the threshold considered by us for its further studies was 30 % os at 6 months , while the proportion of patients surviving was below this , 26.4 % at 6 months . the impact of time to failure post upfront multimodality treatment on os with palliative chemotherapy was seen in this study . patients with time to failure below 3 months had lower os than patients who had failure between 3 and 6 months posttreatment completion . previous treatment with radiation , poor ps , previous history of weight loss , nonoropharyngeal location , and poor differentiation are the known poor prognostic features in the patients treated with palliative chemotherapy in head and neck cancers . patients having two or more of these features ( poor risk status ) have a survival of around 6 months with first - line platinum chemotherapy . in our study , majority of patients ( 84 patients , 84 % ) had previous radiation and all had oral cancer primaries . in addition , nearly three - fourth of the patients had exposure to platinum and had failed within 6 months . as this metronomic combination has failed to reach the prespecified proportion , we need to consider other options in the patients who can not afford cetuximab . the mechanism of resistance to methotrexate in head and neck cancers is driven by abcg2 protein . second - line treatment with erlotinib after first - line failure provides response rates of around 15 - 20 % in our experience . at this end , we now planned to study the combination of triple drug metronomic ( methotrexate , celecoxib , and erlotinib ) in this poor risk cohort . metronomic chemotherapy combination of methotrexate and celecoxib failed to meet its prespecified efficacy limit and hence should not be used in such patients .\noutput:\n" }, { "from": "agent", "value": "purpose : oral cancer patients with platinum - resistant disease and or early failures have limited treatment options . this analysis was planned to study the efficacy of metronomic chemotherapy in this group of patients.materials and methods : this was a retrospective analysis of oral cancer patients who had squamous cell carcinoma and had an early failure and / or platinum - insensitive failure . early failure was defined as a failure either within 1 - month of adjuvant radiotherapy or within 6 months of chemoradiation ( ctrt ) . a sample size of 100 patients was selected for this study . if 39 of 100 patients would have survived at 6 months with metronomic chemotherapy , then additional studies would be warranted.results : the ecog ps was 0 - 1 in 92 patients and 2 in 8 patients . the subsite of primary was buccal mucosa in 38 patients ( 38 % ) , anterior two - third tongue ( oral tongue ) in 51 patients ( 51 % ) , and alveolus in 11 patients ( 11 % ) . the median estimated overall survival was 110 days ( 95 % confidence interval [ ci ] : 85 - 134 days ) . the proportion of patients surviving at 6 months was 26.4 % ( 95 % ci : 17.9 - 35.6 ) . conclusion : metronomic combination of methotrexate and celecoxib failed to meet its prespecified efficacy limit and should not be used in these patients as routine ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: although previously published studies have documented a high perioperative risk in patients with liver failure undergoing general surgery , such as , elective abdominal surgery ( 1 - 4 ) , thoracotomy ( 5 ) , and trauma operations ( 6 , 7 ) , little information is available on clinical outcomes following orthopedic surgery in this group of patients . ziser et al . ( 8 ) , in their retrospective review of 733 cirrhotic patients undergoing any type of surgical procedure , reported that patients undergoing major orthopedic procedures including hip surgery , spine fusions , and operations for long bone fractures had a substantially higher perioperative complication rate than patients undergoing non - orthopedic surgery . whilst elective total hip arthroplasty ( tha ) is generally regarded as safe , with an associated perioperative mortality rate of less than 1 % in the general population ( 9 - 11 ) , data are extremely limited on the safety and outcome of hip arthroplasty in patients with advanced liver disease . only two recent studies ( 12 , 13 ) , to the best of our knowledge , have evaluated the perioperative risks of hip arthroplasty in cirrhotic patients . the purpose of this study was to document perioperative morbidity and mortality in patients with liver cirrhosis undergoing hip arthroplasty . we retrospectively reviewed the complete medical records of 30 cirrhotic patients who had undergone hip arthroplasty at three participating academic institutions between october 1994 and may 2001 . cirrhosis was diagnosed primarily by biopsy , and when biopsy was not performed , abdominal ultrasonography or computed tomography was used for the diagnosis of cirrhosis , in conjunction with a history of liver disease and abnormal liver function test results . there were 26 males and 4 females with a mean age of 60 yr ( range , 15 - 63 yr ) at the time of index operation . the procedures included 17 primary thas , 8 bipolar hemiarthroplasties , and 5 revision thas . of the 25 primary hip arthroplasties , the diagnoses leading to surgery were osteonecrosis of the femoral head in 13 , hip fracture in 10 , and osteoarthritis in 2 . preoperative data included age , gender , levels of serum albumin , total bilirubin and creatinine , the presence of ascites , esophageal varices , or encephalopathy , and prothrombin time . a modification of the child 's classification by pugh ( 14 ) was used as a measure of liver dysfunction . the severity of cirrhosis was graded as class a when the child - pugh score was 5 or 6 points , class b from 7 to 9 , and class c from 10 to 15 ( a higher score indicates more severe cirrhosis ) . perioperative complications searched for were as follows : postoperative bleeding ( gastrointestinal or surgical site ) , coagulopathy , wound ( dehiscence or infection ) , encephalopathy , cardiovascular ( congestive heart failure , myocardial infarction , or arrhythmia ) , pulmonary ( pneumonia , pulmonary embolism , or ventilatory dependence ) , renal ( acute tubular necrosis , hepatorenal syndrome , or ascites ) , and infection ( bacteremia or fungemia ) . postoperative bleeding was defined as hemorrhage requiring transfusion , and gastrointestinal and surgical site bleedings were distinguished from each other based on a review of the medical records . coagulopathy ( whether on the basis of reduced hepatic synthesis , disseminated intravascular coagulation , normal consumption , or dilutional mechanisms ) was noted in those patients with a decreased platelet count , fibrinogen concentration , and increased activated partial thromboplastin time . new onset or worsening of ascites or encephalopathy was also registered as a postoperative complication within 30 days of hip arthroplasty . we chose this 30 - day perioperative time limit because a shorter period may have missed complications and deaths directly related to events that had begun during hip surgery or hospitalization . twelve variables were investigated to determine risk factors in liver cirrhosis patients who underwent hip arthroplasty ; age , gender , the presence of ascites or varices , prothrombin time , the levels of albumin , bilirubin , and creatinine , the type of surgery ( primary tha , bipolar hemiarthroplasty , or revision tha ) , the type of anesthesia ( general or spinal ) , operation time , and estimated operative blood loss . statistical analysis was performed using the sas statistical software package ( sas institute , cary , nc , u.s.a . ) . multivariate logistic regression models were used to identify factors differentiating complicated and uncomplicated hip arthroplasties in cirrhotic patients . variables deemed significant by multivariate analysis at p 0.05 were considered risk factors associated with perioperative morbidity and mortality in liver cirrhosis patients who underment hip arthroplasty . according to assessments of liver cirrhosis severity using the child - pugh scoring system , 19 patients ( 63.3 % ) were class a , 9 ( 30.0 % ) class b , and 2 ( 6.7 % ) were class c. eight ( 26.7 % ) of the 30 patients had one or more perioperative complications . of these , a superficial wound infection was the most common , with a rate of 10 % ( 3 of 30 hips ) . other postoperative complications included 2 surgical site bleedings , 2 coagulopathies , 2 encephalopathies , 1 gastrointestinal bleeding , 1 pneumonia , and 1 arrhythmia . in the analysis of the cirrhotic patients by individual child - pugh 's class , perioperative complications occurred in 1 ( 5.3 % ) of 19 class a cirrhotics , 5 ( 55.6 % ) of 9 class b , and 2 ( 100 % ) of 2 class c ( table 1 ) . two patients with class c died from aspiration pneumonia and disseminated intravascular coagulation , respectively , during the first postoperative month . of the twelve variables that were investigated to identify risk factors for complicated hip arthroplasty in patients with liver cirrhosis , a high level of creatinine was solely associated with increased perioperative mortality ( p = 0.0499 ) . no statistically significant associations were found in the other variables including age , gender , the presence of ascites or varices , prothrombin time , the levels of albumin and bilirubin , the type of surgery , the type of anesthesia , operation time , and estimated operative blood loss . however , combining all of the categories included in the child - pugh scoring system , a significantly increased risk of perioperative complications was noted in cirrhotic patients who had a higher child - pugh score ( p = 0.0001 ) ( table 2 ) . previous studies ( 1 - 7 , 15 - 18 ) have well documented high rates of perioperative complications in patients with liver failure undergoing anesthesia and surgery , especially those undergoing major orthopedic procedures ( 8 ) . however , data are extremely limited on the safety and outcome of hip or knee arthroplasty in patients with advanced liver disease ( 12 , 13 , 19 ) . ( 8 ) evaluated 733 patients with a diagnosis of liver cirrhosis who had undergone some type of surgical procedure , and reported a perioperative complication rate of 30.1 % and a mortality rate of 11.6 % within 30 days of surgery . of these , 26 procedures were hip and pelvic surgery , arthroplasty , or fractures , and this subgroup showed a substantially increased perioperative complication rate of 53.8 % . recently , hsieh et al . ( 13 ) reported on the outcomes of 45 hip arthroplasties that had been performed over a period of 20 yr in 38 patients with liver cirrhosis , with a perioperative 30 - day complication rate of 26.7 % . they found that advanced cirrhotics ( child - pugh 's b and c patients ) had a higher risk of complications than child - pugh 's a cirrhotics ( p = 0.004 ) . ( 12 ) also reported a 20.7 % major complication rate for cirrhotic patients who received either total hip or knee arthroplasty . in accordance with these previous studies , we observed a high perioperative complication rate ( 26.7 % , 8 of 30 ) in cirrhotic patients that had undergone hip arthroplasty . of the twelve variables evaluated in our series , a high level of creatinine was found to be the only risk factor associated with perioperative mortality . however , combining all of the categories included in the child - pugh scoring system , a higher child - pugh score was another important risk factor of perioperative morbidity . our findings were also consistent with the previous observations that there was a trend toward an increased perioperative risk for hip arthoplasty in cirrhotic patients with more advanced liver disease . ( 16 ) reported a mortality rate within 30 days of surgery of 28 % for patients with chronic liver failure who had undergone non - hepatic surgery , and that 2 of 5 patients who underwent unspecified orthopedic surgery died . hsieh et al . ( 13 ) reported that 18 of 38 cirrhotic patients undergoing hip arthroplasty died during the protracted study period of 20 yr . ( 12 ) reported a 10.3 % perioperative mortality rate for cirrhotic patients who received either total hip or knee arthroplasty , and this mortality rate increased to 15.8 % ( 3 of 19 ) in cirrhotic tha patients . however , a relatively lower rate of perioperative mortality ( 6.7 % , 2 of 30 ) was noted in the present study as compared with previous series that enrolled patients with liver cirrhosis undergoing orthopedic surgery over a long time span . although it may be attributed to the small number of patients with severe liver cirrhosis ( child - pugh 's class c ) in our series , we believe that the improvement of medical care of cirrhotic patients and refinement in surgical techniques that have occurred during past decade may contribute to the lower mortality rate . ( 12 ) also suggested that less extensive operative procedures , such as bipolar hemiarthroplasty , would be associated with more favorable outcomes than those of primary or revision thas , but our findings showed no statistically significant difference among the different surgical procedures , which we attribute to the small sample size . in conclusion , we continue to perform hip arthroplasty in patients with cirrhotic liver disease , but we should warn patients with a higher child - pugh score and those with an increased creatinine level about their increased perioperative risk of complications or death . cirrhotic patients should be aware that they are at increased risk for surgical complications because of their disease , albeit the mortality rates are relatively low in less severe cirrhotics .\noutput:\n" }, { "from": "agent", "value": "we retrospectively reviewed the complete medical records of 30 patients with a diagnosis of liver cirrhosis who had undergone hip arthroplasty at three academic institutions between october 1994 and may 2001 . there were 26 males and 4 females with a mean age of 60 yr at index operation . surgical procedures included 17 primary total hip arthroplasties ( tha ) , 8 bipolar hemiarthroplasties , and 5 revision thas . according to the child - pugh scoring system , 19 cirrhotic patients were categorized as class a , 9 as class b , and 2 as class c. eight ( 26.7 % ) of the 30 patients had one or more perioperative complications . of these , wound infection was the most common , with a rate of 10 % ( 3 of 30 hips ) . other perioperative complications included surgical site bleeding , coagulopathy , encephalopathy , gastrointestinal bleeding , pneumonia , and arrhythmia . death occurred in 2 ( 6.7 % ) of the 30 patients ; both were child - pugh 's c cirrhotics . a higher child - pugh score ( p = 0.0001 ) and a high level of creatinine ( p = 0.0499 ) were associated with significantly increased perioperative complications or death . our findings suggest that surgeons should be vigilant about perioperative complications in patients with advanced cirrhotic liver disease who undergo hip arthroplasty , albeit the mortality rates are relatively low in less severe cirrhotics ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the 3d human primary cell culture of oral keratinocytes ( tissues ) and media ( containing specially prepared phenol red , 5 g / ml gentamicin , and 0.25 g / ml amphotericin b ) were purchased from mattek corporation ( ashland , ma ) . the oral ( buccal ) keratinocytes were grown in millipore millicell tissue - culture plate inserts in serum - free media at 37 c with 5 % co2 . the resultant 3d cultures showed high degree of differentiation and were similar to buccal epithelial . the 3d tissues were incubated with 100 l of one of the following mixtures for 2 h at 37 c : ( a ) 1 mm nac , ( b ) 5 mg / ml qyd , or ( c ) an nacqyd mixture consisting of 1 mm nac and 4.5 mg / ml qyd . after the incubation , the tissues were rinsed with phosphate - buffered saline , placed in new plates with fresh media and irradiated with 12 gy . the irradiation took place at the facilities of city of hope , duarte , ca . total rna was extracted using the rneasy plus mini kit ( qiagen , germantown , md ) . rna of at least 2 identically treated 3d tissues was combined and used for analysis . using an agilent 2100 bioanalyzer ( agilent technologies , palo alto , ca ) , and by evaluating the a260 / 280 absorbance ratio , the integrity and quality of rna was determined . only rna with absorbance ratio , a260 / 2801.9 , andrna was converted to double - stranded cdna and amplified using in vitro transcription with t7 polymerase . the in vitro transcription reaction included aminoallyl utp ( aa - dutp ) , and the aa - dutp nucleotides were later conjugated to cy5 nhs ester ( ge healthcare life sciences , pittsburg , pa ) . a quantity of 0.025 mg / ml fragmented cy5 - labeled cdna was hybridized overnight at 42 c using a hybbag mixing system with 1 onearray hybridization buffer ( phalanx biotech , san diego , ca ) and 0.01 mg / ml sheared salmon sperm dna ( promega , madison , wi ) . following hybridization , the arrays were washed according to the onearray protocol ( phalanx biotech , san diego , ca ) . a molecular devices axon 4100a scanner was used to measure the raw cy5 intensities produced by each of the microarrays . genepix pro software was used to measure the signals which were stored in gpr format . rosetta resolver system ( rosetta biosoftware , usa ) was used to analyze the data from all microarrays in each experimental set . testing was performed in triplicate by combining technical replicates and performing statistical analyses using the proprietary modeling techniques of rosetta resolver . average expression values were calculated using the error - weighted approach , which is specifically geared towards combining replicated hybridizations to improve measurement precision and accuracy . p - values were generated to test the null hypothesis that expression is absent ( referred to asp - value detected ) , thereby providing an error - based statistical test for deciding whether a transcript is truly present . this test is especially important for determining whether genes with low average intensities are significantly above background . rosetta resolver does not calculate p - values based strictly on fold changes , but rather uses error - model - based hypothesis tests , which take into account fold change and expression level . since three technical replicate hybridizations were performed and later averaged , care was taken to ensure high repeatability between technical replicates . first , raw and normalized log2 data for each sample were plotted using the r function boxplot . control and flagged probes were not included . a representative box plot is shown in fig .1 . while this analysis is designed to identify hybridizations that have intensity distributions different from those of their technical replicates , we did not find any instances of this . this analysis also ensures that the normalization has correctly centered the distributions of each replicate microarray . next , we compared scatter plots of raw and normalized log2 data for each sample using the r function pairs . only data with a p - value detected 0.01 were includedcorrelation values were calculated from both raw and normalized log2 intensities for each technical repeat . only probes with p - value detectedall correlation values were 0.961 , and scatter plots confirmed high repeatability among technical replicates . in our research article , we focused on differentially expressed genes underlying the different treatments described herein in our analysis of the transcriptomic data . prior to this , we performed enrichment analyses using david bioinformatics as a qc metric given our expectations in irradiated and nac qyd treated samples . up - regulated andgenes with | fold change | 1.5 and p - value 0.05 were used . gene symbols were used as input into david bioinformatics and default settings were used throughout . a benjamini - adjusted p - value 0.05 was used as a threshold for significance . we hypothesized that non - treated , irradiated samples ( compared to non - treated , non - irradiated control samples ) would display patterns of gene expression consistent with the physiological effects of irradiation . similarly , we hypothesized that irradiated samples pre - treated with nac qyd would display patterns of gene expression consistent with a protective effect of nac qyd . table 2lists the selected enriched categories from our qc enrichment analysis ( table s1 contains all enrichment analysis results ) . for example , up - regulated genes in non - treated , irradiated samples were strongly enriched for mitochondrial respiration , which is a known response to irradiation that leads to oxidative stress , , . also , up - regulated genes in the nacnotably , nac qyd treatment suppresses irradiation - induced apoptosis , so the enrichment results likely reflect anti - apoptotic mechanisms at work in these samples . overall , these results confirmed the quality of the microarray data and facilitated further interpretation of the data presented in lambros et al . . the 3d human primary cell culture of oral keratinocytes ( tissues ) and media ( containing specially prepared phenol red , 5 g / ml gentamicin , and 0.25 g / ml amphotericin b ) were purchased from mattek corporation ( ashland , ma ) . the oral ( buccal ) keratinocytes were grown in millipore millicell tissue - culture plate inserts in serum - free media at 37 c with 5 % co2 . the resultant 3d cultures showed high degree of differentiation and were similar to buccal epithelial . the 3d tissues were incubated with 100 l of one of the following mixtures for 2 h at 37 c : ( a ) 1 mm nac , ( b ) 5 mg / ml qyd , or ( c ) an nacqyd mixture consisting of 1 mm nac and 4.5 mg / ml qyd . after the incubation , the tissues were rinsed with phosphate - buffered saline , placed in new plates with fresh media and irradiated with 12 gy . the irradiation took place at the facilities of city of hope , duarte , ca . total rna was extracted using the rneasy plus mini kit ( qiagen , germantown , md ) . rna of at least 2 identically treated 3d tissues was combined and used for analysis . using an agilent 2100 bioanalyzer ( agilent technologies , palo alto , ca ) , and by evaluating the a260 / 280 absorbance ratio , the integrity and quality of rna was determined . only rna with absorbance ratio , a260 / 2801.9 , andrna was converted to double - stranded cdna and amplified using in vitro transcription with t7 polymerase . the in vitro transcription reaction included aminoallyl utp ( aa - dutp ) , and the aa - dutp nucleotides were later conjugated to cy5 nhs ester ( ge healthcare life sciences , pittsburg , pa ) . a quantity of 0.025 mg / ml fragmented cy5 - labeled cdna was hybridized overnight at 42 c using a hybbag mixing system with 1 onearray hybridization buffer ( phalanx biotech , san diego , ca ) and 0.01 mg / ml sheared salmon sperm dna ( promega , madison , wi ) . following hybridization , the arrays were washed according to the onearray protocol ( phalanx biotech , san diego , ca ) . a molecular devicesaxon 4100a scanner was used to measure the raw cy5 intensities produced by each of the microarrays . genepix pro software was used to measure the signals which were stored in gpr format . rosetta resolver system ( rosetta biosoftware , usa ) was used to analyze the data from all microarrays in each experimental set . testing was performed in triplicate by combining technical replicates and performing statistical analyses using the proprietary modeling techniques of rosetta resolver . average expression values were calculated using the error - weighted approach , which is specifically geared towards combining replicated hybridizations to improve measurement precision and accuracy . p - values were generated to test the null hypothesis that expression is absent ( referred to asp - value detected ) , thereby providing an error - based statistical test for deciding whether a transcript is truly present . this test is especially important for determining whether genes with low average intensities are significantly above background . rosetta resolver does not calculate p - values based strictly on fold changes , but rather uses error - model - based hypothesis tests , which take into account fold change and expression level . since three technical replicate hybridizations were performed and later averaged , care was taken to ensure high repeatability between technical replicates . first , raw and normalized log2 data for each sample were plotted using the r function boxplot . control and flagged probes were not included . a representative box plot is shown in fig .1 . while this analysis is designed to identify hybridizations that have intensity distributions different from those of their technical replicates , we did not find any instances of this . this analysis also ensures that the normalization has correctly centered the distributions of each replicate microarray . next , we compared scatter plots of raw and normalized log2 data for each sample using the r function pairs . only data with a p - value detected 0.01 were included . a representative scatter plot is shown in fig . correlation values were calculated from both raw and normalized log2 intensities for each technical repeat . only probes with p - value detectedall correlation values were 0.961 , and scatter plots confirmed high repeatability among technical replicates . in our research article , we focused on differentially expressed genes underlying the different treatments described herein in our analysis of the transcriptomic data . prior to this , we performed enrichment analyses using david bioinformatics as a qc metric given our expectations in irradiated and nac qyd treated samples . up - regulated and down - regulated gene lists were analyzed separately in david bioinformatics . genes with | fold change | 1.5 and p - value 0.05 were used . gene symbols were used as input into david bioinformatics and default settings were used throughout . a benjamini - adjusted p - value 0.05 was used as a threshold for significance . we hypothesized that non - treated , irradiated samples ( compared to non - treated , non - irradiated control samples ) would display patterns of gene expression consistent with the physiological effects of irradiation . similarly , we hypothesized that irradiated samples pre - treated with nac qyd would display patterns of gene expression consistent with a protective effect of nac qyd . table 2 lists the selected enriched categories from our qc enrichment analysis ( table s1 contains all enrichment analysis results ) . indeed , we found enriched categories that were consistent with our hypotheses . for example , up - regulated genes in non - treated , irradiated samples were strongly enriched for mitochondrial respiration , which is a known response to irradiation that leads to oxidative stress , , . also , up - regulated genes in the nacnotably , nac qyd treatment suppresses irradiation - induced apoptosis , so the enrichment results likely reflect anti - apoptotic mechanisms at work in these samples . overall , these results confirmed the quality of the microarray data and facilitated further interpretation of the data presented in lambros et al . . table s1 table showing enrichment analysis using david bioinformatics . both conditions ( non - treated , irradiated and nac - qyd pre - treated , irradiated ) go cc = gene ontology cellular component , mf = molecular function , and bp = biological process . counttable s1 table showing enrichment analysis using david bioinformatics . both conditions ( non - treated , irradiated and nac - qyd pre - treated , irradiated ) go cc = gene ontology cellular component , mf = molecular function , and bp = biological process . count = the number differentially expressed genes annotated with a given enriched term .\noutput:\n" }, { "from": "agent", "value": "cancer patients who receive radiation are often afflicted by oral mucositis , a debilitating disease , characterized by mouth sores and difficulty in swallowing . oftentimes , cancer patients afflicted with mucositis must stop life - saving therapies . thus it is very important to prevent mucositis before it develops . using a validated organotypic model of human oral mucosa , a 3 - dimensional cell culture model of human oral keratinocytes , it has been shown that a mixture ( nac qyd ) of n - acetyl cysteine ( nac ) and a traditional chinese medicine , qingre liyan decoction ( qyd ) , prevented radiation damage ( lambros et al . , 2014 ) . here we provide detailed methods and analysis of microarray data for non - irradiated and irradiated human oral mucosal tissue with and without pretreatment with nac , qyd and nac - qyd . the microarray data been deposited in gene expression omnibus ( geo ) : gse62397 . these data can be used to further elucidate the mechanisms of irradiation damage in oral mucosa and its prevention ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: air - blowing equipment is often used in dentistry and oral surgery , and there are many reports of subcutaneous or mediastinal emphysema with the use of these machines . furthermore , emphysema has been reported with jaw corrective surgery , injuries and alternating washes in root - canal therapy . however , there are no previous reports of subcutaneous emphysema after the maxillary sinus - lift procedure . herean 80 - year - old man with a history of en bloc resection of squamous cell carcinoma of the hard palate ( t4an0m0 ) complained of mastication difficulties due to the maxillary defect , and water and air leakage into the maxillary sinus . maxillary segmentectomy included resection of the alveolar ridge from the left central incisor to the right pterygoid process of the sphenoid bone ( fig . 1 ) . the resection site was reconstructed with a forearm flap , and the maxillary sinus was completely closed . however , these teeth were not strong enough to support a large jaw prosthesis that would cover the right maxillary defect , and residual teeth were missing . however , computed tomography ( ct ) revealed that the bone mass of the left molar region was inadequate for implantation of these fixtures ( fig . 2 ) . the soft tissue from the canine region to the molar tooth region was incised and elevated to expose the underlying lateral wall of the left maxillary sinus . a 125 mm window was created in the bone of the maxillary sinus anterior wall with a piezoelectric instrument to expose the underlying schneiderian membrane , which is the lining of the maxillary sinus cavity . through careful instrumentation , the membrane was carefully peeled from the inner aspect of the sinus cavity ( fig . the newly formed space within the bony cavity of the sinus inferior to the intact membrane was grafted with artificial bone , and artificial bone was placed on the alveolar crest to raise the alveolar crest ( fig . figure 2 : the bone mass in the left molar region was inadequate for implantation of fixtures . a 125 mm section of bone has been removed at the maxillary sinus anterior wall with a piezoelectric instrument . ( b ) artificial bone has been grafted in the formed sinus cavity and placed on the alveolar bone . a 125 mm section of bone has been removed at the maxillary sinus anterior wall with a piezoelectric instrument . ( b ) artificial bone has been grafted in the formed sinus cavity and placed on the alveolar bone . two hours after the surgery , the patient complained of sudden malar swelling ( fig . marked swelling was present from the left infraorbital region to the buccal region , and we suspected postoperative bleeding . there were a few hematomas in the wound , but an apparent bleeding point was absent . the ct images revealed that the artificial bone grafted inferior to the membrane had not leaked into the maxillary sinus , and there was no apparent damage of the maxillary sinus membrane . however , the marked malar swelling was associated with air pockets at the alar base and in the angulus oculi medialis region and subcutaneous malar tissue , and no hematoma was evident ( fig . we made a diagnosis of subcutaneous emphysema and administered an intravenous drip containing antibiotics to the patient for 3 days . we confirmed emphysematous improvement and the graft situation of the artificial bone on the ct images at 12 days postoperatively . figure 4 : after sinus - lift surgery , marked swelling is obvious from the left buccal region to the angulus oculi medialis . emphysema ( indicated by arrows ) is visible from the left buccal region to the angulus oculi medialis . after sinus - lift surgery , marked swelling is obvious from the left buccal region to the angulus oculi medialis . emphysema ( indicated by arrows ) is visible from the left buccal region to the angulus oculi medialis . emphysema of the maxillofacial region caused by dental treatment , oral surgical procedures or trauma is frequently reported . therefore , the mucous membrane of the maxillary sinus might have had a small hole , and air might have entered the subcutaneous tissue via the bone window when the air pressure in the maxillary sinus increased with nose blowing . one of the complications of the sinus lift is damage of the maxillary sinus membrane , and perforation of the sinus membrane occurs in 1035 % of sinus - lift procedures , although membrane perforation is reduced to 7 % when osteotomy is performed using the piezoelectric technique . the thickness of the sinus membrane is 1 mm , so the membrane is easily damaged , and a small hole may not be apparent during the operation . the maxillary sinusis sometimes perforated by the extraction of teeth in contact with the maxillary sinus floor . perforation is common with the presence of a maxillary sinus septum or a history of surgery in the sinus region . rhymes reported that if the vertical section of the attached gingiva reaches the infraversion , then , during tooth extraction , it is easy to cause emphysema because air readily invades the loose tissue . furthermore , an inflow of air from the gap is reported to occur easily because of the texture when the periosteum or fascia is torn . , surgeons should take care not to tear the periosteum during periosteum detachment in mucoperiosteal flap creation . emphysema with sinus lift has not previously been reported and may not be anticipated with this procedure . patients are usually requested not to blow their noses after extraction of teeth in contact with the maxillary sinus or palatal closure of a fistula . however , we did not consider this precaution necessary with the sinus - lift procedure . it is important to advise patients to avoid increasing the intraoral pressure , for example , by blowing the nose vigorously or playing musical instruments , as these activities could cause introduction of more air . therefore , it is important to warn patients about nose blowing , coughing , sneezing and mucous plugging during the postinjury and postoperative periods . special attention should be paid to postoperative supportive care to avoid increased subcutaneous air diffusion in patients who have undergone open surgery . however , it is necessary for oral surgeons to consider the possibility of postoperative subcutaneous emphysema after a maxillary sinus lift and to inform patients accordingly .\noutput:\n" }, { "from": "agent", "value": "an 80 - year - old man with a history of en bloc resection of squamous cell carcinoma of the hard palate ( t4an0m0 ) was performed a lateral - window sinus lift of the edentulous area of the left maxillary molar region to facilitate future placement of dental implants.two hours after the surgery , the patient complained of sudden malar swelling . marked swelling was present from the left infraorbital region to the buccal region . the swelling was associated with air pockets at the alar base and in the angulus oculi medialis region and subcutaneous malar tissue . emphysema appeared after the patient blew his nose . therefore , the mucous membrane of the maxillary sinus might have had a small hole , and air might have entered the subcutaneous tissue via the bone window when the air pressure in the maxillary sinus increased with nose blowing . it is important to advise patients to avoid increasing the intraoral pressure after sinus - lift procedure ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: this tumor affects mainly extremities of the body , pelvis , head and neck , and meningitis , but hemangiopericytoma is rarely found in urogenital system . until 2009 , only 42 cases of this neoplasia involving the kidney were reported in the world literature . because of the rarity of this injury until to date , no therapeutic management and ideal diagnosis were established as well as progress and prognosis of the disease . we report a case of renal hpc diagnosed and treated at urological service of the irmandade santa casa de misericrdia de so paulo . in november 2011 , a 52 - year - old , white and previously healthy woman was admitted at our because of an increase in abdominal volume . the patient does not have a history of smoking or use of illicit substances . in march 2012she had blood hypertension and took medicine for this affection , and also mentioned to lose 10 kg in that period . her ultrasonography test of urinary tract showed evidence of tumors in topography of the right kidney . the abdominal computed tomography ( ct ) scan revealed a cystic - solid expansive formation , multiloculated , heterogenous in the right kidney that replaced the parenchyma in the medial and inferior third . the formation measured 23.2 x18 .8 x18 .7 cm with special emphasis of solid portions and superimposition of septal segments that dislocated superiorly the liver and gallbladder , crossing the medium line and opposing medially to the pancreas , portal and aortic vein with signs of vascular compromising ( figure 1 ) . figure 1tomography showing abdominal tumor the patient had undergone radical nephrectomy , which is a procedure with technical difficult because of tumor proportion , without intercurrence or necessity of blood transfusion , and even intensive care in immediate postoperative . the anatomopathological study ( figure 2 ) confirmed the diagnosis of hpc , and immunohistochemical analysis showed tumoral cells positive for bcl - 2 ( figure 3 ) , cd99 ( figure 4 ) , vimentin ( figure 5 ) , cd34 ( figure 6 ) , and negative for s - 100 . mitotic index score was 2 ( 13 mitoses per 10 high - power fields ) . figure 2histological analysis with hematoxylin - eosin figure 3immunohistochemical with positive cd99 staining figure 4immunohistochemical with positive bcl - 2 staining figure 5immunohistochemical with positive vimentin staining figure 6immunohistochemical with positive cd34 staining in return visit at outpatient unit , the patient remained asymptomatic and without local or systemic complications . we removed points of surgical incision and requested abdominal ct and control chest radiography for 4 months . during reassessments on this periodthe patient was in good general status , normotensive and did not need anti - hypertensive medicine . radiography exam showed changes and ct revealed only sings of previous manipulations in topography of right kidney and mild increased paracaval lymph nodes , 1.0 cm . currently , 7th months after surgery , the patient is clinically well and without intercurrence . hpc is classified as vascular tumor of soft tissues from the pericytes , modified cells of smooth muscle tissue that were described by zimmerman in 1923 . such cells are organized around capillaries and post - capillary veins , and they are responsible to modulate blood flow and permeability of these vessels . our patient was at average age of diagnosis of this neoplasia , about 40.3 years old ( 16 to 68 years old ) , which suggest that such tumor affect more frequently in young patients than other types of renal cell cancer . no significant difference is found concerning the incidence of this neoplasia between men and women , and no age variation between sexes in the diagnosis . other symptoms already described , in order of frequency , are : hematuria , hypoglycemia and arterial hypertension . a study reported that hematuria was found in six patients in which an invasion of pyelocaliceal system by tumor occured . blood hypertension , however , is believed to occur because of the production of renin by the neoplasia and , as observed in our patient , it often disappear after surgical treatment . the most common site of metastasis of renal hpc is the lung , which was described in two case and patients had a poor prognosis . imaging exams , such as ultrasonography , ct or magnetic resonance did not show specific finding of the tumor that were able to collaborate in the differential diagnosis from other renal tumors . however , yagmani reported that these tumors can have standard characteristic in early phase of blood angiography of principal arteries , presence of vessels surrounding the tumor and well - marked stain , delimiting the tumor . macroscopically , most tumors are well circumscribed lesions or a thin capsule , associated to complex network of vessels and , sometimes , with small satellite nodules around the main mass . tumor size reported in the literature range between 2 and 25 cm . in general , there is a cellular proliferation with small variability in cellularity , a staghorn vascular pattern with packed pericytes around vascular endothelium , and minimal collagenization that can vary both in size and form . the technique used is based on hematoxylin and eosin stain ( figure 2 ) and silver associated with immunohistochemistry , using antibodies against cd31 , cd34 , cd99 , s - 100 , vimentin , citokeratin and epithelia antigen membrane ( renal ) . only the combination of these two is can provide the diagnosis , which in our case enabled the precise diagnosis of tumoral mass . such tumors include juxtaglomerular origin , which often is presented as blood hypertension , especially in young adults . other vascular neoplasias , histiocytosis , neural and of smooth muscle must be excluded before the definitive diagnosis of hpc . the main treatment for this disease is surgery , and exeresis must be as radical as possible in order to avoid incomplete resection and recurrence . therefore , an appropriate surgical plan associated with a previous study of tumor vascular architecture ( ct angiography or arteriography ) must be done . radiotherapy , chemotherapy or adjuvant or neoadjuvant immunotherapy seem to be inefficient to treat hpc . although , the majority of renal hpcs are benign , outcomes can not be precisely foreseen by histological appearance , however , rigorous follow - up must be conducted to detect long - term recurrence . enzinger and smith observed survival of 77 % in 10 years in patients with 0 to 3 mitoses / 10 versus 29 % in those patients with 4 or more by field . similarly , survival was 81 % in patients with tumoral necrosis versus 29 % in those who had necrotic areas in the tumor . 6.5 cm , survival in 10 years reached 95 % and 63 % for large tumors . because hpc is rare and present a vague clinical picture associated with imaging exams that do not indicate a specific disease , the precisely diagnosis of hemangiopericytoma is made only after surgery and with the immunohistochemical result . best treatment consists in complete surgical excision because complementary treatment such as chemotherapy and / or radiotherapy is not efficient . descrito pela primeira vez em 1942 , o hemangiopericitoma ( hpc ) um raro tumor perivascular resultante da proliferao descontrolada dos pericitos capilares . acometem principalmente extremidades , pelve , cabea e pescoo , e meninges , sendo raramente encontrados no sistema urogenital . at 2009 , apenas 42 casos dessa neoplasia envolvendo o rim foram relatados na literatura mundial . devido a raridade dessas leses , at os dias atuais , no esto estabelecidas condutas teraputicas e diagnsticas ideais , nem a evoluo e o prognstico da doena . relatamos um caso de hpc renal diagnosticado e tratado no servio de urologia da irmandade santa casa de misericrdia de so paulo . paciente de 52 anos de idade , do gnero feminino , branca , previamente hgida , apresentou , em novembro de 2011 , aumento do volume abdominal . em maro de 2012 comeou o acompanhamento ambulatorial no servio de urologia , hipertensa em uso de medicaes e referindo perda de 10 kg nesse perodo ; trouxe ultrassonografia das vias urinrias com evidncia de tumorao em topografia do rim direito . tomografia computadorizada ( tc ) de abdome evidenciou formao expansiva slido - cstica , multisseptada , heterognea , com origem no rim direito , substituindo o parnquima , no tero mdio e inferior , medindo 23,2 x18 ,8 x18 ,7 cm , com realce das pores slidas e dos septos de permeio , deslocando superiormente o fgado e a vescula biliar , cruzando a linha mdia e rechaando medialmente o pncreas , veia porta e aorta , sem sinais de comprometimento vascular ( figura 1 ) . figura 1tomografia evidenciando tumorao abdominal foi submetida a nefrectomia radical , procedimento com dificuldade tcnica devido s propores da tumorao , porm sem intercorrncias , no necessitando de transfuso sangunea e nem de cuidados intensivos no ps - operatrio imediato . a paciente evoluiu sem complicaes , dreno com baixo dbito e boa diurese , tendo alta no 3 dia aps a cirurgia . estudo anatomopatolgico ( figura 2 ) confirmou o diagnstico de hpc , e a anlise imuno - histoqumica mostrou clulas tumorais positivas para bcl - 2 ( figura 3 ) , cd99 ( figura 4 ) , vimentina ( figura 5 ) , cd34 ( figura 6 ) , sendo negativo para s - 100 . o ndice mittico teve escore de 2 ( 13 mitoses por 10 campos de grande aumento ) . figura 2anlise histolgica com hematoxilina - eosina figura 3imuno - histoqumica com marcador cd99 positivo figura 4imuno - histoqumica com marcador bcl - 2 positivo figura 5imuno - histoqumica com marcador vimentina positivo figura 6imuno - histoqumica com marcador cd34 positivo no retorno ambulatorial , permanecia assintomtica e sem complicaes locais ou sistmicas . foram retirados os pontos da inciso cirrgica e solicitado tc abdominal e radiografia de trax controle em 4 meses . reavaliao nesse perodo , novamente encontrava - se em bom estado geral , normotensa e sem necessidade de usar anti - hipertensivos , sem qualquer queixa . a radiografia no mostrou alteraes e a tc revelou apenas sinais de manipulao pregressa em topografia de rim direito e linfonodos pericavais discretamente aumentados , 1,0 cm . atualmente no 7 ms ps - operatrio , a paciente mantm - se clinicamente bem , sem intercorrncias ps - operatrias . hpc classificado como um tumor vascular de tecidos moles originado a partir de pericitos , clulas modificadas de msculo liso , descritas por zimmerman , em 1923 . tais clulas se arranjam ao redor de capilares e veias ps - capilares , sendo responsveis por modular o fluxo sanguneo e pela permeabilidade de tais vasos . a paciente relatada encontrava - se na mdia de idade de diagnstico dessa neoplasia , prximo de 40,3 anos ( 16 a 68 anos ) , sugerindo que tal tumor ocorre com maior frequncia em pacientes jovens que outros tipos de carcinomas de clulas renal . quanto a incidncia entre homens e mulheres , e nem variao de idade entre os gneros ao diagnstico . o quadro clnico inespecfico . em 66 % dos casos relatados na literatura , o sintoma inicial foi de tumorao abdominal indolor , assim como o relatado neste caso . outros sintomas j descritos , em ordem de frequncia , so : hematria , hipoglicemia e hipertenso arterial . hematria foi detectada em seis pacientes , nos quais houve invaso do sistema pielo - calicinal pelo tumor . j a hipertenso arterial acredita - se que seja decorrente de produo de renina pela neoplasia e , assim como evidenciado em nossa paciente , geralmente regride aps o tratamento cirrgico . o stio mais frequente de metstases do hpc renal o pulmo , descrito em dois casos , nos quais houve pior prognstico dos doentes . exames de imagem , como ultrassonografia , tc ou ressonncia magntica , no demonstram achados especficos do tumor que pudessem colaborar para o diagnstico diferencial entre outras neoplasias renais . por outro lado , yaghmai mostrou que esses tumores podem ter um padro caracterstico na fase precoce da angiografia arterial das artrias principais , presena de grandes vasos circundando o tumor e uma mancha bem demarcada , delimitando o tumor . macroscopicamente a maioria dos tumores se manifesta como leses bem delimitadas ou com uma fina cpsula , associada a uma ampla rede de vasos e , por vezes , com ndulos satlites pequenos encontrados separadamente da massa . geralmente , h proliferao celular com pequena variao da celularidade , com padro vascular em chifre de alcecom pericitos embalados em torno de endotlio vascular , e mnima colagenizao , podendo variar tanto em forma quanto em tamanho . a tcnica utilizada baseia - se na colorao por hematoxilina - eosina ( figura 2 ) e de prata , em associao com imuno - histoqumica , utilizando anticorpos contra cd31 , cd34 , cd99 , s - 100 , vimentina , citoqueratinas e antgeno de membrana epitelial ( renal ) . apenas a combinao dos dois capaz de prover o diagnstico , o que permitiu o diagnstico de certeza da massa tumoral do caso apresentado . o padro histolgico e a imunofenotipagem fornecem informao para o diagnstico diferencial com outras neoplasias vasculares e outros tumores mesenquimais . tais tumores incluem os de origem justaglomerular , que geralmente apresentam - se com hipertenso arterial , especialmente em adultos jovens . outras neoplasias vasculares , histiocitrias , neurais e do msculo liso devem ser excludas antes de se definir o diagnstico de hpc . cirurgia considerada o tratamento principal para tal patologia , e a exrese deve ser o mais radical possvel , a fim de evitar resseco incompleta e recidiva . portanto , um apropriado plano cirrgico , associado a um estudo da arquitetura vascular tumoral ( angio - tc ou arteriografia ) prvio , deve ser realizado . radioterapia , quimioterapia ou imunoterapia adjuvantes ou neoadjuvantes no pareceram ser eficazes para o hpc . embora a maioria dos hpc renais seja benigna , o desfecho no pode ser precisamente previsto pela aparncia histolgica , mas deve ser realizado acompanhamento rigoroso para detectar recorrncia a longo prazo . o principal fator associado ao prognstico parece ser o padro histolgico . nos pacientes com 0 a 3 mitoses / 10 versus 29 % naqueles pacientes com 4 ou mais por campo . de forma similar , a sobrevida foi de 81 % nos pacientes sem necrose tumoral versus 29 % naqueles que apresentaram reas necrticas no tumor . em tumores 6,5 cm , a sobrevida em 10 anos alcanou 95 % e foi de 63 % para tumores maiores . por ser patologia rara e apresentar - se com quadro clnico vago , associado a exames de imagem que no indicam uma patologia especfica , o diagnstico exato de hemangiopericitoma d - se apenas no ps - operatrio , com o resultado imuno - histoqumico . o melhor tratamento consiste na exciso cirrgica completa , visto que o tratamento complementar , com quimioterapia e / ou radioterapia , no se mostrou efetivo .\noutput:\n" }, { "from": "agent", "value": "hemangioperycytoma is a rare perivascular tumor that seldom involves the urogenital system . this tumor often appears with an unspecific clinical picture , and sometimes is associated with hematuria or hypertension . diagnosis is based on a combination of histological and immunohistological findings . we report a case of a 52 - year - old patient with renal hemangiopericytoma who underwent surgical treatment at our service . this report also includes a literature review on the subject ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: however , persons successfully treated with art also have an increased risk for developing many chronic conditions ( e.g. , subclinical atherosclerosis , coronary heart disease ( chd ) , diabetes mellitus , renal disease , malignancies ) . chd and myocardial infarction have been reported in relatively young hiv - infected patients and some reports found an association between increased frequency of myocardial infarction and protease inhibitors ( pi ) or abacavir use . it is now understood that inflammation is a major component in the pathogenesis of atherosclerosis . the adverse effects of art ( e.g. , high levels of total cholesterol , ldl cholesterol , and triglycerides ) could also have an additional influence on accelerated atherosclerosis development . traditional risk factors such as male sex , older age , and cigarette smoking may contribute to the appearance of cardiovascular risks and disease in hiv - infected patients . in the last few decadesmany studies have been conducted to analyze the influence of some potentially healthy food ingredients or vitamin supplements on atherosclerosis biomarkers . extra virgin olive oil ( evoo ) is an ingredient believed for centuries to have a favorable influence on health , although some of its features were better defined only recently . besides its high content of oleic acid , which is monounsaturated and less prone to lipid peroxidation , evoo has some other important components such as phenolic compounds . the favorable effect on systolic blood pressure , hdl cholesterol level , and ldl oxidation could be attributed to these phenolic compounds . interleukin - 6 ( il - 6 ) is a pro - inflammatory cytokine that is synthesized during tissue damage or infection . in hepatocytes , il - 6 stimulates the synthesis of acute - phase proteins such as c - reactive protein ( crp ) , fibrinogen , hepcidin , and serum amyloid a . crp is a pentameric protein molecule whose level during acute infection may increase to 1000 times normal values . however , with improved sensitivity of the test ( e.g. , high - sensitivity crp and hscrp ) it became an early atherosclerosis marker . glutathione - related metabolism enzymes such as glutathione peroxidase ( gsh - px ) and superoxide dismutase ( sod ) are involved in reactive oxygen species ( ros ) processing , making them less toxic . gsh - px and sod are today recognized as oxidative stress biomarkers , found to be disturbed in cardiovascular diseases . malondialdehyde ( mda ) is a final lipid peroxidation product involved in the atherosclerosis process , as shown in animal and human studies . several evoo intervention studies showed that il - 6 and hscrp were decreased , gsh - px mrna was expressed at higher levels , enzyme activity was higher , and lipid peroxides ( mda ) decreased . we conducted an exploratory study to examine the effect of evoo on atherosclerosis biomarkers in a group of hiv - infected men undergoing antiretroviral therapy . the primary outcome measures were changes of atherosclerosis biomarkers in hiv - infected patients on antiretroviral regimen after evoo consumption . secondary outcome measures were changes in atherosclerosis biomarkers after evoo consumption in patients treated with pi and abacavir , respectively . we recruited hiv - infected men on a stable antiretroviral regimen ( 6 months ) and who were currently receiving 1 of the following combinations : 1 ) nucleoside / nucleotide analogue reverse transcriptase inhibitors ( nrti / ntrti ) + protease inhibitors ( pi ) ( n = 10 ) , 2 ) nrti / ntrti + non - nucleoside reverse transcriptase inhibitors ( nnrti ) ( n = 28 ) , and 3 ) nnrti + pi ( n = 1 ) . the inclusion criteria for enrollment of participants were : hiv - seropositivity , male sex ( 18 to 75 years of age ) , being treated with antiretroviral drugs , undetectable hiv rna viral load for at least 6 months ( by ultrasensitive amplicor hiv - 1 monitor test , version 1.5 ( roche diagnostics , indianapolis , usa ) , and glucose levels within the reference range . we excluded hiv - patients with underlying acute / chronic diseases ( e.g. , diabetes or kidney diseases ) , except history of chd . four of the 43 eligible patients , who initially agreed to participate , dropped out before the beginning of the study . finally , 39 participants were included in the study and were interviewed about family history of chd , vitamin supplements administration , and side effects of ongoing therapy , and were given a 14 - point questionnaire on mediterranean food consumption . clinical examination was performed by doctors and nurses in the outpatient department for hiv - infection at the university hospital for infectious diseases . the study was approved by the local institutional ethics committee and all participants provided written informed consent . this study was registered at clinicaltrials.gov with clinicaltrials.gov identifier : nct00925795 . a single - blind , randomized , crossovereach group consumed evoo and refined olive oil ( roo ) as a placebo , but in different order ( sequence 1 : first evoo ; then roo . original manufacturers declarations were removed from both types of olive oils and evoo was designated as oil number 1 and roo as oil number 2 . intervention periods for oil administration lasted 20 days each , with 14 days of interruption ( washout period ) modeled on similar studies . it was emphasized not to cook olive oil , but to pour it over meals . during the washout period , compliance with oil consumption was assessed by participant self - report after each intervention period and registered on a visual analogue scale with percentage expression . participants who self - administered more than 90 % of the whole amount of a particular olive oil in 1 sequence were considered compliant . before the study , we analyzed a total phenolic content of several different olive oils by the folin - ciocalteu method , as previously described . we decided to use evoo and roo , which contained 236 and 57 mg , respectively , of phenolic compounds per kilogram of oil . before the first , and after both intervention periods , we collected a blood sample in fasting state from all participants . in all 3 samples taken from each participant , we performed laboratory analysis for parameters as follows . erythrocyte sedimentation rate ( esr ) , was measured by westergren method , white blood cell count was measured on a beckman coulter lh 750 hematology analyzer ( beckman coulter , inc , brea , california , usa ) as a part of complete blood count ( cbc ) . hscrp concentration was measured by cardiophase siemens using particle - enhanced immunonephelometry on bn prospec system instrument ( siemens healthcare diagnostics products gmbh , marburg , germany ) . interleukin - 6 ( il - 6 ) concentration was measured by elisa quantikine test ( r & d systems europe , abingdon , great britain ) . oxidized ldl ( ox - ldl ) , was measured by elisa test ( drg diagnostics gmbh , marburg , germany ) and malondialdehyde ( mda ) was analyzed by the modified thiobarbituric acid reactive substances ( tbars ) method originally described by yagi . catalytic concentrations of glutathione peroxidase ( gsh - px ) and superoxide dismutase ( sod ) were measured in lysate of erythrocytes prepared by centrifuging edta blood on 2350 g / 10 min , washing erythrocyte pellet with saline , and centrifuging again at 2350 g / 5 min . catalytic concentration of gsh - px was measured through glutathione oxidation - reduction reactions by ransel kit and catalytic concentration of sod was measured by the rate of inhibition of 2 - ( 4 - iodophenyl ) - 3 - ( 4 - nitrophenyl ) -5-phenyltetrazolium chloride by ransod sd 125 kit ( both kits from randox laboratories ltd . , serum glucose level was analyzed by glucose oxidase method using a fisher diagnostics kit ( thermo fisher scientific , middletown , virginia , usa ) . triglycerides ( tg ) and total cholesterol ( tc ) were measured by thermo reagent kits ( electron corporation inc , victoria , australia ) . high - density lipoprotein ( hdl ) and low - density lipoprotein ( ldl ) cholesterol were determined by standard enzymatic automated methods using herbos kits ( herbos diagnostics , croatia ) . all of the above biochemistry parameters were analyzed on a beckman coulter 400 instrument ( beckman coulter , inc , brea , california , usa ) . fibrinogen and von willebrand factor activity were determined by multifibrenu reagent and by vwf : rco assay ( siemens healthcare diagnostics products gmbh , marburg , germany ) , respectively . all coagulation assays were measured in citrated plasma samples on a bcs xp siemens instrument ( siemens healthcare diagnostics , marburg , germany ) . sample size ( n = 35 ) was determined by power analysis where value was 0.05 with power ( 1 - ) 80 % . the kolmogorov - smirnov test was used to assess the normality of distribution of investigated parameters . fornon - normally distributed parameters , data were expressed as median with interquartile range . to determine differences in baseline characteristics of the 2 groups of participants , we used the mann - whitney test . the values p 0.05 were considered statistically significant . since this was an exploratory study , adjustments for multiple comparisons were not implemented . to assess the effect of period , treatment , and sequence , linear mixed models were used for statistical analysis . the linear mixed model enabled a comparison of atherosclerosis biomarkers results even in incomplete groups of participants ( for example , participants who adhered to only 1 olive oil ) . ( medcalc software , mariakerke , belgium ) and sas program , version 9.1.3 , ( sas institute inc , cary , north carolina ) . we recruited hiv - infected men on a stable antiretroviral regimen ( 6 months ) and who were currently receiving 1 of the following combinations : 1 ) nucleoside / nucleotide analogue reverse transcriptase inhibitors ( nrti / ntrti ) + protease inhibitors ( pi ) ( n = 10 ) , 2 ) nrti / ntrti + non - nucleoside reverse transcriptase inhibitors ( nnrti ) ( n = 28 ) , and 3 ) nnrti + pi ( n = 1 ) . the inclusion criteria for enrollment of participants were : hiv - seropositivity , male sex ( 18 to 75 years of age ) , being treated with antiretroviral drugs , undetectable hiv rna viral load for at least 6 months ( by ultrasensitive amplicor hiv - 1 monitor test , version 1.5 ( roche diagnostics , indianapolis , usa ) , and glucose levels within the reference range . we excluded hiv - patients with underlying acute / chronic diseases ( e.g. , diabetes or kidney diseases ) , except history of chd . four of the 43 eligible patients , who initially agreed to participate , dropped out before the beginning of the study . finally , 39 participants were included in the study and were interviewed about family history of chd , vitamin supplements administration , and side effects of ongoing therapy , and were given a 14 - point questionnaire on mediterranean food consumption . clinical examination was performed by doctors and nurses in the outpatient department for hiv - infection at the university hospital for infectious diseases . the study was approved by the local institutional ethics committee and all participants provided written informed consent . this study was registered at clinicaltrials.gov with clinicaltrials.gov identifier : nct00925795 . a single - blind , randomized , crossovereach group consumed evoo and refined olive oil ( roo ) as a placebo , but in different order ( sequence 1 : first evoo ; then roo . original manufacturers declarations were removed from both types of olive oils and evoo was designated as oil number 1 and roo as oil number 2 . intervention periods for oil administration lasted 20 days each , with 14 days of interruption ( washout period ) modeled on similar studies . it was emphasized not to cook olive oil , but to pour it over meals . during the washout period , compliance with oil consumption was assessed by participant self - report after each intervention period and registered on a visual analogue scale with percentage expression . participants who self - administered more than 90 % of the whole amount of a particular olive oil in 1 sequence were considered compliant . before the study , we analyzed a total phenolic content of several different olive oils by the folin - ciocalteu method , as previously described . we decided to use evoo and roo , which contained 236 and 57 mg , respectively , of phenolic compounds per kilogram of oil . before the first , and after both intervention periods , we collected a blood sample in fasting state from all participants . in all 3 samples taken from each participant , we performed laboratory analysis for parameters as follows . erythrocyte sedimentation rate ( esr ) , was measured by westergren method , white blood cell count was measured on a beckman coulter lh 750 hematology analyzer ( beckman coulter , inc , brea , california , usa ) as a part of complete blood count ( cbc ) . hscrp concentration was measured by cardiophase siemens using particle - enhanced immunonephelometry on bn prospec system instrument ( siemens healthcare diagnostics products gmbh , marburg , germany ) . interleukin - 6 ( il - 6 ) concentration was measured by elisa quantikine test ( r & d systems europe , abingdon , great britain ) . oxidized ldl ( ox - ldl ) , was measured by elisa test ( drg diagnostics gmbh , marburg , germany ) and malondialdehyde ( mda ) was analyzed by the modified thiobarbituric acid reactive substances ( tbars ) method originally described by yagi . catalytic concentrations of glutathione peroxidase ( gsh - px ) and superoxide dismutase ( sod ) were measured in lysate of erythrocytes prepared by centrifuging edta blood on 2350 g / 10 min , washing erythrocyte pellet with saline , and centrifuging again at 2350 g / 5 min . catalytic concentration of gsh - px was measured through glutathione oxidation - reduction reactions by ransel kit and catalytic concentration of sod was measured by the rate of inhibition of 2 - ( 4 - iodophenyl ) - 3 - ( 4 - nitrophenyl ) -5-phenyltetrazolium chloride by ransod sd 125 kit ( both kits from randox laboratories ltd . , serum glucose level was analyzed by glucose oxidase method using a fisher diagnostics kit ( thermo fisher scientific , middletown , virginia , usa ) . triglycerides ( tg ) and total cholesterol ( tc ) were measured by thermo reagent kits ( electron corporation inc , victoria , australia ) . high - density lipoprotein ( hdl ) and low - density lipoprotein ( ldl ) cholesterolwere determined by standard enzymatic automated methods using herbos kits ( herbos diagnostics , croatia ) . all of the above biochemistry parameters were analyzed on a beckman coulter 400 instrument ( beckman coulter , inc , brea , california , usa ) . fibrinogen and von willebrand factor activity were determined by multifibrenu reagent and by vwf : rco assay ( siemens healthcare diagnostics products gmbh , marburg , germany ) , respectively . all coagulation assays were measured in citrated plasma samples on a bcs xp siemens instrument ( siemens healthcare diagnostics , marburg , germany ) . sample size ( n = 35 ) was determined by power analysis where value was 0.05 with power ( 1 - ) 80 % . the kolmogorov - smirnov test was used to assess the normality of distribution of investigated parameters . fornon - normally distributed parameters , data were expressed as median with interquartile range . to determine differences in baseline characteristics of the 2 groups of participantsthe values p 0.05 were considered statistically significant . since this was an exploratory study , adjustments for multiple comparisons were not implemented . to assess the effect of period , treatment , and sequence , linear mixed models were used for statistical analysis . the linear mixed model enabled a comparison of atherosclerosis biomarkers results even in incomplete groups of participants ( for example , participants who adhered to only 1 olive oil ) . ( medcalc software , mariakerke , belgium ) and sas program , version 9.1.3 , ( sas institute inc , cary , north carolina ) . of 39 randomized participants , 35 finished the study ( 4 participants did not participate in the second intervention period ) ( figure 1 ) . there were no differences in baseline clinical and laboratory parameters by the order of olive oil administration ( table 1 ) . all participants who finished the study ( n = 35 ) had an undetectable plasma hiv1 - rna viral load ( 50 copies / ml ) at inclusion into the study . after the study ( median days from inclusion : 164 days , minimum 63 days , maximum 337 days ) , all but 1 individual had a plasma hiv1 - rna viral load 50 copies / ml , and the patient with 50 copies / ml had 76 copies / ml . the median cd4 cell count at inclusion was 474 per l , range 228 to 1648 per l . the median duration of antiretroviral therapy was 4.7 years , range 0.5 to 12.2 years . there were no clinical events during the study period , and 12 ( 34 % ) patients had a past history of clinical aids . the median mediterranean diet score in our participants was 5 ( interquartile range [ iqr ] , 37 ) and was not different by sequence of olive oil administration ( median 5 vs. 6 ; p = 0.460 ) . we found no difference in leukocyte count , esr , hscrp , il - 6 , fibrinogen , tc , hdl cholesterol , tg , mda , gsh - px , sod , ox - ldl , or vwf after evoo administration in the whole study population . there were also no differences after roo intervention , except for a lower ldl cholesterol level ( p = 0.020 for treatment , p = 0.006 for period ) ( table 2 ) . thirty participants reported consuming olive oils 90 % of the time ; 27 participants were compliant to evoo and 26 participants were compliant to roo administration . of those 30 individuals , 23 were compliant to both olive oils , 4 were compliant only to evoo , and 3 were compliant only to roo . in adherent participants ( 90 % ) , we found significantly lower hscrp concentration after evoo administration compared to hscrp concentration after roo administration ( geometric mean [ gm ] , 1.70 mg / l ; 95 % confidence interval [ ci ] , 1.152.52 vs. 2.92 mg / l ; 95 % ci , 1.954.37 ; p = 0.035 ) ( figure 2 ) . when the effect of olive oil administration was analyzed in 10 participants who received pilopinavir / ritonavir , evoo intervention resulted in a 62 % lower esr compared to baseline values ( median , 13 ; iqr , 619 vs. median , 21 ; iqr , 1036 ; p = 0.040 ) . in the same group of participants , we observed 151 % lower hscrp concentrations after evoo administration , compared to baseline values ( median , 0.88 mg / l ; iqr , 0.491.66 vs. median , 2.21 mg / l ; iqr , 1.825.47 ; p = 0.035 ) ( figure 3 ) . participants receiving lopinavir / ritonavir had a higher baseline fibrinogen concentration ( median , 3.9 g / l ; iqr , 3.34.4 ) than participants treated with a nnrti - based art ( median , 3.0 g / l ; iqr , 3.73.4 ) ( p = 0.004 ) . there were no statistically significant changes in clinical and laboratory parameters after olive oil administration in 11 participants receiving abacavir . in this study we compared the effect of 2 different olive oils on atherosclerosis biomarkers in hiv - infected patients . there was no difference in biomarkers of atherosclerosis after consumption of evoo and roo in the whole study population ( n = 35 ) . however , participants with compliance 90 % to at least 1 olive oil ( n = 30 ) had significantly lower hscrp concentration after evoo intervention , compared to roo intervention . there is a possibility that the influence of phenolic compounds was present only in participants with high compliance to evoo . after evoo consumption , 10 patients treated with pi had significantly lower esr and hscrp when compared to baseline values . additionally , baseline values of esr , hscrp , interleukin - 6 , and fibrinogen were significantly increased in pi - treated participants ( n = 10 ) when compared to non - pi - treated participants ( n = 28 ) ( results not shown ) . although a group of 10 participants is not sufficient to reach firm conclusions , these results suggest a higher inflammation rate in pi - treated participants and a more significant effect of evoo on their inflammation biomarkers . as art modifications are relatively frequent in our patient population , there was a small group of eligible patients treated for more than 6 months with pi . of note , the only pi used by our participants was lopinavir / ritonavir . in 2010 , the d.a.d . study group reported an association between myocardial infarction and cumulative exposure to indinavir and lopinavir / ritonavir . pi may increase total cholesterol and triglyceride levels and decrease hdl - cholesterol levels as a consequence of longer action of sterol regulatory element - binding protein - 1 ( srebp - 1 ) and protein kinase c activation . group authors emphasized that a higher risk of myocardial infarction can not be explained by lipid changes alone . madden et al . showed 11 % higher fibrinogen concentrations in patients receiving pi compared to patients treated with nnrti , which may be a consequence of the higher inflammation level related to pi regimen . , there was no difference in biomarkers after both olive oil consumptions compared to baseline values . the major clinical implication of our study is that evoo may decrease the inflammation biomarkers in hiv - infected persons ( such as hscrp ) during the 3 - week period in compliant participants . other atherosclerosis biomarkers that we analyzed ( e.g. , il - 6 , ox - ldl , sod , gsh - px , and mda ) did not change , even in compliant participants . because hiv - infected persons are immunocompromised , it is possible that a longer intervention period is needed to improve atherosclerosis biomarkers , although this could reduce the compliance of participants . non - compliance can not be ruled out , because we did not measure metabolites of olive oil consumption such as tyrosol and hydroxytyrosol in urine . we also did not measure the content of other olive oil ingredients that could have influenced atherosclerosis biomarkers ( e.g. , vitamin c and - tocopherol ) . our intervention periods were only 3 weeks long and it is possible that longer duration of intervention periods might have caused a more significant change in atherosclerotic biomarkers . overall , we found no difference in biomarkers of inflammation after evoo administration in our study population . however , in a subanalysis of participants with high compliance to olive oils , hscrp significantly decreased after evoo administration . hence , there could be a protective effect of evoo consumption on inflammatory markers in hiv - infected patients on stable art , but larger studies are needed to confirm these findings .\noutput:\n" }, { "from": "agent", "value": "backgroundpremature atherosclerosis in hiv - infected patients is associated with chronic infection by itself and adverse effects of antiretroviral treatment ( art ) . extra virgin olive oil ( evoo ) has a beneficial effect on the cardiovascular system because of its anti - inflammatory properties.the objective of this study was to determine whether the consumption of evoo improves inflammation and atherosclerosis biomarkers in hiv - infected patients receiving art.material / methodsthis randomized , crossover , controlled trial included 39 hiv - positive male participants who consumed 50 ml of evoo or refined olive oil ( roo ) daily . four participants dropped out of the study . leukocyte count , erythrocyte sedimentation rate ( esr ) , high - sensitivity c - reactive protein ( hscrp ) , interleukin - 6 , fibrinogen , total cholesterol , ldl cholesterol , hdl cholesterol , triglycerides , malondialdehyde , glutathione - peroxidase , superoxide dismutase , oxidized ldl and von willebrand factor were determined before the first and after each of the 2 intervention periods . intervention and washout periods lasted for 20 and 14 days , respectively.resultsin participants with > 90 % compliance ( n = 30 ) , hscrp concentrations were lower after evoo intervention ( geometric mean [ gm ] , 1.70 mg / l ; 95 % confidence interval [ ci ] , 1.152.52 ) compared to roo administration ( gm , 2.92 mg / l ; 95 % ci , 1.954.37 ) ( p = 0.035 ) . in participants using lopinavir / ritonavir , esr and hscrp concentrations decreased 62 % and 151 % , respectively , after evoo administration . in the whole study population ( n = 35 ) we found no difference in analyzed biomarkers after evoo administration.conclusionsour exploratory study suggests that evoo consumption could lower hscrp in patients on art ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: most tissue macrophages are derived from hematopoietic stem cells and their local expansion within tissues can be due to local proliferation of existing macrophages or due to infiltration of blood - derived monocytes , depending on the circumstances . traditionally characterized as the first line of defense against foreign invaders , research in the past decade has shown that their role extends to developmental processes and maintenance of tissue homeostasis in many ways . to fulfill these many different roles in tissue , macrophages can adopt a myriad of phenotypes based on signals they receive from their environment . from in vitro studiesa nomenclature was proposed similar to the th1 / th2 dichotomy , with m1 macrophages being known as classically activated macrophages induced by interferon gamma ( ifn ) and tumor necrosis factor alpha ( tnf ) and m2 being known as alternatively activated macrophages induced by interleukin ( il ) - 4 and il - 13 . the m2 concept already had to expand to m2a , m2b , and m2c to encompass the many different phenotypes labeled alternatively activated , but these in vitro concepts have been hard to match to in situ tissue macrophages . this is in part caused by a lack of specific markers for the different phenotypes within tissue and by the observation that in situ macrophage phenotypes appear as a continuum rather than discrete entities . macrophages are among the most abundant cells in the respiratory tract and can be broadly divided into two populations depending on their localization : alveolar macrophages ( ams ) that line the surface of alveoli and interstitial macrophages ( ims ) that reside in the space between alveolar epithelium and vascular endothelium . it has been suggested that am do not originate directly from blood monocytes , but instead are derived from ims which therefore serve as an intermediate between blood monocytes and ams . compared with ams , ims are less efficient in phagocytosing but are better at stimulating t - cell proliferation in vitro . in addition , ims as opposed to ams , were also found to produce high levels of il - 10 and thereby inhibit dc migration . although ims and ams have distinct functions , they both are among the first to encounter allergens and other threats to the lung homeostasis . they are both capable of quickly dealing with those without perturbing normal gas exchange because they can adopt the most effective phenotypes based on signals from surrounding tissue . both obstructive ( asthma , copd ) and restrictive respiratory diseases ( pulmonary fibrosis ) changes in the number and phenotype of lung macrophages have been found . in this paperwe will first briefly discuss the in vitro generated phenotypes and then compare this with their role in the pathogenesis of obstructive and restrictive respiratory diseases . classically activated or m1 macrophages develop after being exposed to ifn and tnf or lipopolysaccharide ( lps , which induces tnf production ) under the influence of the transcription factor interferon - regulatory factor 5 ( irf5 ) . they are essential in host defense against intracellular pathogens by generating reactive oxygen species ( ros ) and nitric oxide ( no ) through upregulated expression of inducible nitric oxide synthetase ( inos ) and amplifying th1 immune responses by producing proinflammatory cytokines like il - 12 , il - 1 , and tnf ( see also figure 1 ) . in addition , they show enhanced phagocytosis of microorganisms , antigen - presentation capabilities , and enhanced production and secretion of matrix metalloproteinases ( mmps ) such as mmp7 and mmp9 . the secretion of mmps enables macrophage migration during inflammatory responses , but excessive or unregulated production results in tissue damage . alternatively activated or m2 macrophages were named to indicate that their activation status was distinctly different from the classically activated macrophages . first discovered to be induced by il - 4 and il - 13 , this phenotype was soon found to have more siblings , closely resembling each other but distinctly different in function . a variety of different nameshave been suggested , but for the purpose of this paper we will adopt the names suggested by mosser and edwards and sica and mantovani . they have suggested alternatively activated or m2 macrophages for the phenotype induced by il - 4 / il - 13 and regulatory macrophages or m2 - like cells for the phenotype characterized by high il - 10 production that are induced by a variety of stimuli ( see also figure 1 ) . m2 macrophages , induced by il - 4 / il - 13 under the influence of the transcription factor irf4 , have a role in protection against helminths and are considered wound - healing macrophages because of their association with physiological and pathological tissue remodeling . they are characterized by upregulated expression of mannose receptors and transglutaminase 2 in man and mice and by upregulated expression of arginase - 1 , chitinase -3-like protein - 3 ( chi3l3 , also known as ym1 ) , and resistin - like molecule - ( relm , also known as fizz1 ) in mice only ( see also figure 1 ) . they have poor antigen presenting capabilities and exhibit increased release of iron and clearance of apoptotic cells and extracellular matrix components ( efferocytosis ) . m2 - like macrophages also upregulate mannose receptors and in addition produce high levels of il - 10 ( see also figure 1 ) . they are induced by a number of stimuli that need to be combined with a second signal , which is toll - like receptor ( tlr ) stimulation . the initial signals include glucocorticosteroids , prostaglandin e2 ( pge2 ) , antibody immune complexes , transforming growth factor beta ( tgf ) , and il - 10 itself . they may also be the macrophages that produce tgf in addition to il - 10 , but this has not been rigorously shown due to the overlap in markers between m2 and m2 - like macrophages . transcriptional control of this phenotype is unclear but may involve peroxisome proliferator - activated receptor gamma ( ppar ) and the camp - responsive element - binding protein ( creb ) - ccaat / enhancer - binding protein - ( c / ebp ) - axis . as a result of their high il - 10 production , this can be beneficial during later stages of immune responses to limit inflammation but may also permit tumor progression when associated with tumors . to dateit has been difficult to distinguish genuine m2 macrophages from m2 - like macrophages because they share many markers , most notably the mannose receptor . only il - 10 production would be a reliable marker but is used seldomly to identify m2 - like macrophages . the exact differences in tissue distribution and function of these two phenotypes are therefore difficult to establish from the studies published to date . whenever possible , we will indicate what is known of m2 and m2 - like macrophages in the context of respiratory diseases . over the last few decades the prevalence of asthma has rapidly increased , and currently more than half a million people suffer from asthma in the netherlands ( annual report 2011 dutch lung fund ) . asthma is a heterogeneous disorder of the airways , which are chronically inflamed and contract easily in response to nonspecific stimuli . this so - called airway hyperreactivity is accompanied by increased mucus secretion and airway wall remodeling , which leads to symptoms such as wheezing , coughing , and chest tightness . several distinct forms of asthma have been recognized and can roughly be divided into atopic and the less - studied nonatopic asthma . the majority of asthma patients are atopic , which is a predisposition to mount an immunoglobulin type e ( ige ) response . there is no evidence of allergen - specific ige , and this type is characterized by the infiltration of neutrophils in the lungs . a small portion of asthma patients suffer from severe asthma , which includes both atopic and nonatopic characteristics . severe asthma is defined as being unable to control asthma symptoms despite taking high - dose corticosteroids , also referred to as corticosteroid - resistant asthma . asthma is traditionally considered a t - helper - 2 - ( th2 - ) cell driven inflammatory disorder . activation of a th2 - response is characterized by the release of the cytokines il - 4 , il - 5 , il - 9 , and il - 13 . these th2 - cytokines are responsible for the recruitment of effector cells resulting in eosinophil infiltrates , ige production , and histamine release among other typical asthma symptoms . the innate immune system is increasingly being recognized as an additional important disease mechanism in asthma . cells of the innate immune system actively orchestrate adaptive immune responses in asthma . besides dendritic cells ( dc ) in the lung taking up allergens and pathogens and presenting those to the adaptive immune system , other cells important for innate immune responses in the lung are macrophages . their role , however , in asthma has been greatly underestimated , and therefore their contribution to asthma is mostly unexplored . in asthmait appears that effective phenotype switching is impaired and macrophages can actually contribute to the pathogenesis of this disease . the next part will focus on the roles of each known phenotype in the pathogenesis of asthma . although the inflammatory process in asthma is dominated by a th2 inflammation , increasing evidence supports the parallel development and involvement of both m1 and m2 macrophages in this disease . we have recently shown that during the development of house - dust - mite - induced asthma numbers of m1 macrophages are high in a short model as compared to control mice and decrease with longer exposure . levels of m1 inducers ( ifn and lps or tnf ) were found to be significantly higher in asthmatics , especially in those with severe forms of the disease . elevated serum ifn correlates with the severity of airway inflammation in atopic asthma , and this cytokine has been linked to mechanisms that induce airway hyperreactivity . in agreement with the findings in human asthma , it was shown that both ifn and lps contribute to airway inflammation and airway hyperreactivity in a mouse model of asthma . tnf is implicated in many aspects of asthma pathology , including development of airway hyperreactivity and attraction of eosinophils and neutrophils . in both atopic and nonatopic asthmatics , the amount of lps in house dust has been related to the severity of airway inflammation . inhalation of pure lps by asthmatics is associated with bronchoconstriction and a change in airway hyperreactivity . administration of high doses of lps into the lungs of allergic mice promotes airway hyperreactivity , neutrophilic inflammation , and expression of m1 cytokine il - 12 . in addition , exposure of asthmatic mice to both ifn and lps induced higher numbers of macrophages in the lungs . it was shown that a common irf5 gain - of - function haplotype is associated with asthma and the severity of asthmatic symptoms . these associations were more pronounced in nonatopic asthmatics , and it was suggested that irf5 may only have a profound impact on the pathogenesis and severity of nonatopic asthma and not on atopic asthma . an explanation could be that m1 macrophages are responsible for the recruitment of neutrophils , which are the major effector cells in nonatopic asthma . neutrophils are also dominant in more severe phenotypes of asthma , and the most commonly used therapy for asthma , corticosteroids , is not effective against neutrophilic inflammation . this is in accordance with recent findings that corticosteroid - resistant asthmatics have increased expression of m1 markers on macrophages in bronchoalveolar lavage fluid ( balf ) compared to corticosteroid - sensitive asthmatics , suggesting that m1 macrophages also play a key role in the development of severe corticosteroid - resistant asthma . a few studies have shown that m1 macrophages act preventively in the onset of allergic airway inflammation in mice and suppressed dc maturation . this is consistent with the findings of a study that investigated the role of the m1 cytokine il - 12 during the development allergic airway inflammation in mice . they showed that neutralization of il - 12 during the sensitization phase aggravated development of allergic airway inflammation but neutralization of il - 12 during challenges abolished the development of allergic airway inflammation . these data demonstrate a dual role of il - 12 : it acts preventive during th2 sensitization , but it contributes to allergic airway disease during allergen challenges . the effects of il - 12 neutralization were not shown in ifn knockout mice , suggesting that ifn plays an essential role in the il -12-induced effect . thus , both the presence of m1 skewing factors ( ifn , tnf , or lps ) and the proinflammatory mediators released by m1 macrophages can contribute to asthma . the data imply that m1 macrophages may be beneficial to prevent allergic sensitization , but in already established disease they promote the development of m2 macrophages and induce corticosteroid resistance . besides a role in severe asthma , markers of m1 macrophagesthe cytokines il - 4 and il - 13 are abundantly present in the lungs of asthmatics , and it may therefore not come as a surprise that markers expressed by m2 macrophages have been associated with asthma . elevated levels of chitinase family members have been found in the serum and lungs of patients with asthma , suggesting the presence of increased m2 macrophage numbers . indeed , we showed that asthmatics have higher percentages of macrophages expressing mannose receptor and transglutaminase 2 in bronchial biopsies than in healthy subjects . in addition kim et al . showed that severe asthmatics had higher numbers of il -13-positive m2 macrophages in balf as compared to healthy controls . both chitinase levels and the percentage of mannose receptor - positive macrophages also correlated with asthma severity . higher numbers of m2 macrophages were also found in children undergoing severe exacerbations of asthma . in addition , we have recently shown in several models of house - dust - mite - induced asthma that the number of m2 macrophages positively correlated with the severity of airway inflammation . these clinical and animal model findings demonstrate a correlation between asthma severity and the number of m2 macrophages , but it is unclear whether m2 macrophages actively contribute to the induction and exacerbation of the disease or are just bystanders in allergic airway inflammation responding to the high il - 4 and il - 13 levels . credit to the role of m2 macrophages in the exacerbation of the disease was given by adoptive transfer studies . the transfer of in vitro differentiated m2 macrophages into the airways of male asthmatic mice aggravated airway inflammation . another study using il - 4r - positive m2 macrophages showed that intraperitoneal injection of these macrophages was sufficient to increase the allergic inflammatory response in the lung . in a different model of fungus - induced asthma , moreira et al . showed that transfer of m2 macrophages into the lungs of mice enhanced both inflammation and collagen deposition as compared to asthmatic mice not treated with macrophages . since m2 macrophages and their products have been reported in asthma patients , m2 macrophages may be a target to reduce asthma symptoms . indeed , the study by moreira et al . in mice with fungus - induced asthma also showed that treatment with an inhibitor of m2 macrophage generation resulted in lower airway hyperreactivity , mucus cell proliferation , collagen deposition , and m2 numbers as compared to control mice . in support of these results , inhibition of m2 - expressed transglutaminase 2 reduced ovalbumin - induced airway hyperreactivity , ovalbumin - specific ige levels , and infiltration of inflammatory cells in lung tissue . these studies substantiated previous circumstantial evidence concerning a role for m2 macrophages in the pathogenesis of asthma . unfortunately , the previous studies did not conclusively prove that m2 macrophages play a causative role in the development of allergic airway inflammation . in contrast to what has just been described , nieuwenhuizen et al . recently demonstrated that m2 macrophages are not necessary for allergic airway disease and may only be a consequence of the elevated th2 response . they studied the contribution of m2 macrophages to acute , chronic , and house - dust - mite - induced allergic airway inflammation by using mice with abrogated il - 4r signaling on macrophages . it was demonstrated that airway hyperreactivity , th2 responses , mucus hypersecretion , number of eosinophils , and collagen deposition were not significantly affected by decreased development of m2 macrophages . however , the expression of m2 markers was still higher in mice with macrophage - restricted il - 4 receptor - ( il - 4r ) deficiency as compared to healthy mice . the presence of these small numbers of m2 macrophages may still have been able to reinforce the th2 response . to sum up , m2 markers are correlated with severity of allergic airway disease in humans and mice , suggesting that m2 macrophages contribute to the disease . indeed , elimination of m2 macrophages in established disease by pharmacological interventions remarkably decreased the degree of airway inflammation . however , new data suggest that m2 macrophages are not essential for the development of allergic airway inflammation but only play a bystander role as a consequence of the th2 response . these macrophages could play an important role in the resolution of asthma because of their production of il - 10 . interestingly , a lower level of il - 10 production was found in lung macrophages from asthmatics compared to healthy persons . moreover , macrophages from severe asthmatics produce high levels of il - 6 and il - 8 , but il - 10 was undetectable in these cells compared to macrophages from patients with moderate asthma . studies in mouse models of allergic airway inflammation have investigated the role of il - 10 intensively and found it to be an important mediator in the resolution of airway inflammation , but only few studied the production of il - 10 by macrophages . we have just shown that the number of il -10-positive cells is lower in lungs of mice with house - dust - mite - induced asthma as compared to control mice , and recently it was also shown that lung interstitial macrophages produce high levels of il - 10 and prevent airway inflammation in mice . stimulation of macrophages by ovalbumin uptake and tlr ligands induced increased production of il - 10 by these macrophages , and this resulted in lower levels of il - 5 and ovalbumin - specific ige and a lower number of eosinophils in a mouse model of asthma . although evidence for a role of m2 - like macrophages in asthma is scarce , these findings suggest a protective effect since active il - 10 production by these cells is low in moderate asthma and absent in severe asthma . in a mouse model of asthma il - 10studies on the resolution of asthma may reveal whether an increased production of il - 10 by these macrophages is involved . combining the data available for the different subsets in asthma ( see also figure 2 ) suggests that m1 macrophages can prevent the induction of asthma but during established disease can cause severe corticosteroid - resistant asthma . however , it is still a matter of debate whether they genuinely contribute to asthma pathogenesis or are just innocent bystanders of the inflammation . m2 - like macrophages seem to be beneficial to the resolution of asthma through production of il - 10 but are not present or not functional in asthma , and therefore allergic inflammation can progress . copd is one of the most common respiratory diseases and affects around 320,000 people in the netherlands ( annual report 2011 dutch lung fund ) . it is projected to be the fourth leading cause of death worldwide by 2030 and places a huge economic burden on society . copd is caused by lung inflammation due to inhalation of noxious gasses and particles : in the western world most commonly from cigarette smoking and in developing countries from indoor biomass cooking and heating . the disease is characterized by airflow limitation that is not fully reversible , which is caused by a combination of obstructive bronchiolitis ( also known as chronic bronchitis ) and destruction of alveoli resulting in airspace enlargement ( also known as emphysema ) . the relative contributions of chronic bronchitis and emphysema to the copd phenotype can vary from person to person . exposure to smoke and particles leads to an exaggerated chronic inflammation in lungs of people susceptible to the development of copd . the mucosa , submucosa , and glandular tissue become infiltrated with inflammatory cells and the walls of the respiratory bronchioles become thickened because of edema and fibrosis . chronic mucus hypersecretion is induced by goblet cell hyperplasia and hypertrophy of submucosal glands , which further contributes to occlusion of small airways . not much is known about the role of macrophages in this part of the disease , but pigmented macrophages were found to cluster around small airways and these were associated with peribronchiolar fibrosis . the alveolar destruction that characterizes emphysema is the result of infiltration of inflammatory cells with a prominent role for macrophages . both neutrophils and macrophages are being recruited to the lung because smoke / particle exposure injures epithelial cells that subsequently release cytokines and chemokines to recruit them . they have been postulated to be the main effector cells contributing to the excess tissue damage seen in emphysema because of their ability to produce proteolytic mmps like neutrophil elastase and macrophage elastase ( mmp12 ) . increased numbers of macrophages and neutrophilshave been found in airways and lung parenchyma of patients with copd . however , only the number of parenchymal alveolar macrophages was directly proportional to the severity of lung destruction in emphysematous lung tissue from copd patients . animal studies confirmed the dominant role for macrophages , because deletion of neutrophils in smoke - exposed rats did not prevent cigarette smoke - induced emphysema , whereas deletion of macrophages did . in addition , mice deficient in mmp12 ( mainly produced by macrophages ) were completely protected from cigarette - smoke - induced emphysema even though they could still produce neutrophil elastase . the role of the different macrophage phenotypes in copd is the topic of quite a few studies recently and the subject of much debate as the results have been somewhat counterintuitive . based on studies in mice and results from patient studies , m1 polarization is expected to play an important role in the pathogenesis of copd . however , the results of other studies have questioned this view , and this is nicely illustrated by studies from shaykhiev et al . and hodge et al . . the first ones recently studied the transcriptome of alveolar macrophages from healthy smokers and nonsmokers and compared them to alveolar macrophages from copd smokers . their results showed a mixed phenotype for alveolar macrophages after smoking with downregulation of m1 genes and partial upregulation of m2 genes , which was progressively worse in copd . hodge et al . showed a mixed phenotype in alveolar macrophages of smoking copd patients with some m1 ( mhc ii expression ) and m2 ( efferocytosis ) markers going down and some going up ( proinflammatory cytokine production and dc - sign expression ) . in the next partwe will touch upon this debate as we discuss the separate phenotypes in the pathogenesis of copd . several lines of evidence support not only a role for m1 macrophages but also a role for dysregulated m1 macrophages in the development of copd . first of all , exposure to compounds in smoke appears to induce m1 polarization of macrophages . smoking is the most important risk factor for copd and cigarette smoke contains many thousands of compounds , including lps that can activate macrophages in the lung . indeed , increased expression of inos in alveolar macrophages was found in copd patients , indicating a polarization towards an m1 phenotype . oxidative stress has been shown to be an important contributor to the pathogenesis of copd . smoking itself of coursecauses oxidative stress , and increased inos activity through m1 polarization can add to this stress . furthermore , many studies have shown that smoke exposure enhances the release of the m1 proinflammatory cytokines il - 1 , il - 6 , il - 8 , and tnf . il - 1 , il - 6 , il - 8 , and tnf have all been found to be elevated in copd and in experimental settings have been found to contribute to the development of persistent airway inflammation , emphysema , and mucus production . tnf was found to drive most of the emphysema development in mice after smoking because mice lacking receptors for tnf only developed mild emphysema . in addition , mice overexpressing tnf in lung tissue develop chronic inflammation and emphysema . however , in humans antibodies against tnf seem to be ineffective in copd , questioning the relevance of this cytokine for human copd . in addition to tnf , m1 cytokine il - 1 was also found to play a role . overexpression of il - 1 in lung caused lung inflammation , emphysema , mucus metaplasia , and airway fibrosis in mice . taken together these data suggest cytokines produced by m1 macrophages at least play a role in the pathogenesis of copd . another important m1 - related cytokine with a role in copd is ifn . it is produced by cd8 + t cells that infiltrate the lungs in copd and can cause m1 polarization . inducible overexpression of ifn in lungs of mice caused emphysema with alterations in the balance of mmps and antiproteases . however , in human alveolar macrophages from smokers reduced expression of ifn receptors and reduced ifn signaling were found , suggesting m1 polarization may be impaired after smoking . this of course is in line with the above - cited finding by shaykhiev et al . that m1 genes are downregulated in alveolar macrophages of healthy smokers and smoking copd patients as compared to nonsmokers . m1 macrophages have also been found to produce mmp9 , presumably to enable macrophage migration during inflammatory responses . mmp9 is associated with the breakdown of extracellular matrix in copd as macrophages from patients with copd have a significantly higher production of mmp9 as compared to control macrophages . in addition , overexpression of human mmp9 in mouse macrophages induced emphysema and loss of alveolar elastin pointing at a role for m1 macrophages in copd development . finally , an important property of m1 macrophages that appears to be dysregulated is phagocytosis of microorganisms . m1 macrophages are geared towards killing and disposal of microbial threats and phagocytosis of microorganisms is part of that function . copd is often exacerbated by infections , and there is accumulating evidence that reduced macrophage phagocytosis in copd may be responsible for the persistence of microorganisms in the lungs . this dysfunction of phagocytosis is not restricted to microorganisms but also appears to be present for m2 - related phagocytic functions such as efferocytosis and mannose receptor - mediated uptake . this overall inhibition of phagocytosis irrespective of macrophage phenotype was further confirmed by the later study of hodge et al . that has already been mentioned before . taken together , the available data suggest that a dysregulated m1 response plays a role in copd rather than an increased number of m1 macrophages . some aspects of the m1 activation signature are upregulated in copd ( ros generation , proinflammatory cytokines , production of mmp9 ) , but some aspects are also downregulated ( phagocytosis , ifn responsiveness ) . overexpression of prototypical m1 - inducer ifn may be able to induce emphysema , but so does overexpression of prototypical m2 induced il - 13 . showed that mice overexpressing il - 13 in lung tissue caused lung pathology mirroring human copd with macrophage - and lymphocyte - rich inflammation , emphysema , and mucus metaplasia . unfortunately , macrophages were not further characterized in this study , so it is not known if il - 13 overexpression also induced more alternative activation of macrophages . further evidence for a role for m2 macrophages came from a study by kim et al . who showed that viral infections could induce an il -13-producing m2 phenotype through interactions with natural killer t cells leading to chronic airway inflammation . they also showed higher numbers of il -13-positive m2 macrophages in lung tissue of copd patients . in mice , m2 macrophages produce large amounts of chitinases like ym1 and ym2 . whether their human counterparts are also induced by alternative activationis unclear , but another member of this family , stabilin - 1 interacting chitinase - like protein ( si - clp ) , has been found upregulated in m2 macrophages . whether or not pointing at alternative activation , many members of the chitinase family associate with copd . chitotriosidase levels , for instance , were increased in bronchoalveolar lavage of smokers with copd and they also had more chitotriosidase - positive cells in bronchial biopsies and an elevated proportion of alveolar macrophages expressing chitotriosidase as compared to smokers without copd or never smokers . furthermore , macrophage chitinase - 1 was selectively increased in a subset of patients with severe copd , and serum concentrations of ykl - 40 were significantly higher in smokers with copd as compared to nonsmokers or smokers without copd and correlated negatively with lung function . interestingly , ykl - 40 also stimulated the production of proinflammatory cytokines and mmp9 by macrophages from copd patients , suggesting ykl - 40 itself actually induces more of an m1 phenotype . as mentioned above mmp12 plays an important role in mouse emphysema , and mmp12 was found specifically induced in il -4-stimulated m2 macrophages . furthermore , woodruff et al . showed increased m2 polarization of alveolar macrophages in smokers using mmp12 as a marker for alternative activation , and many others showed that smoke induces mmp12 in macrophages . interestingly , mmp12 production by macrophages was also found to be necessary to terminate both neutrophil and macrophage influx at the end of an inflammatory response and may therefore be an instrument of m2 macrophages to dampen inflammation to be able to start remodeling of damaged tissue . how that ties in with the potential proemphysematous role of m2 macrophages remains an open question . summarizing , there is some evidence for a role of m2 activation in copd , and this evidence points at a role contributing to the development of copd . the data by hodge et al . suggest that , similar to dysfunctional m1 activation , m2 activation is also dysregulated with reduced efferocytosis but increased expression of m2 marker dc - sign . no attempts have been made to distinguish the roles of m2 and m2 - like macrophages in copd . two studies reported il - 10 in the context of copd . a study by hackett et al . showed diminished il - 10 production in lung tissue of copd patients after lps stimulation as compared to lung tissue of patients with normal lung function . takanashi et al . demonstrated that the level of il - 10 and the number of il -10-positive macrophages in sputum from copd patients and healthy smokers was decreased as compared to healthy nonsmokers . this would suggest that m2 - like macrophages are impaired in smoking and copd and therefore can not suppress the ongoing inflammation induced by smoke . combining the data available for m1 , m2 , and m2 - like macrophages ( see also figure 3 ) , it appears copd is a disease of dysfunctional macrophages rather than a disease of one particular polarization state . macrophages in copd are promoting ongoing inflammation and tissue damage but are unable to effectively dampen inflammation because they have lost the ability to phagocytose microorganisms and apoptotic bodies and produce anti - inflammatory cytokines like il - 10 . pulmonary fibrosis is a disease that encompasses a collection of restrictive pulmonary disorders characterized by progressive and irreversible destruction of lung architecture by excessive deposition of extracellular matrix ( ecm ) . while ecm formation usually functions as an essential process of tissue healing after lung injury , continuous damage may result in abnormal wound repair and progress to fibrosis . fibrosis of the interstitium ultimately leads to organ malfunction because of the disturbed architecture of the lung , causing impaired gas exchange and eventually death from respiratory failure . in some cases , fibrotic lesions remain localized to a limited area of the lung because the initial trigger is removed , for example after tuberculosis or a fungal infection , while in others such as in sarcoidosis and idiopathic pulmonary fibrosis ( ipf ) the fibrotic process continues to progress throughout the lungs in a diffuse manner . the chronic and slowly progressing character of the disease together with an unknown aetiology makes it a difficult disease to diagnose and treat . the incidence of ipf appears to be increasing and is currently estimated at 716 cases per 100,000 persons . patients diagnosed with ipf have a poor life expectancy with a median survival of 25 years . currently there are no effective therapies available for these patients , as no therapy has yet been proven to cure or even halt the progression of fibrosis . to describe the pathogenesis of pulmonary fibrosis and to be able to unravel the complex interactions of macrophages , tissue repair after injury can be divided into four different stages : the clotting phase for emergency tissue repair , then the inflammatory phase to fight the inciting agent , followed by formation of scar tissue in the fibrotic phase for more permanent repair , and eventually resolution of scar tissue and restoration of tissue homeostasis in the resolution phase . during fibrosispulmonary fibrosis is thought to be the result of repetitive injury to the epithelial cell layer lining the alveoli . this damage initiates a blood coagulation cascade to prevent severe blood loss and to maintain some sort of homeostasis . this includes platelet accumulation and production of fibrin by epithelial cells , which is essential for fibrin - containing clot formation . to restore the function of damaged tissue , plasminogen activator ( pa ) eventually breaks down this fibrin matrix again . in pulmonary fibrosis , changes in both the coagulation cascade itself and the resolution of the wound - healing clot can affect the disease . impaired fibrin degradation for instance has been shown to worsen epithelial cell survival . impaired resolution of clots can be caused by either the absence of pa or by increased production of pa inhibitors pai - 1 or pai - 2 . it has been difficult to investigate the role of the former and this phase in fibrosis because patients usually present with end - stage disease . nevertheless , the inflammatory response has been extensively studied in lps - induced inflammation in humans ( reviewed by rossol et al . ) . it was shown that epithelial cell damage induces the release of several cytokines and chemokines that triggers an influx of neutrophils , closely followed by monocytes to fight the inciting agent . epithelial cells also release growth factors like tgf , tnf , and epidermal growth factor alfa ( egf ) that stimulate tissue healing by activating fibroblasts , which are the main producers of collagen and other ecm proteins . control of the inflammatory event , however , is essential for a proper wound healing process . dysregulation of the inflammatory phase with a prominent role for m1 macrophages has long been thought to be important to the process of fibrosis . the fact that anti - inflammatory drugs such as corticosteroids have no therapeutic effects in patients with pulmonary fibrosis has made this assumption unlikely . now the new prevailing hypothesis is that pulmonary fibrosis probably develops when the fibrotic phase and / or resolution phase become dysregulated . to progress from the inflammatory phase to the next phase of tissue repair , the release of il - 10 and tgf dampens inflammation and promotes ecm production by myofibroblasts . under the influence of tgf and pdgf produced bydamaged epithelial cells and platelets , fibroblasts differentiate into myofibroblasts , proliferate , and produce ecm proteins . furthermore , they start producing their own tgf to maintain tissue healing . in pulmonary fibrosisthis phase is probably dysregulated as increased numbers of myofibroblasts and increased production of ecm are found in fibrotic lungs . increased numbers of m2 macrophages are also associated with this phase , and these macrophages are therefore suggested to play an important role in the development of fibrosis . eventually repair of the epithelial cell barrier and removal of excess ecm are essential to recover normal lung function . to overcome the loss of alveolar epithelial type i cells ( aec i ) , alveolar epithelial type ii cells ( aec ii ) become hyperplastic and provisionally restore the epithelial cell layer along with the ecm produced by myofibroblasts . normally these type ii cells would revert back to aec i and homeostasis is restored . however , when injury is repetitive this does not seem to occur ; ecm is produced continuously and aec ii continue to proliferate without reverting back to aec i. in a proper tissue healing response , the excess of ecm products is removed to gain full function of the lungs again . macrophages are important cells in degrading and taking up ecm components . in order to doso they produce mmps and their inhibitors ( tissue inhibitors of metalloproteinases , timps ) . a balance between the activities of mmps and timps is important to maintain tissue homeostasis . levels of both mmps and timps are elevated in patients and mouse models of pulmonary fibrosis , but their balance is clearly disrupted as the net result is an excess of ecm in those lungs . macrophages play an important role in the pathogenesis of lung fibrosis , but their role is complex . they are involved in many of the dysregulated tissue healing responses in fibrosis , and they can also adopt many phenotypes . in the next part we will discuss what is known about the contribution of each macrophage phenotype to each stage of fibrosis . we have found no studies reporting on the presence of m1 macrophages in pulmonary fibrosis except for one study by nagai et al . showing that folate - receptor - beta - ( fr - ) positive macrophages were higher in patients with ipf as compared to controls . these macrophages have previously been shown to produce tnf and oxygen radicals and are therefore very likely m1 macrophages . several lines of evidence suggest that m1 macrophages may play a role in both the inflammatory phase as well as the resolution phase of pulmonary fibrosis . as a reaction towards epithelial cell damage , monocytes are recruited to the site of inflammation and differentiate into m1 macrophages under the influence of proinflammatory cytokines . once activated , m1 macrophages themselves produce tnf , il - 1 , and oxygen radicals to kill and phagocytose microbes to fight an infection or remove an exogenous agent . many studies indicate that these proinflammatory cytokines and oxygen radicals are associated with fibrosis development . in the study by nagai et al . ablation of the fr - expressing m1 macrophages during the inflammatory phase of bleomycin - induced fibrosis abrogated fibrosis development . however , the importance of the contribution of inflammation to established fibrosis has been challenged because anti - inflammatory drugs such as corticosteroids have no therapeutic effects in patients with pulmonary fibrosis . they studied newly recruited inflammatory macrophages in a mouse model of bleomycin - induced lung fibrosis and showed that depletion of tissue - resident macrophages and / or circulating inflammatory monocytes during the inflammatory phase did not affect the onset or degree of fibrosis that developed after this inflammatory phase . another study pointed out that the m1 cytokine tnf has beneficial effects on alveolar epithelial cell recovery and therefore also contributes to resolution . in the resolution phase , macrophages are involved in the degradation of excess ecm and the uptake of matrix components . depletion of macrophages during this recovery phase impaired the resolution of fibrosis by slowing down the degradation of ecm . it is unclear what type of macrophages is responsible for degradation of ecm , but a case can be made for m1 macrophages as these have been shown to produce several mmps including mmp7 and mmp9 . levels of mmp9 have been found to be increased in lungs of ipf patients and this may reflect a failing attempt of the lungs to remove excess ecm and may be caused by a simultaneous increase of the inhibitor timp - 1 . macrophages are also important in the subsequent removal of ecm components through endocytosis - mediated mechanisms . again it is unclear if this is restricted to one particular phenotype , but the receptors involved would suggest more of an m2 phenotype , and this will therefore be discussed in the next part on m2 macrophages . in summary , m1 macrophages are important in the inflammatory phase , but their presence does not appear to affect the subsequent fibrotic phase . during resolution of scar tissue , this may be related to an m1 phenotype , and it may therefore be beneficial to stimulate recruitment of m1 macrophages to reverse fibrosis . there is a great deal of evidence that th2 responses are important in the development of fibrosis , and it appears that il - 13 is the predominant cytokine in the profibrotic responses . levels of il - 13 are higher in patients with pulmonary fibrosis as compared to controls , and macrophages isolated from these fibrotic lungs produce more il - 13 than macrophages from control lungs . it therefore comes as no surprise that m2 macrophages are associated with pulmonary fibrosis , although we could not find publications directly showing numbers of m2 macrophages are increased in lung tissue of patients with pulmonary fibrosis . we did find one study showing higher numbers of m2 macrophages in balf of ipf patients as compared to controls and two studies showing higher numbers of insulin - like growth factor - i ( igf - i ) - positive and pdgf - positive interstitial macrophages in lung tissue of ipf patients as compared to controls . both these markers are important profibrotic mediators , and a recent study by chen et al . showed that expression of igf - i colocalized with arginase - 1 and not with il - 10 expression in macrophages suggesting genuine m2 macrophages express igf - i and not the m2 - like subset . this was a study in mice ; it therefore remains to be investigated whether this is also true in humans . markers found on or produced by m2 macrophages have also been found to be increased in pulmonary fibrosis . levels of galectin - 3 , a carbohydrate - binding lectin that is necessary for alternative activation , were higher in balf of ipf patients as compared to control patients . furthermore , macrophages from ipf patients produced more of the human m2 marker ccl18 than control macrophages , and this correlated negatively with pulmonary function test parameters . ipf patients were also found to have higher serum and pulmonary levels of chitinase - like protein ykl - 40 as compared to controls , although it is still unclear whether chitinases are true markers of alternative activation in human macrophages . this is also the case for arginase - 1 , which is a marker of m2 macrophages in mice but its specificity in humans is debated . nevertheless , lung tissue from ipf patients had higher expression of arginase - 1 in macrophages than normal lung tissue . lastly , circulating monocytes from systemic sclerosis patients with pulmonary fibrosis showed enhanced profibrotic phenotype by increased expression of cd163 , a marker of alternative activation in humans . experimental models of pulmonary fibrosis have revealed more about the role of m2 macrophages in fibrosis of the lung . depletion of macrophages during the fibrotic phase of lung fibrosis reduced the deposition of ecm in this organ . to confirm a role for m2 macrophages , levels of ym1 and arginase - 1the m1 marker inos did not show a reduction in expression , indicating that m2 macrophages are predominantly responsible for the development of fibrosis . furthermore , m2 marker mmp12 was shown to be essential in the development of fibrosis induced by excessive activation of fas and in a model of il - 13 dependent fibrosis . the aforementioned production of igf - i and pdgf contribute to proliferation of fibroblasts and their transformation to ecm - producing myofibroblasts . furthermore , fizz1 ( also known as resistin - like molecule alpha ) was found to increase ecm production in fibroblasts , but a recent paper by pesce et al . this contradictory finding highlights other new findings that also suggest that m2 macrophages could be antifibrotic . a mechanistic study in a model of schistosoma - induced liver fibrosis with specific deletion of the il - 4r on myeloid cells preventing alternative activation of macrophages showed that m2 macrophages are not required for fibrosis development . in addition , related studies with mice lacking arginase - 1 in m2 macrophages showed that the arginase -1-expressing m2 macrophages were required for suppression and resolution of fibrosis . this correlates well with findings that uptake of ecm components appears to be mediated by m2 macrophages . uptake of these components is mediated by different mannose receptors and by glycoprotein milk fat globule epidermal growth factor 8 ( mfge8 ) . mannose receptors of course are a known m2 marker , and for mfge8 this is unclear . both mannose receptor 2 and mfge8 were shown to attenuate fibrosis in different models . to summarize , m2 macrophages are firmly associated with fibrosis development , but new evidence suggests they may actually contribute to resolution of fibrosis . their presence during fibrosis may be explained as a failing attempt to clear the excess ecm . the conflicting roles described in the literature may be the result of difficulties separating the effects of m2 and m2 - like macrophages simply because these two subsets are difficult to distinguish . m2 - like macrophages may be a more likely candidate for the promotion of fibrosis as will be discussed below . the specific role of m2 - like macrophages has not been investigated in lung fibrosis yet , but m2 - like macrophages may be important during the transition from inflammation towards tissue healing . the signature marker of m2 - like macrophages is il - 10 , which is the canonical anti - inflammatory cytokine with profibrotic actions . elevated levels of il - 10 and enhanced production of il - 10 by alveolar macrophages have been reported in several fibrotic diseases , including ipf and in systemic sclerosis patients with interstitial lung disease . its anti - inflammatory actions in lung are illustrated by a study from armstrong et al . , showing that il - 10 inhibited tnf production by alveolar macrophages after lps stimulation . in addition , several studies in mice using the model of bleomycin - induced fibrosis suggest that il - 10 attenuates bleomycin - induced inflammation and can thereby attenuate fibrosis development . sun et al . found that inducible il - 10 overexpression in clara cells induced fibrosis by fibrocyte recruitment and activation of macrophages towards an m2 phenotype . the increased levels of il - 10 found in lungs of ipf patients may therefore contribute to the fibrotic process . the production of the profibrotic , anti - inflammatory cytokine tgf would also fit with this role of dampening inflammation and promoting tissue repair by this subset of macrophages . whether tgf production is restricted tothey may be recruited or induced by damage to the epithelium to dampen inflammation and start repair . in the event of ongoing damagethey are continually induced or recruited and may contribute to fibrosis by overexpression of il - 10 . since corticosteroids are also capable of inducing m2 - like macrophages , this would explain why these drugs are not effective against fibrosis and may even be disadvantageous . this is illustrated by our finding that when corticosteroids are specifically delivered to liver macrophages in a model of liver fibrosis , fibrosis actually becomes worse . overall , current data on the role of macrophages in the development of pulmonary fibrosis show that macrophages are important cells in the pathogenesis of this disease ( see also figure 4 ) . m1 macrophages are important in the inflammatory phase and may also be important for resolution of the disease , although this hypothesis needs testing . new data suggest that m2 macrophages may actually protect against development of fibrosis while m2 - like macrophages contribute to fibrosis . therefore , key to understandinghow these two phenotypes contribute to pulmonary fibrosis are studies differentiating between m2 and m2 - like macrophages . the literature on lung macrophages summarized in this paper clearly shows that macrophages are important in maintaining tissue homeostasis in the lung . through their ability to change phenotypesthey are able to regulate responses to homeostatic threats without impairing the functionality of the organ . the available literature also shows that when phenotype switching becomes dysfunctional or when some aspects of a particular phenotype become dysfunctional , pathologies develop . however , data on the distribution of macrophage subsets in healthy lung tissue and during disease is sorely lacking for humans as well as experimental models of respiratory diseases . in general , asthma , copd , and pulmonary fibrosis are diseases characterized by changes in macrophage subsets in the lung ( m1 , m2 , and m2 - like ) . it seems likely that changes in the interactions between the different subsets , that is , the balance , and changes in their function are a cause for disease , rather than the presence of one particular subset . the next challenge will be to specifically improve a particular function of a subset in vivo or specifically change a phenotype as a novel therapeutic approach for obstructive and restrictive respiratory diseases .\noutput:\n" }, { "from": "agent", "value": "macrophages are among the most abundant cells in the respiratory tract , and they can have strikingly different phenotypes within this environment . our knowledge of the different phenotypes and their functions in the lung is sketchy at best , but they appear to be linked to the protection of gas exchange against microbial threats and excessive tissue responses . phenotypical changes of macrophages within the lung are found in many respiratory diseases including asthma , chronic obstructive pulmonary disease ( copd ) , and pulmonary fibrosis . this paper will give an overview of what macrophage phenotypes have been described , what their known functions are , what is known about their presence in the different obstructive and restrictive respiratory diseases ( asthma , copd , pulmonary fibrosis ) , and how they are thought to contribute to the etiology and resolution of these diseases ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the internet is a technology that facilitates accessing various kinds of information resources and information exchange easily via an inexpensive and safe way . although a standardized definition of internet addiction has not been uniformly agreed upon , some researchers define the internet addiction as having less ability to control enthusiasm for internet activities , losing the importance of the time without being connected to the internet , extreme nervousness and aggressive behaviour when deprived , and progressive deterioration in work , and social and family functionings . researchers point that the internet addiction may be seen at every age in both sexes and begin at earlier ages than other addictions . prevalence statistics of internet addiction among adolescents vary widely from 2 % to 20 % across cultures and societiesfor this reason , the internet addiction may cause physical and social problems as well as psychological disturbances . a number of studies have underlined the unfavorable effects of internet addiction on physical and mental well - being and most of the adolescents with internet addiction were also reported to have another psychiatric disorder . mood disorders , substance use disorders , attention - deficit hyperactivity disorder ( adhd ) , disruptive behaviour disorders , anxiety disorders , sleep disorders , eating disorders , and epileptic seizures are some proven internet addiction - related clinical situations . others have argued that the internet addiction is actually a behaviour pattern which plays role in some of the negative cognitions that compensate for failed areas of life just as seen in depression . in this context , excessive use of the internet can be seen as a rewarding behavior , and through learning mechanisms , it may be used as an insufficient strategy to cope with some negative feelings . temperament traits of novelty or sensation seeking are reported to be significantly higher in substance users than in nonusers . most authors agree that these traits increase the risk of drug addiction in general , presumably because of an increased tendency to experiment with drugs . in studies investigating the temperament features of adolescents with internet addiction , it was revealed that students with internet addiction were easily affected by feeling , emotionally less stable , imaginative , absorbed in thought , self - sufficient , experimenting , and preferred their own decisions . adolescents with internet addiction were also shown to have higher scores on neuroticism and psychoticism temperament categories than those of the control group . however , to our knowledge , there is not a study in the literature addressing the correlation between affective temperament profiles and the internet addiction . the first aim of this study was to investigate internet addiction and the relevance to the sociodemographic properties among a sample of turkish adolescent population . second , it was aimed to compare the affective temperament profiles and emotional and behavioural characteristics of adolescents with or without the internet addiction . the study population included high school students attending erzurum ataturk high school in turkey in the 2010 - 2011 academic year ( n = 325 ) . the study sample included 303 students who were present in classes on the day when data were collected , who agreed to participate in the study , and who filled in the questionnaires completely ( response rate = 93.2 % ) . the ethical committee approval was obtained from the institute of health sciences of ataturk university . the students who were given information about the study and who accepted to participate in the study were included . also , approval was obtained from the directorate of school education , affiliating with the ministry of education . four instruments were used to collect data : a sociodemographic characteristics data form , internet addiction scale , the strengths and difficulties questionnaire , and the temperament evaluation of memphis , pisa , paris , and san diego autoquestionnaire . we developed a 12 - item sociodemographic questionnaire with items pertaining to age , sex , grade , average monthly household income , extent and type of internet use ( e.g. , where do you use the internet ? ) , and presence of the computer in the home . the ias is a self - report instrument consisting of 31 items ( e.g. , i have attempted to spend less time on the internet but i have been unable to do so . ) based on the diagnostic and statistical manual of mental disorders , fourth edition , substance dependence criteria , and 2 additional criteria recommended by griffiths . the ias is a highly reliable and internally consistent measure ( cronbach = .95 ) . the scale was translated into turkish , and psychometric properties of the turkish version of the scale were evaluated among high school students revealing a highly significant test - retest reliability . an interitem reliability reduced the initial scale from 31 to 27 items ( with cronbach of .94 ) . scale items are rated on a 5 - point likert scale ( 1 , never ; 2 , rarely ; 3 , sometimes ; 4 , frequently ; 5 , always ) , with higher scores representing greater internet addiction . a cutoff score of 81 ( 327 items ) was suggested as indicative of internet addiction . the sdq was developed to determine adolescents ' areas of strengths and problematic behaviours . the tool contains 25 questions which asks about behavioural characteristics , some of which are positive , and some of which are negative . these questions are listed under five subheadings : ( 1 ) conduct problems ; ( 2 ) hyperactivity - inattention ; ( 3 ) emotional symptoms ; ( 4 ) peer problems ; and ( 5 ) prosocial behaviour . the validity and reliability of the turkish version of sdq was performed by gvenir et al . with an acceptable internal consistency ( cronbach 's alpha = 0.73 ) . the autoquestionnaire version of the temperament evaluation of memphis , pisa , paris , and san diego ( temps - a ) is a self - report instrument developed by akiskal et al . . the complete questionnaire measures affective temperamental traits , present in the subject 's whole life , represented in five dimensional scales : depressive , cyclothymic , hyperthymic , irritable , and anxious . in this study , the turkish version was used . statistical package for social sciences software ( spss 15 , chicago , il , usa ) was used for the analysis . pearson 's chi - square test was used to analyze the differences in means and proportions between groups . spearman 's or pearson 's correlation tests were used to evaluate the association between the ias and the subscales of the sdq and the temps - a . a p value of 0.05 was considered significant . a total of 210 boys ( 69.2 % ) and 92 girls ( 30.8 % ) completed the scale and questionnaires . of the sample , 20 ( 6.6 % ) the proportion of boys who were classified as internet addicts was 6.2 % . for girls , the corresponding proportion was 7.6 % ; the difference was not statistically significant . having a computer in the home was found to be significantly related with internet addiction . table 1 lists the baseline subject characteristics by the presence or absence of internet addiction . the mean ias scores were significantly higher in adolescents who had a computer in home than those who had not ( p 0.001 ) . additionally , students who had been using internet for more than two years were found to score higher on the ias than those who had been using internet for two years or less ( p 0.001 ) . the ias scores were also significantly higher in adolescents who had been using the internet in home than in those who had been using the internet in other places ( p 0.001 ) . the prevalence rate of anxious temperament for internet addicts was 15 % , whereas that for nonaddicts , it was 2.8 % ( ptemperament subtypes and their distribution in terms of the internet addiction status are shown in table 2 . the mean ias scores were found to be higher in adolescents with anxious temperament ( 63.925.3 ) than those without anxious temperament ( 47.918.1 ) ( p 0.05 ) . presence or absence of other temperament subtypeswas not associated with significantly different scores on the ias . according to pearson 's correlation coefficient , significant correlations were detected between internet addiction and dysthymic ( r = 0.199 ; p 0.01 ) , cyclothymic ( r = 0.249 ; p 0.01 ) , hyperthymic ( r = 0.156 ; p 0.01 ) , irritable ( r = 0.254 ; p 0.01 ) , and anxious ( r = 0.205 ; p 0.01 ) temperaments . adolescents with and without internet addiction were also compared according to their temps - a and sdq scores ( table 3 ) . although no difference was observed in temps - a scores , students with internet addiction scored higher on conduct problems ( p 0.05 ) and total difficulties ( p 0.05 ) subscales of sdq than students without internet addiction . moreover , there was a positive and statistically significant correlation between ias and conduct problems ( r = 0.146 ; p 0.05 ) , hyperactivity - inattention ( r = 0.133 ; p 0.05 ) , emotional symptoms ( r = 0.138 ; p 0.05 ) , and total difficulties ( r = 0.160 ; p 0.01 ) . in the present study , the prevalence of internet addiction was found to be 6.6 % , which is similar with the rate found in other studies evaluating similarly aged students . according to our findings , the risk of becoming an internet addict increases with the increase in the accesibility of internet . additionally , internet use with a duration of more than two years was also found to be related to increased internet addiction risk . in our study , presumably because of low participation rates in girls , there was no significant difference between boys and girls according to ias scores . contrary to our finding , turkey statistical institute has stated that computer and internet use was more prevalent among boys than in girls in 2010 data . other studies from turkey have also shown that boys were more prone to the effects of harmful internet use . in a study which evaluated 535 primary school students using child behavior checklists , adhd scores have been found to be higher in adolescents with internet addiction than in those without . additionally , yen et al . , evaluating 2793 college students , revealed that there was a relationship between the internet addiction and attention deficit hyperactivity disorder ( adhd ) . they have also shown that the most prominent relation between the internet addiction was with attention deficit symptom cluster . similarly , in the present study , internet addiction scores were found to be positively related to attention deficit and hyperactivity scores . according to the rewarding withdrawal syndrome , because of the d2 receptor deficiency , children with adhd have marked tendency to predisposition for pathological gambling , substance and alcohol use , and impulsive and compulsive behaviours . the internet addiction , according to the reward deficiency hypothesis , may function as an unnatural reward and may accompany adhd symptoms by this way . dependent personality traits have been shown to be related with impulsivity , novelty seeking , psychoticism , and social relation problems in several studies . landers and lounsbury evaluated 117 undergraduate students and found that the internet usage was negatively related to three of the big five traits , agreeableness , conscientiousness , and extraversion as well as two narrow traits ; optimism and work drive , and positively related to tough - mindedness . in a study conducted among college students in turkey , psychoticism was shown to be the only personality dimension related to establishing new relationships and having internet only friends . moreover , extroversion was the only personality dimension that is related to maintaining long - distance relationships and supporting daily face - to - face relationships . in our study , a positive and highly significant correlation was found between the internet addiction scores and depressive , cyclothymic , hyperthymic , irritable , and anxious temperament scores . furthermore , the frequency of anxious temperament was found to be significantly higher in students with internet addiction than those without . behavioural addictions demonstrate the core features of physical and psychological addictions such as mental rumination , mood variability , tolerance , withdrawal , interpersonal conflict , and relapse . according to the self - medication hypothesis , the patients usually use the substances to change their unwanted temperament status , to reduce their unbearable anxiety , and to cope with cognitive impairments . this can be seen in the internet addiction , which is also a behavioral addiction . namely , repeating efforts to get online may be a way of decreasing the severity of withdrawal symptoms such as anxiety . additionally , the explanation of increased internet addiction frequency in individuals with anxious temperament may be related to self - medication hypothesis . adolescents who are deprived of emotional and psychological support have been reported to be under increased risk for internet addiction . morahan - martin and schumacher revealed that 22.7 % of the internet users had trouble with peer and family relations and had difficulty in work and school activities because of the internet usage . in our study sample , total strength scores and conduct problems scores of the sdq have been found to be significantly higher in the students with internet addiction . also , there was a positive correlation between the internet addiction scores and total difficulties , conduct problems , hyperactivity - inattention , and emotional symptoms scores . according to these findingsfirst , since the sample of this study included students of a high school , the results of the study can not be generalized to the larger population in turkey . second , the sample size was modest to draw definite conclusions . also , high school education was not mandatory in turkey when this study was conducted . families in the east and southeast of turkey invest more in the education of their sons than their daughters . finally , the cross - sectional research design of the present study could not confirm causal relationships of temperament profiles and behavioural problems with internet addiction . according to the findings of the present study , internet addiction is a relatively common phenomena among the adolescents . there is a relation between the internet addiction and attention deficit and hyperactivity symptoms and also with anxious temperament . furthermore , behavioural problems are more frequent in adolescents who have problematic internet use . because of the cross - sectional nature of this study , it is not possible to define the direction of the causality of the results . there is a need for further prospective studies evaluating the temperament features of adolescents who are at risk for the internet addiction in larger study populations .\noutput:\n" }, { "from": "agent", "value": "the purpose of this study was to investigate the association of affective temperament profiles and emotional and behavioural characteristics with internet addiction among high school students . the study sample included 303 high school students . a sociodemographic characteristics data form , internet addiction scale ( ias ) , the strengths and difficulties questionnaire , and the temperament evaluation of memphis , pisa , paris , and san diego autoquestionnaire were used to collect data . of the sample , 6.6 % were found to be addicted to internet . having a computer in the home ( p < 0.001 ) and using the internet for more than two years ( p < 0.001 ) were found to be related to higher scores on the ias . the prevalence rate of anxious temperament for internet addicts was more than that for nonaddicts ( p < 0.001 ) . dysthymic ( r = 0.199 ; p < 0.01 ) , cyclothymic ( r = 0.249 ; p < 0.01 ) , hyperthymic ( r = 0.156 ; p < 0.01 ) , irritable ( r = 0.254 ; p < 0.01 ) , and anxious ( r = 0.205 ; p < 0.01 ) temperaments ; conduct problems ( r = 0.146 ; p < 0.05 ) , hyperactivity - inattention ( r = 0.133 ; p < 0.05 ) , emotional symptoms ( r = 0.138 ; p < 0.05 ) , and total difficulties ( r = 0.160 ; p < 0.01 ) were found to be correlated with ias scores . according to these findings , there is a relation between the internet addiction and affective temperament profiles , especially with anxious temperament . furthermore , emotional and behavioural problems are more frequent in adolescents who have problematic internet use ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: diabetes mellitus ( dm ) has been known as a potentially disabling chronic disease with multiple complications . in the kingdom of saudi arabia ( ksa ) , diabetes has emerged as a major public health problem that has reached an epidemic stage . the crude prevalence of diabetes has been documented as 23.7 % , accounting for 37.8 % of saudis aged between 30 and 70 years . with the advances in the healthcare facilities in the kingdom , therefore , the complications associated with longer duration of the disease have become one of the challenges faced by health care institutions . of these complications , a retinal vascular disorder , retinopathy is considered the leading cause of blindness in the working age population and accounts for considerable adult work disability . its presence may also indicate and predict other diabetic complications . it is documented that more than 77 % of patients who survive for over 20 years with dm are affected by retinopathy . untreated diabetic retinopathy ( dr ) not only leads to blindness , which is a personal catastrophe for the individual but also increases the economic burden of health care servicesin the community . dr is characterized by signs of retinal ischemia ( retinal microvascular abnormalities , microaneurysms , hemorrhages , intra - venous caliber abnormalities , cotton - wool spots , and neovascularization ) and / or signs of increased retinal vascular permeability . vision loss can result from several mechanisms , including neovascularization leading to vitreous hemorrhage and / or retinal detachment , macular edema , and retinal capillary nonperfusion . depending on these signs , retinopathy is classified into nonproliferative diabetic retinopathy ( npdr ) and proliferative retinopathy ( pdr ) . a number of studies show marked differences in the prevalence of retinopathy in patients with type 2 diabetes . of the estimated 10.2 million us adults40 years and older known to have dm , the estimated crude prevalence rates for retinopathy was 40.3 % , while an urban population - based study from india documented the prevalence of dr to be 18 % . similar to global prevalence differences the prevalence of dr reported in studies from the middle east also shows varied figures : united arab emirates ( uae ) ( 19 % ) , kuwait ( 812 % ) , oman ( 42.4 % ) , egypt ( 42 % ) , and jordan ( 64 % ) . the studies from different regions of saudi arabia also show variable prevalence : al - hassa ( 30 % ) , madinah ( 36.8 % ) , aseer region ( 11.3 % ) , riyadh ( 31 % ) , and taif ( 36.1 % ) . the risk factors associated with this complication are also not uniform in all the studies from different geographical regions . the risk factors and epidemiological determinants mostly documented in various studies are age , gender , obesity , duration of disease , presence of hypertension , dyslipidemia , uncontrolled diabetes , and geographical area . considering the variability of the prevalence of dr in different geographical regions andit is importance as a complication due to the fact that it not only results in serious consequences , it is a key indicator of systemic diabetic microvascular complications . it is , therefore , considered as a sentinel indicator of the impact of diabetes . this study has the principal aim of describing the most recent prevalence of dr and the associated risk factors in the type 2 diabetic patients attending the diabetes center at abha , ksa for follow - up . the objective of the present study was to assess the proportion and grades of retinopathy and its risk factors in diabetes type 2 patients . the diagnosed diabetic patients are referred to this center from different hospitals and primary health care centers ( phccs ) in this region . the sample size for this studywas calculated according to swinscow , as 350 with the estimated prevalence of dr = 35.24 ( average of dr prevalence reported from different geographical regions of saudi arabia ) . to compensate for the missing patientsa total of 10,576 type 2 diabetic patients were registered in this center from january 2008 to december 2013 . every 26 patient 's medical record was selected , and the patients were then contacted for their permission and to provide the relevant data in the questionnaire . the last medical investigation results shown in the records were noted in the checklist . to maintain confidentiality , data were collected anonymously with the approval of the research ethical committee of the college of medicine , king khalid university . the demographic parameters were age , gender , occupation , and family history of diabetes . clinical parameters noted were : duration of diabetes , age at onset of diabetes , control of blood sugar ( hemoglobin a1c [ hba1c ] 7 % was considered as controlled , 7 - 9 % as uncontrolled and 9 % poorly controlled ) , use of anti - diabetic drugs , dyslipidemia , obesity ( classified as overweight body mass index [ bmi ] 25.029.9 kg / m , obese 30.039.9 kg / m and morbidly obese 40.0 kg / m ) , blood pressure ( grouped as normotensive and hypertensive receiving antihypertensive drugs ) . complications of diabetes included ischemic heart disease , peripheral vascular disease , cerebrovascular accident , cataract , neuropathies ( diagnosed on clinical findings ) , nephropathy ( presence of microalbuminuria / gross albuminuria or high creatinine level ) . the diagnosis and grading of dr were done by slit lamp ( with a volk 90 d lens ) examination and colored fundus photographs using a topcon trc - nw6 nonmydriatic fundus camera by a trained ophthalmologist in the diabetic clinic and findings were recorded in patients ' files . retinopathy was classified into npdr and pdr , npdr was further subdivided into mild ( microaneurysms confined mainly to the area temporal to the fovea ) , moderate ( vascular changes seen in one to two quadrants of the retina ) , and severe ( vascular changes seen in more than two quadrants ) . the statistical package for social studies ( spss ) ( spss version 17.0 . in : cary nc , editor . descriptive statistics ( number , the percentage for categorical variables , mean , standard deviation [ sd ] , and range for continuous variables ) and chi - square tests ( ) was used to test for the association . odds ratio ( or ) with 95 % confidence interval ( 95 % ci ) were generated to quantify relationships with each risk factor . their ages ranged from 20 to 90 years , with a mean sd of 54.6 ( 12.3 ) years and a median of 54.0 years . the mean age of male and female diabetic patients were 54.93 years and 54.25 years . the mean age of patients with dr was significantly higher ( p 0.001 ) in comparison to patients without dr ( 57.3 vs. 53.1 years ) . the mean age of onset for dm was 43.91 years with dr while it was 46.30 years for diabetics ( p = 0.03 ) . a significant difference was observed in the mean duration of diabetes ( 13.47.9 years vs. 6.86.7 respectively , p 0.001 ) between patients with dr and diabetics without retinopathy [ table 1 ] . baseline characteristics of participants with and without diabetic retinopathy the overall prevalence of dr was 146 ( 36.4 % ) . mild npdr was in 57.5 % of the patients , moderate npdr in 19.9 % and severe npdr in 11.0 % while 11.6 % of diabetic patients had pdr . analysis of baseline characteristics and different risk factors with different grades of retinopathy showed a significant difference in mean duration among the four grades of retinopathy ; ( p = 0.001 ) . post - hoc test revealed that the duration of dm was significantly different for pdr ( p = 0.003 ) in comparison to npdr . similarly , the total mean cholesterol was different among the four grades ( p = 0.019 ) . this difference was found to be with the severe grade of npdr ( post - hoc test ) however , no significant difference was observed in the levels of high - density , low - density lipoprotein and other risk factors ( data not shown ) . grades of retinopathy and association with maculopathy table 3 presents the potential risk factors of dr . in univariable analysis , the rate of retinopathy was significantly associated with older age group , younger age at onset , longer duration of disease , poorly controlled blood sugar , the presence of hypertension ( receiving drug treatment ) , insulin use , and the presence of multiple complications . gender , higher bmi and dyslipidemia including total cholesterol , high - density lipoproteins ( hdl ) , low - density lipoproteins ( ldl ) levels and smoking did not appear as significant risk factors . unadjusted or and 95 % ci for risk factors of diabetic retinopathy in multivariable logistic regression analysis [ table 4 ] , longer duration of diabetes , younger age of onset and the use of insulin appeared as the strongest predictors of dr . odds of having retinopathy were higher among patients who had developed diabetes at a younger age ( 45 years ) compared with patients who had developed diabetes aged more than 45 years ( adjusted or [ aor ] = 0.44 , 95 % ; ci : 0.21 , 0.90 ) . patients with a lengthy duration of diabetes ( 5 years or more ) were more than twice as likely to develop retinopathy than the patients with shorter duration of diabetes ( aor = 2.48 , 95 % ; ci : 1.254.94 ) . the use of insulin with or without oral hypoglycemic drugs for the treatment of diabetes was almost 3 times likely to result in retinopathy . logistic regression analysis results - aor and 95 % ci for factors that might be associated with the dr in abha , saudi arabiaabnormal glucose metabolism has reached epidemic proportions in the kingdom , with the prevalence of diabetes at 23.7 % . this has led to a considerable increase in the burden of diabetic complications including dr , which appears to be highly prevalent in the general adult saudi population . the overall prevalence of dr in our study was 36.4 % , which is nearly the same as the global documented estimated prevalence of 34.6 % in individuals with diabetes . it is also close to what was found in taiwan 35.0 % , southern india and the reports from studies in different regions of kingdom of saudi arabia : al - hassa 30 % , madinah 36.8 % , taif 36.1 % , and riyadh 31 % our result shows a lower prevalence of dr than what is reported in the uk 50 % , usa 40.3 % , oman 42.4 % , egypt 42 % , and jordan 64 % . the prevalence of dr in our study is higher than those documented in many other studies ; 21.9 % in australia , 26.11 % in spain , 19 % in uae , 812 % in two different studies in kuwait and 18 % in india . the difference of prevalence could be explained by the fact that most of these studies were population based and also that different tools of measurement were used . the prevalence of dr reported by al - khaldi from aseer region was 11.3 % , which is much lower than the results of our study in the same region . the variation could be due to the difference in study location and difference in the method of diagnosis . their study was conducted in a single phcc while our study was conducted at a diabetic clinic to which all patients from the phccs in the region are referred for annual screening , their diagnosis of retinopathy was based on fundoscopic examination , while in our study the diagnosis was made by colored photographs and slit lamp examination as it was the standard technique used in other studies . regarding the grades of retinopathy in our study , the proportion of mild grade of retinopathy is higher than that reported from oman and madina ( ksa ) but our finding is in agreement with that documented from hassa ( ksa ) . the present study showed a lower prevalence of pdr than that of madina ( ksa ) but higher than that reported from uae and oman , and similar to the study in hassa ( ksa ) . our study is in agreement with a review article which indicated that in patients with dr , severe vision impairment was not as common as mild vision impairment . the results of our study indicate that retinopathy increases with younger age at onset of diabetes and showed a significant association between dr and duration of diabetes , which is consistent with most of the previous studies . a study from sweden documents that prevalence of dr reached 100 % after 30 years of diabetes . our study found no significant gender difference in the development of dr , which is in accord with multiple studies mostly from the middle east and saudi arabia but it is in contrast to a study from sweden , which documents higher rates for women than men ; and studies from madina , india , and uae where dr was observed to be more prevalent in male diabetics . many studies on dr have documented the close association of chronic hyperglycemia ( with high hba1c ) and the development of the condition . however , a longitudinal study by aiello et al . reported that the prevalence of dr in long - standing diabetes is not dependent on the control of the disease . similarly , the degree of glycemic control did not show any significant association with dr in the study sample in madina ( ksa ) and from uae . our finding showed significant association in univariable analysis but failed to reveal the same in multiple logistic regression . hypertension has been documented as a risk factor in studies from jordan , oman , and also by a longitudinal uk prospective diabetes study group . report from uae reveals that dr is marginally significantly associated with hypertension . while in contrast , many studies including those from hassa ( ksa ) , riyadh ( ksa ) and from south india were not able to find any significant role of hypertension in the development of dr . in our study , the univarent analysis showed hypertension as a risk factor for dr , but this was not significant after adjusting for confounders . bmi and smoking did not appear as significant risk factors as reported by the studies in uae and tehran ; the latter finding is in contrast to a report from madina and south india that documented smoking to be associated with an increased prospect of dr . similar to van leiden 's study and the study in riyadh , the present study found that high total cholesterol , abnormal ldl , and hdl levels did not have a positive association with the development of dr , but contrasting results were observed in studies in hassa ( ksa ) jordan and oman . in our study , the total cholesterol level was significantly higher in the severe grade of dr , which may indicate that it could be a risk of the progression of dr to severe retinopathy , a finding that emphasizes the importance of good lipid control as a preventive measure for the progression of retinopathy . the univariable analysis revealed that the age of the patient , the number of other complications and presence of neuropathy and nephropathy were significant risks for dr , but these were not supported by multiple regression analysis . this finding is consistent with the study in oman in which similarly aged patients , poor control of diabetes ( with hba1c 9 ) , high systolic blood pressure and complications were documented as insignificant after multiple regression analysis . in the present study study , the strongest determinants for the development of dr were younger age at onset , longer duration of diabetes and the use of insulin , which may be due to the fact that most of the type 2 dm patients with longer duration ultimately end up using insulin . all these three risk factors have been documented in most of the studies related to dr . the limitation of our study is that a predictive inference can not be drawn from our observational data since a more extensive study is required . despite this limitation , our study provides a picture of the prevailing situation in this region , and the data is sufficient to exhibit the enormity of this complication in diabetic patients and emphasize the main priorities of attention in regional programmes for screening retinopathy in all patients with diabetes type 2 at an early stage in the phcc with recommended tools ( presently not available in the phcc ) and prevent its progression . our findings clearly demonstrate that retinopathy is a common complication of diabetes in diabetic patients at abha , aseer region and that the situation is no different from other regions of saudi arabia . this is in contrast to a previous study from the same region that documented the prevalence as much lower in this region . we support the idea that the retina of a diabetic patient provides a summary measure of lifetime exposure to the effects of hyperglycemia , and which emphasizes the fact that screening for dr at the initial stage of diabetes may prevent disability from blindness caused by dr . small investments in prevention , awareness and care can dramatically improve the quality of life of patients with long - standing diabetes .\noutput:\n" }, { "from": "agent", "value": "objectives : to assess the proportion and grades of retinopathy and its risk factors in diabetes type 2 patients.materials and methods : this was a cross - sectional study of 401 type 2 diabetic patients . a questionnaire and checklist were used to collect the data . retinopathy was diagnosed and graded by fundus photographs and slit lamp examination . the duration of diabetes , age of patients , age at onset of diabetes , body mass index , hemoglobin a1c level , blood pressure , and complications were noted.results : the mean age of male and female patients was 54.93 and 54.25 years ; 57.6 % were males . the mean age of onset and mean duration of diabetes were 43.91 and 13.4 years , respectively . the proportion of retinopathy was 36.4 % . grades of retinopathy were : mild 57.5 % , moderate 19.9 % , severe nonproliferative 11 % , and proliferative retinopathy 11.6 % ; 7.2 % of patients had maculopathy . retinopathy was significantly associated with older age , younger age at onset , longer duration of disease , poorly controlled blood sugar , hypertension , insulin use ; the presence of neuropathy and nephropathy appeared as a significant risk . younger age at onset , longer duration , and insulin use appeared as the strongest predictors for diabetic retinopathy.conclusions : more than a third ( 36.4 % ) of the diabetic patients attending a diabetic center had retinopathy . the control of the risk factors may reduce both prevalence and consequences of retinopathy ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: we are born in organizations , educated by organizations , and most of us spend much of our lives working for organizations . we spend much of our leisure time paying , playing , and praying in organizations . most of us will die in an organization , and when the time comes for burial , the largest organization of all the state must grant official permission . we are born in organizations , educated by organizations , and most of us spend much of our lives working for organizations . we spend much of our leisure time paying , playing , and praying in organizations . most of us will die in an organization , and when the time comes for burial , the largest organization of all the state must grant official permission . in many societies , thus , bureaucracy can be viewed as the predictable extension of social organizations within the societies . an organization is defined as a social system of consciously coordinated activities or forces of two or more persons explicitly created to achieve specific ends . not surprisingly , leading social scientists hold that 3 interrelated social processes , namely , urbanization , industrialization , and bureaucratization , are the most influential factors that have transformed american community life over the generations . indeed , immigration and globalization are contributing factors for such transformations . the institutional complex of major concern to us is health care that exemplifies the structures and functions of the bureaucracy . the structural aspect seeks to explain a feature of society as the predictable consequence of certain structural characteristics of society . the functional aspect , on the other hand , seeks to explain a feature of society in terms of the beneficial consequences it has for the larger social system . it is of interest to note that institutions are crescive in nature and have a strain of consistency , which means that institutions build over time and that they are all interrelated . for example , the institutions such as the family and health care are interrelated because the family is the unit of health because it is the unit of living . in brief , institutions are socially approved patterns of behavior . a medical industrial organization as an institution , therefore , can not be fully understood unless it is examined in itself as well as in relation to other institutions such as the family , social welfare , government , education , religion , and other organizational structures in the society . a society , from one perspective , can be viewed as falling somewhere between 2 polar pure types , ideal types , or mental constructs as either gemeinschaft ( g1 ) or gesellschaft ( g2 ) in orientation , or perhaps rural and urban ( fig 1 ) . the society - culture - personality ( scp ) model from a macroscopic perspective represents the global village , a nation , a community , an institution , or a group . there are a multitude of subsystems , comparable to subsystems in the human body , operating in any of these aggregates . bureaucracy , therefore , is the typical social and cultural milieu in which health care workers carry out their individual and common tasks in a society . thus , a health care professional does not simply work in a clinic , a hospital , or a department of a medical industrial complex ; but he or she works in a bureaucratic setting of a health care institution within a particular community of a specified society located either in a g1 or a g2 type of environment ( fig 1 ) . therefore , the purpose of this article is to present select concepts and theories of bureaucratic structures and functions so that chiropractic physicians and other health care professionals can use them in their respective practices . the scp model can be applied as an organizational instrument for assisting chiropractors in the diagnosis and treatment of their patients irrespective of locality . society - culture - personality forms an interlocking social system ( fig 1 ) . by definition , a social system is a pattern relationship of roles ; and as these roles become highly complex structures , they are called institutions ( i ) , that is , ways of taking care of the basic human needs of a society . as mentioned previously , a society , from one perspective , can be viewed as falling somewhere between 2 polarpure types , ideal types , or mental constructs , such as g1 and g2 in orientation . bureaucracy is a pyramiding of unit organizations of the social system in any complex society . bureaucracy contains several subsystems within the larger social system : the authority system , the power system , the status system , the organizational system , the security system , and the role system ( fig 1 ) . these are as follows ( fig 1 ) : freedom the employee is bound by contract to perform various functions during the day 's work , but is free to do what he / she wants after hours . hierarchythe structure of a bureaucracy is in the form of a hierarchy , with each member answerable to a higher authority or authorities . the members have defined spheres of competence and authority , and the duties and obligations of each group are specifically stated . positions are filled by a contract , and both the organization and the individual are bound by its terms . the procedure in a bureaucratic setting is highly regularized ; communication takes place through channels and according to established forms . disciplinethe members are supposed to carry out the work of their office , keep the secrets of the organization , and maintain an in - group feeling against outsiders . hierarchical form of social organization rationally geared to the achievement of precisely specified objectives by means of a division of labor based on demonstrated competence . as bureaucracy has come to define and to regulate important functions of other institutions within this society , health care has increasingly adopted such bureaucratic characteristics as positions and official record keeping . indeed , the appearance of bureaucratic administration in almost every sphere of life has not left the health care professions untouched . bureaucracy influences relations between chiropractic physicians and patients , between physicians and nurses , and other health - related professionals , permeating and influencing the whole structure of health services and the community as a whole . the structural aspects of bureaucracy in relation to the health care institution ( fig 1 ) can be analyzed from the viewpoint of typologies . alvin gouldner suggested that 3 patterns of bureaucracy are clearly distinguishable : mock , representative , and punishment centered . in mock bureaucracy , the informal organization of personnel circumvents the formal organization ; nonenforcement and nonobedience of rules are informally arranged by superordinates and subordinates with little tension or conflict ensuring . representative bureaucracy is marked by the endorsement and support of the rules by both groups ; tension and conflict are relatively absent . punishment - centered bureaucracy involves insistence on enforcement of the rules by one group and evasion of rules by the other ( either pattern can be adopted by the superordinate or subordinate groups ) ; consequently , tension and conflict are common in this type of work situation . stable patterns of behavior based on structural roles and specialized tasks are apparent . as a general rule , any organization large enough inhibits face - to - face relationships in a bureaucracy . when large numbers of people are added to an organization so that its goals may be accomplished , a hierarchy of authority emerges as a line - ranking of positions from top to bottom . each considers his or her function indispensable to the organization and expects his or her point of view to take precedence , especially in allocating funds for example in a medical industrial complex . the concepts of individual initiative , team work , along with authority are additional structural and functional factors that need to be taken into consideration within the medical industrial organization . a. earl swift asserts that all organizational behavior is ultimately founded upon human nature . human nature , according to swift , allows for 3 distinct decision - making systems , namely , individualism , collaboration , along with authority and power . individual initiative , also known as liberty , is a crucial aspect for an effective and successful organization . collaboration , commonly referred to as teamwork , is another significant factor in organizational relationships . teamwork does not allow any individual to manipulate and to dominate other employees because the group provides a check against individuals with bad motives , denying them the power to tyrannically dominate or exploit other people . when group decisions based upon consensus are established , a democratic approach to organizational relationships is fostered . authority and power are additional factors that should be taken into consideration if an organization is to continue to fulfill its mission and objectives . the board of trustees , as the chief policy - making group of a medical industrial organization , is there to enforce the mission and culture to ensure a proper balance of individualism , community , and authority . by establishing homeostasis , it allows for a diverse workforce to work together , as a professional community , to achieve the goals of the organization . under most circumstances , however , organizations work most effectively when all three types of decision making are balanced relatively equally , and it is the authoritarian aspect of the organization that controls this balance . given the above statements on the health care enterprise , the structural aspects of bureaucracy ( fig 1 ) are indeed linked to their functional dimensions as they relate to the health care institution ( fig 2 ) . thus , the structure and function of bureaucratic organizations are essential ingredients of analysis to bring about optimum levels of quality , affordability , availability , accessibility , and continuity in a health care institution irrespective of location whether g1 ( rural ) or g2 ( urban ) in orientation ( fig 3 ) . the functional aspect of bureaucracy in relation to the health care institution of a community or a society is closely linked to the interactional changes within a health care organizational setting such as a clinic or a hospital . furthermore , functional changes within the health care bureaucracy are affected when transactional and transformational changes are initiated in the system ( fig 2 ) . before scpthat catalyst is social meaningful interaction ( smi ) ( fig 2 ) . as a person internalizes the culture of a society into his or her own personality , he or she develops a personality that is at once unique and distinctive and more or less adjusted to the demands of a society . in the development of smi , the actor enters society and establishes rapport . after this has been accomplished , social contact , the simplest unit of relationship between 2 or more persons , is possible . communication , which is involved in social contact , is the basis of smi . in a sense , it is smi . social contact plus communication results in social interaction , which is a sustained , reciprocal , purposeful , meaningful , and ( within limits ) predictable series of relationships between 2 or more socialized human beings . in the smi process , each actor takes the other ( s ) into account , is aware of the other ( s ) , and appraises the other ( s ) . for example , interaction can take place between 2 individuals , between the individual and the group , between the individual and culture , and between the individual and mass communication . the smi is linked to socialization , a learning process in a social environment where the value - attitude system of a culture is internalized . it is important that chiropractic and other health care professionals recognize the implication of smi in terms of both quality and quantity to gain an understanding of the health care enterprise . for example , a chiropractic physician and chiropractic student should recognize the fact that patients , although presently in seeming isolation , are family members , and their reactions and behaviors demonstrate their family 's influence on their level of understanding and their attitude about the meaning and purpose of health care . the family , conversely , socializes the patient into a system of health care expectations that has been developed by the bureaucratic model . in the socialization process , other agencies , peer groups , and community pressure groups influence the patients view concerning health and illness . as previously stated , health care as an institution , therefore , can not be fully understood unless it is examined in itself as well as in relation to other institutions such as the family , social welfare , government , education , religion , and other organizational structures in the society . every social institution has some sort of structure or framework that helps to put concepts or purposes of the institution into the world of action so that it can serve the interest of society and the members who compose it . the family as a social institution has its framework or structure within which it can carry out the purposes for which it exists . the first is the family of origin ( orientation ) in which our earliest experiences take place . the second is the family of marriage ( or procreation ) in which we may enact the role of parent . it is within the network of familial relationships that we develop our attitudes and values toward health and illness . attitudes are tendencies to feel and act in certain ways . values , on the other hand , are measures of desirability . the family is the most universal of all human institutions . it varies widely in structure from the consanguineal type ( ie , extended kin groups that include a wide variety of related persons ) to conjugal families consisting simply of an adult pair ( male and female ) and their children . the conjugal family acts as a source of refuge in mass society a place where the individual may engage in genuinely personal relationships in a world that is largely impersonal . in the past , many authors have given us a description of different types of families . sorokin , for example , presents 3 types : the compulsive , the contractual , and the familistic . in the compulsive family , the bond holding members together is not love but force ; and the relationship is based on exploitation , cruelty , and deprivation . the contractual type brings profit and advancement to the participants but is devoid of love and hatred . the familistic type is based on mutual love between the spouses ; and it is characterized by devotion , sacrifice , solidarity , sharing , permanence , and stability . sorokin feels that the 3 types of families have been present regardless of one 's society but have changed in proportion with time . the contractual family , however , is the largest one in today 's western world . the type of family a person comes from can help us understand the behaviors of the patient and members of the family toward the sick person . for example , in severe coronary cases , increasing demands are made on the family to adjust their customary routines to the patient 's needs . one can expect , therefore , that if the family type was close ( familistic ) in which each member was concerned about the others before the illness , then there could be a greater willingness for members of the family to adjust their roles to help the sick person . on the contrary , if the family type was contractual and / or compulsive , then the family members would be less willing to make the sacrifices to aid the sick individual . structure within the institution of the family plays an essential role in the way stress is handled during a sudden crisis . the outcome of such a crisis will depend upon the type of familial relationship before the episode . for exampleresearch done at the family medicine unit at harvard medical school have demonstrated rather clearly that : common crises such as death of grandparents , change of residence , a loss of a father 's job , and a child 's being subjected to unusual pressure , occur four times more frequently in the two week period prior to the appearance of streptococcal infection than in the 2 weeks afterward . common crises such as death of grandparents , change of residence , a loss of a father 's job , and a child 's being subjected to unusual pressure , occur four times more frequently in the two week period prior to the appearance of streptococcal infection than in the 2 weeks afterward . the same studies have shown that : age , intimacy of contact , and family organization influenced the susceptibility to streptococcal infection . children of school age were most susceptible , and a spread of infection to other family members sharing the same bedroom was likely . age , intimacy of contact , and family organization influenced the susceptibility to streptococcal infection . children of school age were most susceptible , and a spread of infection to other family members sharing the same bedroom was likely . additional research demonstrates that streptococcal and staphylococcal infections are family disorders , and successful management responses requires consideration of the family group . another kind of crisis in which the type of family plays an important role is the biological inheritance factor . if one learns that he or she is a cause of disease that affects children , or learns that he or she is a recipient of a disease of a familiar nature , this knowledge can bring about complicated emotional problems in family interaction . for example , the birth of a deformed infant may be accompanied by a guilt reaction on the part of both parents . one can speculate about the emotional disturbances of the family in the specific case of muscular dystrophy that is carried by the female and attacks the male . the need of a parent to deny knowledge about such discomforting facts is understandable ; however , there is a tendency for the parent to believe that the facts must be disproved and to continually seek out advice to get different answers . at this stage of the crisis , there is a great need to see the family as a unit of treatment . whether or not the family is viewed as such will depend partially upon the type of familial relationships before the episode . another important role of the family is the patient - physician relationship concerning the care at the end of life . although many health care professionals are often uncomfortable discussing death and dying with their patients and families and feel that such discussion would be too difficult emotionally and thus ineffective for the patient and family , a recent study has shown that the reverse is true . almost 90 % of caregivers ( ie , the family ) feel that such collaboration was not stressful , whereas 20 % found it beneficial . . it can be the equivalent of a full - time job for 20 % of caregivers and result in further financial burden . the average annual costs for caregiving in the united states can range from $ 3 billion to $ 6 billion . these stressors often lead families to seek long - term care ( ltc ) placement . caregivers who are older ( 65 years of age ) and who feel a greater sense of burden are more likely to have their loved one in an ltc facility . although many caregivers experience symptoms of anxiety and depression ( 15 % - 20 % ) before placement in an ltc facility , these symptoms did not change after placement , which is particularly true for spouses . two recent studies found that caregivers often experience a sense of relief after the passing of a loved one when it was preceded by ongoing suffering and significant burden to the caregiver . one study suggests that , in addition to the known risk of psychiatric morbidity of caregiving , there is a 60 % higher risk of caregiver 's death when compared with noncaregiver 's controls . in recognizing the burden of caregiving , rabow et al recently proposed 5 areas of opportunities for caregivers to be of service to the familythese are ( a ) promote communication , ( b ) promote advanced care planning and decision making , ( c ) support home care , ( d ) demonstrate empathy for patients and their family , and ( e ) participate in family grief and bereavement . in providing compassion and empathy , health care , an institution within american society , is like other institutions whereby structural subsystems and functional components are intertwined ( fig 3 ) . using a medical industrial complex , for example , one could identify certain organizational and functional goals such as education , research , and health care services . the organizational structure and functional components of the medical industrial bureaucracy are composed of a hierarchy of offices and positions . the board of trustees is the chief policy - making group within the medical industrial complex . it is made up partially of community representatives who safeguard the interests of the community within the organization . every department and service within the medical industrial complex have a hierarchy . within the hierarchy , the title and office that one holds confer status upon one , which varies depending upon the position in the organization . from the functional perspective , a professional person in a health care organization is exposed to the laws of authority , professional and bureaucratic ; both are essential for the functioning of the intricate health care enterprise . professional authority rightly has the freedom to act on the basis of professional skill and judgment on behalf of the individual patient in the particular situation regardless of bureaucratic rules . skipper and mumford asserted that the professional person derives his or her basic authority from outside the bureaucracy . for example , the health care professionals come to work in a hospital ( or a clinic ) with their own professional license to practice . on the other hand , the bureaucratic authority of the organization rightly demands regularity and conformity to regulations that make for dependability and predictability within the organizational network . thus , the medical staff usually defines the line in its activities , whereas the management authority is often restricted to matters of providing the means by which the doctor 's orders may be successfully carried out . from the viewpoints of the functions of bureaucracy in the health care institution , it is important to note that max weber 's approach is essentially formal , outlining the blueprint character of bureaucracythe rule of rules rather than of men , the role of hierarchy , specialization , and experience , the development of the office as a career . the functions of bureaucracy ( fig 2 ) are also linked to 5 factors that are directly related to the positive outcomes in any health care organization . these variables are quality , availability , accessibility , affordability , and continuity . in the functioning of the health care bureaucracy , the factors noted above may bring about sociopsychological pressures to the professionals within the organization . the acronymsara ( surprise - anxiety - rejection - acceptance ) is most relevant in analyzing the functional changes of personality within the system . thus , it may be hypothesized that the interaction between the various units in a health care bureaucratic system will either be associative , tending toward a mutual sharing of responsibility , power , and authority , or disassociative , tending toward the tension and conflict situations ( fig 2 ) . if one takes the variable of power into consideration , certain associative and dissassociative patterns are possible . one of the significant patterns today is the relationship between and among health care professionals . as the recipients of the chiropractic physician 's orders for his or her patterns , the nurse is obligated to carry out these orders in a professional competent manner ; but at the same time , he or she is a hired employee of the hospital , clinic , or doctor 's office and consequently subject to all the rules and regulations of the administrative organization . * furthermore , the demands of patient care , especially those of an emergency nature , can not be accomplished within the framework of administrative rules . thus , the nurse can be in a conflict situation between the expectations of the chiropractic physician that his or her orders be carried out and the expectations of the administration that administrative procedures will be complied with . the dysfunctions of bureaucracy were pointed out by men like veblen , dewey , and warnotte who documented concepts of trained incapacity , occupational psychosis , and professional deformation respectively . refers to that condition in which one 's abilities function as inadequacies or blind spots , preventing one from adjusting correctly to the changed situation . thus , skills and training that have been successfully applied in the past may under changed conditions result in inappropriate responses . dewey 's concept of occupational psychosis is founded upon some observations from the humdrum activities of life in which people develop certain preferences , antipathies , discriminations , and points of interest . by psychosis , dewey means a profound character of the mind . these psychoses originate from demands put upon the individual by the organizing of his occupation role . however , there are forces at work that tend to lessen the severity of the potential problems resulting from the social structure of a medical industrial complex . coe asserts that : one of these is the ideology of service , an historical legacy of the middle ages , expressed in modern terms as commitment to a job . a second force is the development of informal groups within the formal organization which permit certain activities to be accomplished regardless of the potential blocks of the social structure . one of these is the ideology of service , an historical legacy of the middle ages , expressed in modern terms as commitment to a job . a second force is the development of informal groups within the formal organization which permit certain activities to be accomplished regardless of the potential blocks of the social structure . insofar as the chiropractic physician and nurse are concerned , the relationship shifts from time to time and from place to place . it varies according to the generation each belongs to , to the size of the community and the hospital setting , and to the field of specialization in nursing and medicine . the getzels - guba model gives us further insight into the structural and functional aspects of organizational bureaucracy . the nomothetic or normative dimension of the model is composed of institutions , roles , and expectations . the idiographic or personal dimension of the model is characterized by the individual , personality , and need - disposition . social behavior is the result of the interactions between 2 sets of motives : the nomothetic / normative dimension and the idiographic / personal dimension . the getzels - guba model asserts that , within an institution , an individual has a purposeful role and is required to meet certain expectations as a member of the organization . need - disposition and role expectation can be viewed as structural elements in patient / chiropractic physician rapport and in professional and ethical functions . if there is a lack of homeostasis between needs / structures and roles / functions within an organization , it may produce stress , strain , and anxiety that may negatively affect professional relationships and the continuity of health care . according to w. edwards deming 's out of the crisis , principles such as efficiency and effectiveness need to be aligned so that the members of the health care organization take part in shared decision making . if a health care organization lacks these principles , it may lead to identity and role confusion at work ( in a hospital or a clinic ) , creating additional stress and strain that may affect the proper functioning of the organization . the patient , who is the customer in the health care organization , can be affected positively or negatively if such issues within the health care organization remain unsolved . if stress , strain , and anxiety are created from occupational relationships ( and remain unresolved ) , this could result in what gregory bateson et al refer to as the double bind theory . given this theory , the recipient of double bind is given contradictory messages , causing confusion in self - concept that may lead to an element of uncertainty within the personality of the individual . for example , a medical organization may instill in their employees the importance of teamwork and shared decision making ; but when employees actually voices their concern , they are greeted with resistance and disapproval . this element of uncertainty along with identity and role confusion can lead to what emile durkheim called anomie ( commonly known as a lack of norms ) . this type of behavior within a medical industrial organization can increase the level of stress and strain , leading to neurosis ; and if it remains untreated , it can result in psychosis that affects the functioning within the organizational system . society - culture - personality forms an interlocking social system ( fig 1 ) . by definition , a social system is a pattern relationship of roles ; and as these roles become highly complex structures , they are called institutions ( i ) , that is , ways of taking care of the basic human needs of a society . as mentioned previously , a society , from one perspective , can be viewed as falling somewhere between 2 polarpure types , ideal types , or mental constructs , such as g1 and g2 in orientation . bureaucracy is a pyramiding of unit organizations of the social system in any complex society . bureaucracy contains several subsystems within the larger social system : the authority system , the power system , the status system , the organizational system , the security system , and the role system ( fig 1 ) . these are as follows ( fig 1 ) : freedom the employee is bound by contract to perform various functions during the day 's work , but is free to do what he / she wants after hours . hierarchythe structure of a bureaucracy is in the form of a hierarchy , with each member answerable to a higher authority or authorities . the members have defined spheres of competence and authority , and the duties and obligations of each group are specifically stated . positions are filled by a contract , and both the organization and the individual are bound by its terms . the procedure in a bureaucratic setting is highly regularized ; communication takes place through channels and according to established forms . disciplinethe members are supposed to carry out the work of their office , keep the secrets of the organization , and maintain an in - group feeling against outsiders . hierarchical form of social organization rationally geared to the achievement of precisely specified objectives by means of a division of labor based on demonstrated competence . as bureaucracy has come to define and to regulate important functions of other institutions within this society , health care has increasingly adopted such bureaucratic characteristics as positions and official record keeping . indeed , the appearance of bureaucratic administration in almost every sphere of life has not left the health care professions untouched . bureaucracy influences relations between chiropractic physicians and patients , between physicians and nurses , and other health - related professionals , permeating and influencing the whole structure of health services and the community as a whole . the structural aspects of bureaucracy in relation to the health care institution ( fig 1 ) can be analyzed from the viewpoint of typologies . alvin gouldner suggested that 3 patterns of bureaucracy are clearly distinguishable : mock , representative , and punishment centered . in mock bureaucracy , the informal organization of personnel circumvents the formal organization ; nonenforcement and nonobedience of rules are informally arranged by superordinates and subordinates with little tension or conflict ensuring . representative bureaucracy is marked by the endorsement and support of the rules by both groups ; tension and conflict are relatively absent . punishment - centered bureaucracy involves insistence on enforcement of the rules by one group and evasion of rules by the other ( either pattern can be adopted by the superordinate or subordinate groups ) ; consequently , tension and conflict are common in this type of work situation . stable patterns of behavior based on structural roles and specialized tasks are apparent . as a general rule , any organization large enough inhibits face - to - face relationships in a bureaucracy . when large numbers of people are added to an organization so that its goals may be accomplished , a hierarchy of authority emerges as a line - ranking of positions from top to bottom . each considers his or her function indispensable to the organization and expects his or her point of view to take precedence , especially in allocating funds for example in a medical industrial complex . the concepts of individual initiative , team work , along with authority are additional structural and functional factors that need to be taken into consideration within the medical industrial organization . a. earl swift asserts that all organizational behavior is ultimately founded upon human nature . human nature , according to swift , allows for 3 distinct decision - making systems , namely , individualism , collaboration , along with authority and power . individual initiative , also known as liberty , is a crucial aspect for an effective and successful organization . collaboration , commonly referred to as teamwork , is another significant factor in organizational relationships . teamwork does not allow any individual to manipulate and to dominate other employees because the group provides a check against individuals with bad motives , denying them the power to tyrannically dominate or exploit other people . when group decisions based upon consensus are established , a democratic approach to organizational relationships is fostered . authority and power are additional factors that should be taken into consideration if an organization is to continue to fulfill its mission and objectives . the board of trustees , as the chief policy - making group of a medical industrial organization , is there to enforce the mission and culture to ensure a proper balance of individualism , community , and authority . by establishing homeostasis , it allows for a diverse workforce to work together , as a professional community , to achieve the goals of the organization . under most circumstances , however , organizations work most effectively when all three types of decision making are balanced relatively equally , and it is the authoritarian aspect of the organization that controls this balance . given the above statements on the health care enterprise , the structural aspects of bureaucracy ( fig 1 ) are indeed linked to their functional dimensions as they relate to the health care institution ( fig 2 ) . thus , the structure and function of bureaucratic organizations are essential ingredients of analysis to bring about optimum levels of quality , affordability , availability , accessibility , and continuity in a health care institution irrespective of location whether g1 ( rural ) or g2 ( urban ) in orientation ( fig 3 ) . the functional aspect of bureaucracy in relation to the health care institution of a community or a society is closely linked to the interactional changes within a health care organizational setting such as a clinic or a hospital . furthermore , functional changes within the health care bureaucracy are affected when transactional and transformational changes are initiated in the system ( fig 2 ) . before scpthat catalyst is social meaningful interaction ( smi ) ( fig 2 ) . as a person internalizes the culture of a society into his or her own personality , he or she develops a personality that is at once unique and distinctive and more or less adjusted to the demands of a society . in the development of smi , the actor enters society and establishes rapport . after this has been accomplished , social contact , the simplest unit of relationship between 2 or more persons , is possible . communication , which is involved in social contact , is the basis of smi . in a sense , it is smi . social contact plus communication results in social interaction , which is a sustained , reciprocal , purposeful , meaningful , and ( within limits ) predictable series of relationships between 2 or more socialized human beings . in the smi process , each actor takes the other ( s ) into account , is aware of the other ( s ) , and appraises the other ( s ) . for example , interaction can take place between 2 individuals , between the individual and the group , between the individual and culture , and between the individual and mass communication . the smi is linked to socialization , a learning process in a social environment where the value - attitude system of a culture is internalized . it is important that chiropractic and other health care professionals recognize the implication of smi in terms of both quality and quantity to gain an understanding of the health care enterprise . for example , a chiropractic physician and chiropractic student should recognize the fact that patients , although presently in seeming isolation , are family members , and their reactions and behaviors demonstrate their family 's influence on their level of understanding and their attitude about the meaning and purpose of health care . the family , conversely , socializes the patient into a system of health care expectations that has been developed by the bureaucratic model . in the socialization process , other agencies , peer groups , and community pressure groups influence the patients view concerning health and illness . as previously stated , health care as an institution , therefore , can not be fully understood unless it is examined in itself as well as in relation to other institutions such as the family , social welfare , government , education , religion , and other organizational structures in the society . every social institution has some sort of structure or framework that helps to put concepts or purposes of the institution into the world of action so that it can serve the interest of society and the members who compose it . the family as a social institution has its framework or structure within which it can carry out the purposes for which it exists . the first is the family of origin ( orientation ) in which our earliest experiences take place . the second is the family of marriage ( or procreation ) in which we may enact the role of parent . it is within the network of familial relationships that we develop our attitudes and values toward health and illness . it varies widely in structure from the consanguineal type ( ie , extended kin groups that include a wide variety of related persons ) to conjugal families consisting simply of an adult pair ( male and female ) and their children . the conjugal family acts as a source of refuge in mass society a place where the individual may engage in genuinely personal relationships in a world that is largely impersonal . in the past , many authors have given us a description of different types of families . sorokin , for example , presents 3 types : the compulsive , the contractual , and the familistic . in the compulsive family , the bond holding members together is not love but force ; and the relationship is based on exploitation , cruelty , and deprivation . the contractual type brings profit and advancement to the participants but is devoid of love and hatred . the familistic type is based on mutual love between the spouses ; and it is characterized by devotion , sacrifice , solidarity , sharing , permanence , and stability . sorokin feels that the 3 types of families have been present regardless of one 's society but have changed in proportion with time . the contractual family , however , is the largest one in today 's western world . the type of family a person comes from can help us understand the behaviors of the patient and members of the family toward the sick person . for example , in severe coronary cases , increasing demands are made on the family to adjust their customary routines to the patient 's needs . one can expect , therefore , that if the family type was close ( familistic ) in which each member was concerned about the others before the illness , then there could be a greater willingness for members of the family to adjust their roles to help the sick person . on the contrary , if the family type was contractual and / or compulsive , then the family members would be less willing to make the sacrifices to aid the sick individual . structure within the institution of the family plays an essential role in the way stress is handled during a sudden crisis . the outcome of such a crisis will depend upon the type of familial relationship before the episode . research done at the family medicine unit at harvard medical school have demonstrated rather clearly that : common crises such as death of grandparents , change of residence , a loss of a father 's job , and a child 's being subjected to unusual pressure , occur four times more frequently in the two week period prior to the appearance of streptococcal infection than in the 2 weeks afterward . common crises such as death of grandparents , change of residence , a loss of a father 's job , and a child 's being subjected to unusual pressure , occur four times more frequently in the two week period prior to the appearance of streptococcal infection than in the 2 weeks afterward . the same studies have shown that : age , intimacy of contact , and family organization influenced the susceptibility to streptococcal infection . children of school age were most susceptible , and a spread of infection to other family members sharing the same bedroom was likely . age , intimacy of contact , and family organization influenced the susceptibility to streptococcal infection . children of school age were most susceptible , and a spread of infection to other family members sharing the same bedroom was likely . additional research demonstrates that streptococcal and staphylococcal infections are family disorders , and successful management responses requires consideration of the family group . another kind of crisis in which the type of family plays an important role is the biological inheritance factor . if one learns that he or she is a cause of disease that affects children , or learns that he or she is a recipient of a disease of a familiar nature , this knowledge can bring about complicated emotional problems in family interaction . for example , the birth of a deformed infant may be accompanied by a guilt reaction on the part of both parents . one can speculate about the emotional disturbances of the family in the specific case of muscular dystrophy that is carried by the female and attacks the male . the need of a parent to deny knowledge about such discomforting facts is understandable ; however , there is a tendency for the parent to believe that the facts must be disproved and to continually seek out advice to get different answers . at this stage of the crisis , there is a great need to see the family as a unit of treatment . whether or not the family is viewed as such will depend partially upon the type of familial relationships before the episode . another important role of the family is the patient - physician relationship concerning the care at the end of life . although many health care professionals are often uncomfortable discussing death and dying with their patients and families and feel that such discussion would be too difficult emotionally and thus ineffective for the patient and family , a recent study has shown that the reverse is true . almost 90 % of caregivers ( ie , the family ) feel that such collaboration was not stressful , whereas 20 % found it beneficial . . it can be the equivalent of a full - time job for 20 % of caregivers and result in further financial burden . the average annual costs for caregiving in the united states can range from $ 3 billion to $ 6 billion . these stressors often lead families to seek long - term care ( ltc ) placement . caregivers who are older ( 65 years of age ) and who feel a greater sense of burden are more likely to have their loved one in an ltc facility . although many caregivers experience symptoms of anxiety and depression ( 15 % - 20 % ) before placement in an ltc facility , these symptoms did not change after placement , which is particularly true for spouses . two recent studies found that caregivers often experience a sense of relief after the passing of a loved one when it was preceded by ongoing suffering and significant burden to the caregiver . one study suggests that , in addition to the known risk of psychiatric morbidity of caregiving , there is a 60 % higher risk of caregiver 's death when compared with noncaregiver 's controls . in recognizing the burden of caregiving , rabow et al recently proposed 5 areas of opportunities for caregivers to be of service to the family . these are ( a ) promote communication , ( b ) promote advanced care planning and decision making , ( c ) support home care , ( d ) demonstrate empathy for patients and their family , and ( e ) participate in family grief and bereavement . in providing compassion and empathy , health care , an institution within american society , is like other institutions whereby structural subsystems and functional components are intertwined ( fig 3 ) . using a medical industrial complex , for example , one could identify certain organizational and functional goals such as education , research , and health care services . the organizational structure and functional components of the medical industrial bureaucracy are composed of a hierarchy of offices and positions . the board of trustees is the chief policy - making group within the medical industrial complex . it is made up partially of community representatives who safeguard the interests of the community within the organization . every department and service within the medical industrial complex have a hierarchy . within the hierarchy , the title and office that one holds confer status upon one , which varies depending upon the position in the organization . from the functional perspective , a professional person in a health care organization is exposed to the laws of authority , professional and bureaucratic ; both are essential for the functioning of the intricate health care enterprise . professional authority rightly has the freedom to act on the basis of professional skill and judgment on behalf of the individual patient in the particular situation regardless of bureaucratic rules . skipper and mumford asserted that the professional person derives his or her basic authority from outside the bureaucracy . for example , the health care professionals come to work in a hospital ( or a clinic ) with their own professional license to practice . on the other hand , the bureaucratic authority of the organization rightly demands regularity and conformity to regulations that make for dependability and predictability within the organizational network . thus , the medical staff usually defines the line in its activities , whereas the management authority is often restricted to matters of providing the means by which the doctor 's orders may be successfully carried out . from the viewpoints of the functions of bureaucracy in the health care institution , it is important to note that max weber 's approach is essentially formal , outlining the blueprint character of bureaucracythe rule of rules rather than of men , the role of hierarchy , specialization , and experience , the development of the office as a career . the functions of bureaucracy ( fig 2 ) are also linked to 5 factors that are directly related to the positive outcomes in any health care organization . these variables are quality , availability , accessibility , affordability , and continuity . in the functioning of the health care bureaucracy , the factors noted above may bring about sociopsychological pressures to the professionals within the organization . the acronymsara ( surprise - anxiety - rejection - acceptance ) is most relevant in analyzing the functional changes of personality within the system . thus , it may be hypothesized that the interaction between the various units in a health care bureaucratic system will either be associative , tending toward a mutual sharing of responsibility , power , and authority , or disassociative , tending toward the tension and conflict situations ( fig 2 ) . if one takes the variable of power into consideration , certain associative and dissassociative patterns are possible . one of the significant patterns today is the relationship between and among health care professionals . as the recipients of the chiropractic physician 's orders for his or her patterns , the nurse is obligated to carry out these orders in a professional competent manner ; but at the same time , he or she is a hired employee of the hospital , clinic , or doctor 's office and consequently subject to all the rules and regulations of the administrative organization . * furthermore , the demands of patient care , especially those of an emergency nature , can not be accomplished within the framework of administrative rules . thus , the nurse can be in a conflict situation between the expectations of the chiropractic physician that his or her orders be carried out and the expectations of the administration that administrative procedures will be complied with . the dysfunctions of bureaucracy were pointed out by men like veblen , dewey , and warnotte who documented concepts of trained incapacity , occupational psychosis , and professional deformation respectively . refers to that condition in which one 's abilities function as inadequacies or blind spots , preventing one from adjusting correctly to the changed situation . thus , skills and training that have been successfully applied in the past may under changed conditions result in inappropriate responses . dewey 's concept of occupational psychosis is founded upon some observations from the humdrum activities of life in which people develop certain preferences , antipathies , discriminations , and points of interest . by psychosis , dewey means a profound character of the mind . these psychoses originate from demands put upon the individual by the organizing of his occupation role . however , there are forces at work that tend to lessen the severity of the potential problems resulting from the social structure of a medical industrial complex . coe asserts that : one of these is the ideology of service , an historical legacy of the middle ages , expressed in modern terms as commitment to a job . a second force is the development of informal groups within the formal organization which permit certain activities to be accomplished regardless of the potential blocks of the social structure . one of these is the ideology of service , an historical legacy of the middle ages , expressed in modern terms as commitment to a job . a second force is the development of informal groups within the formal organization which permit certain activities to be accomplished regardless of the potential blocks of the social structure . insofar as the chiropractic physician and nurse are concerned , the relationship shifts from time to time and from place to place . it varies according to the generation each belongs to , to the size of the community and the hospital setting , and to the field of specialization in nursing and medicine . the getzels - guba model gives us further insight into the structural and functional aspects of organizational bureaucracy . the nomothetic or normative dimension of the model is composed of institutions , roles , and expectations . the idiographic or personal dimension of the model is characterized by the individual , personality , and need - disposition . social behavior is the result of the interactions between 2 sets of motives : the nomothetic / normative dimension and the idiographic / personal dimension . the getzels - guba model asserts that , within an institution , an individual has a purposeful role and is required to meet certain expectations as a member of the organization . need - disposition and role expectation can be viewed as structural elements in patient / chiropractic physician rapport and in professional and ethical functions . if there is a lack of homeostasis between needs / structures and roles / functions within an organization , it may produce stress , strain , and anxiety that may negatively affect professional relationships and the continuity of health care . according to w. edwards deming 's out of the crisis , principles such as efficiency and effectiveness need to be aligned so that the members of the health care organization take part in shared decision making . if a health care organization lacks these principles , it may lead to identity and role confusion at work ( in a hospital or a clinic ) , creating additional stress and strain that may affect the proper functioning of the organization . the patient , who is the customer in the health care organization , can be affected positively or negatively if such issues within the health care organization remain unsolved . if stress , strain , and anxiety are created from occupational relationships ( and remain unresolved ) , this could result in what gregory bateson et al refer to as the double bind theory . given this theory , the recipient of double bind is given contradictory messages , causing confusion in self - concept that may lead to an element of uncertainty within the personality of the individual . for example , a medical organization may instill in their employees the importance of teamwork and shared decision making ; but when employees actually voices their concern , they are greeted with resistance and disapproval . this element of uncertainty along with identity and role confusion can lead to what emile durkheim called anomie ( commonly known as a lack of norms ) . this type of behavior within a medical industrial organization can increase the level of stress and strain , leading to neurosis ; and if it remains untreated , it can result in psychosis that affects the functioning within the organizational system . this discussion examined some select concepts of bureaucratic structures and functions so that chiropractic physicians and other health care professionals can use them accordingly . we have focused upon the relationships of scp and smi upon the structural and functional aspects of bureaucracy in the health care institution of a society . it is hoped that present and future chiropractic physicians and other health care professionals will internalize and make use of these select concepts and theories in their future roles as health care givers ( figs 1 and 2 ) . implicit in our analysis of the health care bureaucratic structures and functions in a society is the focus that future chiropractic and other health care professionals integrate , synthesize , and actualize values and virtues such as empathy , integrity , excellence , diversity , compassion , caring , and understanding with a deep commitment to self - reflection so that they can deliver care that involves the ingredients of quality , affordability , availability , accessibility , and continuity for their patients . if these values are taught constructively in any health care bureaucracy , then future health care professionals will be able to transmit the traditions of excellence , dedication , and creativity within the health care profession . on balance , it is asserted that chiropractic physicians recognize the implications of the structures and functions of the health care bureaucracy for the prognosis , treatment , and diagnosis of a patient especially because a bureaucracy is a phenomenon of every highly urbanized and industrialized society today . indeed , it is an environment in which chiropractic physicians and other health care professionals are educated and trained , the organization in which the overwhelming majority will work through their lives . as bureaucracy has tended to define and to regulate the important functions of all institutions within this society , health care has increasingly been transformed into a bureaucratic activity both structurally and functionally . stable patterns of behavior based on structured statuses , roles , and specialized tasks are linked to life or death issues . the explosive growth of scientific knowledge , the rapid increases in technology , and the impact of globalization produce ever more specialization to be incorporated and coordinated in the present health care structures and functions . such a concern of care epitomizes the statement promulgated by wilson hoff , we must recognize that the adequacy of health services depends as much upon the organization of health personnel and the combinations with other resources as is does upon their numbers alone . indeed , a concern for care further documented the diction noted by prof frances weld peabody of harvard medical school , namely , the secret of the care of the patient is in the caring of the patient .\noutput:\n" }, { "from": "agent", "value": "objectivethe purpose of this article is to present select concepts and theories of bureaucratic structures and functions so that chiropractic physicians and other health care professionals can use them in their respective practices . the society - culture - personality model can be applied as an organizational instrument for assisting chiropractors in the diagnosis and treatment of their patients irrespective of locality.discussionsociety - culture - personality and social meaningful interaction are examined in relationship to the structural and functional aspects of bureaucracy within the health care institution of a society . implicit in the examination of the health care bureaucratic structures and functions of a society is the focus that chiropractic physicians and chiropractic students learn how to integrate , synthesize , and actualize values and virtues such as empathy , integrity , excellence , diversity , compassion , caring , and understanding with a deep commitment to self - reflection.conclusionit is essential that future and current chiropractic physicians be aware of the structural and functional aspects of an organization so that chiropractic and other health care professionals are able to deliver care that involves the ingredients of quality , affordability , availability , accessibility , and continuity for their patients ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the concept of the fetal genome is no longer that of a static framework inherited from paternal and maternal sources but a malleable scaffold constantly adapting to stimuli . this is most evident in studies involving fetal programming due to the effects of nutritional variation and glucocorticoid exposure . here , we examined the resulting fetal molecular preconditioning due to antenatal steroid therapy using a protein - restriction mouse model . this model was first designed in a previous study as a novel approach to evaluate postnatal adaptive responses due to varied prenatal nutritional conditions and the addition of stress or steroids . molecular evidence revealed that prenatal programming secondary to maternal protein restriction rendered an inherent susceptibility to neural compromise in neonates and any further addition of antenatal steroids may be detrimental to these already injury - prone offspring . thus , an examination of underlying molecular mechanisms in the fetus was warranted to elucidate the effects seen postnatally . understanding any subtle changes in the fetus induced by these factors and their correlation with phenotypic outcomes in the adult would facilitate early detection of either well - being or disease . current biomolecular techniques such as microarray analysis have allowed the investigation of global gene expression and subsequently , the parallel data mining of gene transcripts of interest as well as the discovery of new gene involvement . moreover , gene expression profiles through clustering of significant genes have shown promising potential as diagnostic panels . all these have led to the rapid identification of biomarkers for disease conditions and their associated regulatory pathways . using these advancements , a panoramic view of genetic movement in uterofemale c57bl / 6n mice about 6 weeks old provided by the institute for animal experimentation , tohoku university graduate school of medicine , were maintained under controlled lighting ( 12 - hour light cycles ) and temperature ( 24c ) . these were allowed for free access to food ( ain - 93 g : oriental yeast co. , ltd . , tokyo , japan ) and water during a 2 - week acclimatization period after which each female was time mated with a male . pregnant females ( n = 36 ) were then housed singly and administered either control ( c ) or protein restricted ( pr ) diets ad libitum all throughout pregnancy ( embryonic stage , e0 to e17 ) . these were then further subdivided into 6 groups and subjected to either plain normosaline solution ( c - s , pr - s ) or 100 g / kg dexamethasone sodium phosphate ( decadron , msd k.k . , tokyo , japan ) in normosaline solution ( c - d / s , pr - d / s ) by subcutaneous injection daily during late gestation ( e10 to e17 ) . maternal weights on days e0 , e10 , and e17 were recorded , as well as fetal weights on e17 . on embryonic day 17 , whole brain samples collected from 2 male and 2 female fetuses from each litter were supercooled in liquid nitrogen and stored at 80c . a total of 6 toray 3d - gene mouse oligo chip 24 k ( toray industries , inc . , tokyo , japan ) microarrays were analyzed per treatment . each chip utilized a 0.5 g portion of combined total rna from a matched pair of male and female samples . rna was amplified and labeled using an amino allyl messageamp ii arna amplification kit ( life technologies japan ltd . ) according to the manufacturer 's instructions . each sample of arna was labeled with fluorescence cy3 or cy5 and cohybridized at 37c for 16 hours . hybridization signals were scanned using scan array express ( perkin elmer , ma , usa ) and global background analysis was performed using genepx pro ( mds analytical technologies , ca , usa ) . all 36 arrays were then normalized together as one experiment to reduce nonbiological variability . to validate microarray results , qpcr was performed on 2 selected genes , microtubule - associated protein 1b ( mtap1b ) and 3 - hydroxy -3-methylglutaryl - coa synthase 1 ( hmgcs1 ) , using the c and c - d / s treatments . total rna was extracted from whole fetal brains ( n = 6 per treatment ) using qiazol lysis reagent ( qiagen , hilden , germany ) and cleaned with an allprep dna / rna mini kit ( qiagen , hilden , germany ) according to the manufacturer 's protocol . complimentary dna was synthesized using the superscript iii first - strand synthesis system ( invitrogen , carlsbad , ca ) and quantitative pcr was conducted with express sybr greener supermix with premixed rox ( invitrogen , carlsbad , ca ) on an eppendorf realplex mastercycler ( eppendorf , hamburg , germany ) . amplified transcripts were quantified and normalized against hypoxanthine phosphoribosyltransferase 1 ( hprt1 ) . microarray data were subjected to t - test analyses with standard bonferroni correction for multiple comparisons . the p value was set at 0.05 and a threshold of 1.5-fold was applied to determine significantly regulated genes . these were subjected to an ontological review and a subset of neurodevelopmental genes for genetic profiling was determined by hierarchical clustering . targeted gene transcripts of interest on the microarrays were treated to one - way anova with post - hoc analysis ( bonferroni post - test ) . confirmation of selected genes by qpcr was validated through fold change analysis ( threshold of 1.5-fold ) . data management , statistical analysis , and gene ontology were performed using geworkbench software ( https://gforge.nci.nih.gov/frs/?group_id=78 ) and mgi gene ontology tools ( http://www.informatics.jax.org/gotools/ ) . mean maternal weight gain patterns , between groups , were similar before ( e0 to e10 ) and during treatment ( e10 to e17 ) . mean fetal brain to body weight indices on sampling day e17 were not significantly different ( figure 1 ) . microarray analyses of 23,522 probe transcripts presented 10,946 genes without absent calls or unreadable hybridization signals . there were more upregulated genes as compared to downregulated genes across all treatment groups ( figure 2 , table 1 ) . the combined number of significant genes regulated from all treatment groups versus the control was 332 ( figure 3 ) . subsequent gene ontology analysis revealed that ongoing cell organization and biogenesis , developmental processes , and transport were most rampant in the global expression survey . the discovery of genes uniquely activated per treatment and sharing similar ontologies facilitated individual treatment characterization ( table 2 ( a ) ) . associated genes were found for protein restriction , cell adhesion genes in both pr - d / s only ( col1a1 , atp1b2 , ctnnd1 , rpsa , and fat4 ) , and pr - s only ( cdh2 , edil3 , and astn1 ) ; for dexamethasone treatment , stress response genes in both c - d / s only ( brsk1 , rarres2 ) , and pr - d / s only ( klk8 , myo6 , ndufa6 , col1a1 , mapk8 , and phlda3 ) ; and for both protein restriction , dexamethasone treatment , and dna metabolism genes for pr - d / s only ( tcf3 , mapk8 ) . overall , neurodevelopmental genes were overrepresented among those significantly regulated ( table 2 ( b ) ) and were associated with nervous system development ( pbx3 , eif2b5 , nlgn1 , mark4 , atp2b2 , nrxn3 , ncam1 , tnik , slitrk1 , cdh2 , synj1 , palm , nrp1 , rpl24 , mtap2 , rpgrip1 , pou3f2 , gabrb3 , lrp6 , sulf2 , ank3 , ccdc88a , atrx , nr2c2 , opa1 , abi2 , mtap1b , tcf3 , syne1 , mapk8 , golga2 , atxn2 , gfra1 , snap91 , slitrk5 , celsr2 , emx2 , klk8 , myo6 , scn2a1 , sema3c , and kif5c ) ; generation of neurons ( pbx3 , nlgn1 , atp2b2 , ncam1 , tnik , slitrk1 , cdh2 , synj1 , palm , nrp1 , rpl24 , mtap2 , rpgrip1 , pou3f2 , gabrb3 , lrp6 , ank3 , ccdc88a , abi2 , mtap1b , tcf3 , syne1 , mapk8 , golga2 , atxn2 , gfra1 , slitrk5 , snap91 , celsr2 , emx2 , klk8 , myo6 , sema3c , kif5c , robo2 , arhgef2 , brsk1 , pou3f4 , and sox11 ) ; neuron differentiation ( pbx3 , nlgn1 , atp2b2 , ncam1 , tnik , slitrk1 , cdh2 , palm , nrp1 , rpl24 , mtap2 , rpgrip1 , pou3f2 , gabrb3 , lrp6 , ank3 , ccdc88a , abi2 , mtap1b , tcf3 , syne1 , mapk8 , golga2 , gfra1 , atxn2 , slitrk5 , snap91 , celsr2 , emx2 , klk8 , myo6 , sema3c , kif5c , robo2 , brsk1 , pou3f4 , and sox11 ) ; neurogenesis ( pbx3 , eif2b5 , nlgn1 , atp2b2 , ncam1 , tnik , slitrk1 , cdh2 , synj1 , palm , nrp1 , rpl24 , mtap2 , rpgrip1 , pou3f2 , gabrb3 , lrp6 , ank3 , ccdc88a , abi2 , mtap1b , tcf3 , syne1 , mapk8 , golga2 , atxn2 , gfra1 , slitrk5 , snap91 , celsr2 , emx2 , klk8 , myo6 , sema3c , kif5c , robo2 , arhgef2 , brsk1 , pou3f4 , and sox11 ) ; neuron development ( pbx3 , abi2 , mtap1b , syne1 , mapk8 , golga2 , nlgn1 , atxn2 , gfra1 , snap91 , slitrk5 , celsr2 , atp2b2 , ncam1 , tnik , slitrk1 , klk8 , cdh2 , myo6 , sema3c , palm , kif5c , nrp1 , rpl24 , robo2 , mtap2 , rpgrip1 , brsk1 , pou3f2 , gabrb3 , ank3 , and ccdc88a ) ; and neuron projection development ( abi2 , mtap1b , syne1 , mapk8 , golga2 , nlgn1 , atxn2 , gfra1 , snap91 , slitrk5 , celsr2 , ncam1 , tnik , slitrk1 , klk8 , cdh2 , myo6 , sema3c , palm , kif5c , nrp1 , rpl24 , robo2 , mtap2 , brsk1 , pou3f2 , ank3 , and ccdc88a ) . a subset of 8 genes out of 332 was filtered through the hierarchical clustering method allowing segregation of treatments ( figure 4 ) . an assessment of individual biological themes within the subset revealed neurodevelopmental roles and distinct causal relationships with glucocorticoid treatment and protein restriction ( table 3 ) . the addition of stress or steroids ( - s and - d / s groups ) greatly affected gene regulation leading to further investigation of genes related to glucocorticoid and stress signaling pathways . mapk8 , fkbp5 , mkp - 1 , pp2a , akt , and gsk3 exhibited expression patterns across treatment groups that corresponded to an overall reduction in glucocorticoid receptor ( gr ) activity in the - d / s and - s groups . most significant of which were the marked differences between c - d / s and pr - d / s ( mapk8 , gsk3 , and mtap1b ) emphasizing the disparate effect on varying nutritional conditions due to dexamethasone administration ( figures 5 ( a ) and 5 ( b ) ) . qpcr results demonstrated a good agreement with the microarray data for mtap1b and hmgcs1 ( figure 6 ) . the maternal - fetal compartment serves to cushion the fetus from environmental stimuli , but beyond normal circumstances , prenatal conditioning invariably occurs . microarray analysis allowed for a panoramic view of gene activity along two levels : through the global expression of genes and through individual treatment groups and their association with one another . in general , ongoing cell organization and biogenesis , developmental processes , and transport were most rampant in the global expression survey ( table 2 ( a ) ) . the dominance of these particular gene groups is expected in the developing fetus just as genes for growth and maturation are more likely activated in neonates . regardless , these increased gene frequencies most likely demonstrate consequent fetal reactions to acquired insults from protein restriction and glucocorticoid exposure either as compensatory regulation or protective feedback . they signaled changes within a fetus long previously believed to be immune prior to the conception of the barker theory . this was exemplified by recurring themes in biological processes related to ongoing brain development during fetal stages : multipotent progenitor differentiation and neuronal migration . their increased expression over other gene systems emphasized the significance of fetal neuroplasticity even to the detriment of visceral organ growth similar to physiologic brain sparing . this also underlined the early dependence on brain - controlled pathways that trigger bodily functions during stages when less developed organs have not yet attained full functional independence . the isolation of distinct genes associated with individual factors of protein restriction , dexamethasone , and stress were complimentary to known gene networks . studies of these genes uniquely regulated in both pr - d / s ( col1a1 , atp1b2 , ctnnd1 , rpsa , and fat4 ) and pr - s only ( cdh2 , edil3 , and astn1 ) emphasized the crucial role of nutritional factors in maintaining the integrity of cell interaction . col1a1 , a known marker of fibrosis and aging , has been linked to alterations in oxidative and antioxidant defense capacity in cells due to poor maternal nutrition . on the other hand , modifications in atp1b2 , edil3 , and astn1 during development lead to glial dysfunction . moreover , various studies on nutritional factor effects and progenitor cell differentiation included ctnnd1 , fat4 , and cdh2 . fetal dexamethasone exposure impairs development in various cell types eliciting a dose - dependent stress response . in the brain , the pituitary is the site of action of administered dexamethasone in the blockade of stress induced hypothalamic - pituitary axis ( hpa ) activation . the latter involves the stimulation of brain receptors , primarily , those of glucocorticoid receptors ( gr ) by both exogenous and endogenous corticosterone . during conditions of stress , the hpa axis releases reactive feedback which suppresses increased excitability allowing recovery from stress induced activation and facilitation of memory storage . the addition of dexamethasone can partially deplete the brain of corticosterone and in turn suppress the fetal hpa axis . studies that included the genes uniquely regulated in c - d / s ( brsk1 , rarres2 ) and pr - d / s ( klk8 , myo6 , ndufa6 , col1a1 , mapk8 , and phlda3 ) report their important roles in neuroregulation and adaptation to stress responses during brain development . furthermore , expression patterns of targeted genes related to stress signaling pathways revealed decreased gr activity : mapk8 ( mitogen activated protein kinase 8 ) and fkbp5 ( fk506 binding protein 5 ) , both gr inhibitors , were increased in the - d / s and - s groups ; mkp1 ( mitogen activated protein kinase phosphatase 1 ) and pp2a ( protein phosphatase 2 ) , both map kinase inhibitors , were decreased in the - d / s and - s groups ( figure 5 ( a ) ) . genes associated with pr - d / s only ( tcf3 and mapk8 ) on microarray analysis , as well as two targeted genes ( akt and gsk3 ) all function in metabolic gene networks , especially for glucose metabolism in dna synthesis . here , their specific expression patterns between - d / s groups underscored the most significant observation in this study , which was the apparent harmful effect of dexamethasone to fetuses in highly stressed conditions ( pr - d / s ) . a diagram interrelating the targeted genes of interest with regard to gr activity is shown in figures 7 ( a ) and 7 ( b ) . previous reports have stated that a loss of gr activity reduces dexamethasone inhibition of akt ( thymoma viral protooncogene 1 ) , which in turn decreases akt inhibition of gsk3 ( glycogen synthase kinase 3 ) , a proapoptotic gene . but in the pr - d / s group , a highly stressed condition , dexamethasone was evidently harmful . this disparate pattern between c - d / s and pr - d / s , significant in mapk8 , gsk3 , and mtap1b ( p 0.0001 ) , denotes the possibility of ongoing altered neurodevelopment or even neurodysgenesis ( figure 5 ( b ) ) . the process of data mining revealed the association between regulated genes unique to individual treatment groups and certain biologic processes . their correlation provided a better understanding of underlying pathophysiology and a glimpse of key pathways for future focused studies . one possible application is the development of gene panels for genetic expression profiling as diagnostic tools . hierarchical clustering programs currently allow the generation of gene maps to be capable of distinguishing between phenotypes . in our simulation , highly regulated neurodevelopmental genes were used and these successfully segregated treatments between microarrays ( figure 4 ) . our findings strengthen our previous study 's assertion that fetal programming secondary to maternal protein restriction renders an inherent susceptibility to neural compromise in offspring and that the addition of dexamethasone to this vulnerable group results in further injury . in future studies , the investigation of both sex - specific and transgenerational effects is necessary as glucocorticoids influence endocrinological pathways differently in males and females . also , timing of exposure to glucocorticoids as well as dosage studies is no less relevant especially in the light of reported evidence that a single course of therapy profoundly affects the fetal hpa axis . in conclusion , the effects of antenatal steroid therapy can vary for each fetus according to maternal - fetal factors and concurrent environmental stimuli . further elucidating regulatory networks that can mark the turning point between beneficial or damaging corticosteroid actions would result in valuable adjustments of current treatment protocols . the ability to recognize conditions highly vulnerable to damage would also expand the possibility of tailored medicine more suitable to each individual 's needs . current biomolecular techniques are powerful tools in this field of study but further validation between animal and true clinical models is required .\noutput:\n" }, { "from": "agent", "value": "introduction . prenatal programming secondary to maternal protein restriction renders an inherent susceptibility to neural compromise in neonates and any addition of glucocorticosteroids results in further damage . this is an investigation of consequent global gene activity due to effects of antenatal steroid therapy on a protein restriction mouse model . methods . c57bl / 6n pregnant mice were administered control or protein restricted diets and subjected to either 100 g / kg of dexamethasone sodium phosphate with normosaline or normosaline alone during late gestation ( e10e17 ) . nontreatment groups were also included . brain samples were collected on embryonic day 17 and analyzed by mrna microarray analysis . results . microarray analyses presented 332 significantly regulated genes . overall , neurodevelopmental genes were overrepresented and a subset of 8 genes allowed treatment segregation through the hierarchical clustering method . the addition of stress or steroids greatly affected gene regulation through glucocorticoid receptor and stress signaling pathways . furthermore , differences between dexamethasone - administered treatments implied a harmful effect during conditions of high stress . microarray analysis was validated using qpcr . conclusion . the effects of antenatal steroid therapy vary in fetuses according to maternal - fetal factors and environmental stimuli . defining the key regulatory networks that signal either beneficial or damaging corticosteroid action would result in valuable adjustments to current treatment protocols ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: nearly all organisms require iron because of its ability to catalyze redox reactions , and humans have evolved mechanisms to recycle almost all the iron contained within hemoglobin and cellular enzymes with only minimal daily loss through the gastrointestinal tract . nevertheless , iron - deficiency anemia and anemia of chronic disease ( caused in part by iron - restricted erythropoiesis ) together are responsible for the majority of anemia cases worldwide , and while these conditions cause morbidity and mortality , it has become clear that limiting iron availability is in fact an innate immune strategy against microbes . indeed studies in humans and mice have shown that oral iron supplementation leads to increased mortality due to infection . pathogens that enter and proliferate within a host must acquire iron from the host and have evolved a large and diverse number of mechanisms to accomplish this , and in response , mammals have developed complex mechanisms to keep iron from pathogens . over the last two decades , there has been much effort aimed at understanding the pathophysiology of anemia associated with chronic inflammation / disease , characterized by hypoferremia . this led to the finding that a small peptide , hepcidin , initially identified as an antimicrobial peptide , is a master regulator of systemic iron stores . hepcidin is produced mainly by the liver and its production is regulated by inflammation / iron levels , hypoxia , and erythropoiesis ; hepcidin is elevated in anemia of chronic inflammation . hepcidin can bind to ferroportin 1 ( fpn1 ) , an iron export protein found on macrophages , enterocytes , and other cell types , and in doing so causes fpn1 internalization and degradation . the vast majority of bodily iron stores is complexed with heme in hemoglobin in red cells , and senescent red cells are broken down and phagocytosed by specialized macrophages in the spleen , which are highly efficient in recycling iron from hemoglobin . nevertheless , pathogens have evolved complex mechanisms to obtain heme from blood or tissues as an alternate source of iron . while the heme synthesis pathway has been well characterized in mammals , much lesswe identified the feline leukemia virus subgroup c receptor ( flvcr ) , a 12 - transmembrane domain protein and member of the major facilitator superfamily , as a heme exporter in mammalian cells . heme exported from cells through flvcr is rapidly bound by plasma proteins including hemopexin and albumin , which can then transport the heme to other sites for utilization . although macrophages express high levels of flvcr , consistent with a role for macrophages in recycling heme / heme iron from phagocytosed senescent red cells , the role of flvcr in regulating heme - iron after infection remains unexplored . macrophages upregulate heme oxygenase - 1 ( hmox1 ) , a heme - degrading enzyme , in response to inflammation or infection ; therefore we hypothesized that macrophages dynamically regulate flvcr in response to inflammation or infection . we analyzed flvcr ( also referred to as mfsd7b ) mrna levels as well as that of the other key heme and iron regulatory genes , fpn1 ( also referred to as slc40a1 ) , hmox1 , and ferritin light chain ( ftl ) in macrophages treated with lps . we found that flvcr mrna decreases quickly upon lps stimulation , similar to fpn1 , before recovering to baseline 2448 hours later . the return to baseline flvcr expression coincides with the major increase in hmox1 and ftl1 expression , suggesting an initial need for increased heme in macrophages after infection accomplished by flvcr downregulation , then at later time points , heme is degraded by hmox1 and iron is sequestered in ferritin . while macrophage sequestration of heme and iron may be one aspect of antimicrobial defense , macrophages need heme and iron for the reactive oxygen ( ros ) production and bacterial killing . these observations suggest that , upon infection , macrophages initially transiently increase intracellular heme and iron in order to kill bacteria before shifting to a strategy focused on iron sequestration . the j774a .1 cell line ( henceforth referred to as j774 ) was obtained from atcc and maintained in cdmem : dmem medium ( gibco ) supplemented with 10 % inactivated fbs , penicillin / streptomycin / l - glutamine ( 1 unit / ml , 1 g / ml , and 2 mm ; gibco ) , hepes ( 10 mm ; gibco ) , - mercaptoethanol ( 0.05 m ; sigma ) , and mem - non - essential amino acids ( 0.1 mm ; gibco ) . bone - marrow - derived macrophages ( bmdm ) were prepared by euthanizing 68 - week - old male c57bl / 6 mice and sterilely dissecting both femurs . the bone marrow was flushed from the femur with hbss , homogenized into single cell suspension by pipetting , and centrifuged at 400 g 4 minutes ( 4c ) and supernatant aspirated . the cells were then resuspended at 510 cells / ml in bmdm media : rpmi1640 ( gibco ) supplemented with 20 % inactivated fbs , 30 % l929 - conditioned media ( lcm ) , penicillin / streptomycin / l - glutamine ( 1 unit / ml , 1 g / ml , 2 mm ; gibco ) , - mercaptoethanol ( 0.05 m ; sigma ) , and 10 ml plated / 10 cm sterile nontissue culture - treated petri dish ( corning ) . after 4 - 5 daysbmdm were harvested by trypsin / versene treatment and replated at lower density as below for stimulation assays . all mice were bred and maintained in a specific pathogen - free barrier facility at the university of washington . experiments were performed in compliance with the university of washington institutional animal care and use committee regulations . j774 or bmdm were plated at 510 cells / well in 12 - well tissue culture plates in cdmem ( j774 ) or bmdm media and allowed to adhere overnight . the following day , the media were exchanged for fresh cdmem with varying concentrations of hemin or lps ( e. coli o111 : b4 ; sigma ) for varying durations . for later experiments , including those using tlr4 ; ly96 bmdm , o111 : b4 ultrapure lps from invivogen was used . pam3csk4 was obtained from emc microcollections and polyinosinic : polycytidylic acid ( pic ) from amersham . at the appropriate time points , media were aspirated from stimulation wells and macrophages lysed with rlt buffer ( qiagen ) and stored at 80c . rna was then purified from lysate using rneasy plus mini kit ( qiagen ) and reverse - transcribed using iscript reverse transcriptase ( biorad ) . multiplex quantitative real - time pcr ( qpcr ) was performed on cdna using the kapa probefast biorad icycler reaction mix ( kapa biosystems ) with gene - specific primers obtained from integrated dna technology ( idt ) . primer sequences : - actin ( f 5 - accttctacaatgagctgcg - 3 , r 5 - ctggatggctacgtacatgg - 3 , 5 - / 5cy5 / tctgggtcatcttttcacggttggc / 3iabrqsp / - 3 ; flvcr ( f 5 - atctggaacctgtgcagaaaca - 3 , r 5 - attgaataaaatgctccagtcatgat - 3 , probe 5 / hex / cccctttgttctcctgctggtcagttatg / iabkfq / - 3 ) ; hmox1 ( f 5 - ctgctagcctggtgcaagatact - 3 , r 5 - gtctgggatgagctagtgctgat - 3 , probe 5 - / fam / agacaccccgagggaaacccca / iabkfq / - 3 ) ; fpn1 ( f 5 - ccaaccggaaataaaaccacag - 3 ) , ( r 5 - aggagaaaacaggagcagattag - 3 ) , ( probe 5 - / fam / ccaaccggaaataaaaccacag / iabkfq / - 3 ) ; and ftl1 ( f 5 - cagccatgacctctcagattc - 3 ) , ( r 5 - ccacgtcatcccgatcaaaa - 3 ) , ( probe 5 - / hex / cgcctggtcaacttgcacctg / iabkfq / - 3 ) . flvcr , hmox1 , and - actin primer sets were run together , and fpn1 , ftl1 , and - actin primer sets were run together . gene expression ( mrna rq ) was quantified as fold - change expression using the pffafl method ; - actin was the reference gene and untreated ( 0 ng / ml ) cells were the reference sample . a dilution series of untreated c57bl / 6 macrophage cdna was run for every assay to determine the reaction efficiency for the pfaffl calculation , to ensure that amplification was linear , and to ensure that the samples being assayed were within the linear range of the assay . polarization of bmdm to the m1 and m2 states was performed using established protocols as follows . the following day , either ifn / lps ( 100 u / ml ; 100 ng / ml ) , il4 ( 100 u / ml ) , or nothing was added and cells were lysed at various times afterward as above for rna isolation , cdna production , and qrt - pcr . the promoter binding tf profiling plate array ( signosis ) was used to assess tf binding to the murine flvcr promoter . in brief , this 96 - well plate - based competition assay utilizes an array of biotinylated oligos specific for 48 transcription factors ( in duplicate ) . nuclear extracts from the cell of interest are incubated with purified , pcr - amplified flvcr promoter . the purified promoter competes with biotinylated tf - specific oligos for binding to tfs present in the nuclear extract . if there is no competition , each tf - bound oligo can hybridize to its specific complementary dna on the 96 - well plate and be detected through luminescence . tf that are present in the extract and bind to the flvcr promoter will show decreased signal in the presence of the promoter compared to no promoter . nuclear extracts were prepared from 110 bmdm using the nuclear extraction kit ( signosis ) , and the protein content was determined by the bradford assay .10 g of bmdm nuclear extract was incubated with or without 15 pmol of purified pcr - amplified murine flvcr promoter , processed , and hybridized to the tf array plate following the manufacturer 's protocol . previously , we observed that macrophages expressed high levels of flvcr , consistent with a role for macrophages in recycling heme / heme iron from phagocytosed senescent red cells . to determine whether flvcr expression in macrophages is regulated by heme , j774 macrophages were exposed to increasing doses of hemin for different times and then flvcr , hmox1 , fpn1 , and ftl1 mrna levels were determined by multiplex quantitative rt - pcr ( qpcr ) . while the hmox1 , fpn1 , and ftl1 mrna showed a dose - responsive increase to hemin exposure for 10 hours , flvcr mrna levels did not change ( figure 1 ) . this led us to ask whether flvcr in macrophages might have another role aside from heme regulation after erythrophagocytosis . macrophages are key regulators of systemic iron balance that maintain organismal iron supply while sequestering iron from pathogens . given that much of the body iron store is found in heme , we next tested whether macrophages modulate flvcr expression in response to infection . fpn1 transcription is downregulated in macrophages stimulated by lps ; therefore we stimulated j774 with varying concentrations of lps for different durations and quantified mrna levels of flvcr and key heme / iron regulatory genes . we found that flvcr expression decreased rapidly upon lps stimulation before recovering to baseline at 2448 hours ( figure 2 ( a ) ) . fpn1 increased rapidly and transiently before then decreasing over the first 24 hours ; fpn1 recovery was slower and not complete by 48 hours ( figure 2 ( a ) ) . ftl1 kinetics were similar to those of flvcr though the initial decrease in expression was not as marked as flvcr and at later time points ftl1 increased above baseline ( figure 2 ( a ) ) . the decrease in flvcr expression was dose - responsive between 0 and 100 ng with no further decrease at higher lps doses , as seen in figure 2 ( b ) , which shows heme and iron regulatory gene expression at 10 hours . both flvcr and hmox1 show a dose - responsive decrease and increase in mrna expression , respectively , whereas fpn1 and ftl1 had the maximal drop in expression at the lowest dose of lps , 10 ng / ml ( figure 2 ( b ) ) . we next assessed the effect of lps stimulation on primary murine bone - marrow - derived macrophages ( bmdm ) and again observed a dose - responsive decrease in flvcr similar to the decrease in fpn1 expression ( figure 3 ) . the kinetics of flvcr and fpn1 downregulation in response to lps were similar to that seen in j774 ( data not shown ) . thus , both primary bmdm and macrophage cell lines respond to lps signaling by downregulating heme and iron export . activation of macrophages in vitro or in vivo by various stimuli leads to distinct gene expression patterns , a process referred to as macrophage polarization . lps and ifn treatment leads to m1 macrophage polarization , suited for combating infection and acute inflammation , whereas il4 treatment leads to m2 polarization . most studies on macrophage regulation of iron balance have been done on m1 macrophages , but one study found that in contrast to m1 macrophages , m2 - polarized human macrophages do not sequester iron but rather release iron to the surrounding tissues , promoting proliferation . to determine whether flvcr was differentially regulated in m1 - versus m2 - polarized macrophages , we generated primary murine undifferentiated macrophages ( m0 ) and then treated with either lps and ifn or il4 to generate m1 - and m2 - polarized macrophages . similar to previous reports , we found that hmox1 and ftl1 expression was not upregulated in m2 macrophages ( figure 4 ) . however , both m1 and m2 macrophages downregulated fpn1 mrna , and in contrast to lps treatment alone , fpn1 mrna remained suppressed at 48 hours . interestingly , flvcr expression decreased later and to a much lower extent in m2 versus m1 macrophages . thus , m2 macrophages maintain flvcr expression , possibly to export heme to cells in regenerating tissues . lps binds to the tlr4 receptor complex on macrophages to activate multiple downstream signaling pathways . to confirm that lps - induced flvcr downregulation was mediated by the tlr4 pathway , we stimulated bmdm from tlr4 ; ly96 mice or controls with lps or lps / ifn . ly96 encodes md2 , a coreceptor with tlr4 required for lps signaling . loss of tlr4 and md2 completely reversed lps - induced downregulation of flvcr and fpn1 ( figure 5 ) . to demonstrate specificity , we stimulated wild - type and tlr4 ; ly96 bmdm with the tlr1 / 2 agonist pam3csk4 ( pam3 ) and tlr3 agonist polyinosinic : polycytidylic acid ( pic ) . we found that both pam3 and pic treatment led to flvcr and fpn1 downregulation in both wild - type and tlr4 ; ly96 bmdm ( figure 5 ) . another group recently showed that tlr2 and tlr6 agonists cause fpn1 mrna downregulation in macrophages . thus , decreased transcription of the genes encoding both heme and iron export proteins is a common pathway following tlr activation in macrophages . interestingly , hmox1 was upregulated by lps and pam3 , but not by pic ( figure 5 ) , suggesting distinct regulation of flvcr as compared to other heme regulatory genes . to explore the connection between lps stimulation and flvcr mrna transcription , we used the epdnew eukaryotic promoter database to identify the human flvcr promoter sequence and then queried the promoter sequence for transcription factor ( tf ) binding sites using promo . this analysis revealed many potential binding sites motifs for transcription factors known to be expressed in macrophages such as nf - b , irf - 1 , and c / ebp ( see supplemental figure 1 of the supplementary material available online at http://dx.doi.org/10.1155/2016/4039038 ) . we next used a multiplex tf binding assay to identify tf present in murine bmdm that can bind to the murine flvcr promoter . several of the tf with highest in vitro flvcr promoter binding activity ( figure 6 ) such as stat4 , ap2 , sp - 1 , and irf - 1 had predicted binding sites with the human flvcr promoter ( supplemental figure 1 ) . moreover , stat4 and irf - 1 are known downstream mediators of lps / tlr4 signaling in macrophages . in this study , we found that primary and immortalized murine macrophages downregulate flvcr mrna levels upon lps stimulation , similar to the downregulation of fpn1 expression previously described . macrophages also downregulated flvcr and fpn1 in response to tlr1 / 2 and tlr3 agonists , suggesting that heme and iron sequestration in macrophages is a general response to inflammatory / infectious stimuli . it was previously reported that m1 polarization causes human macrophages to sequester iron through fpn1 downregulation while m2 polarization leads to increased fpn1 protein expression . a more recent study found that fpn1 expression was decreased in murine m0 macrophages polarized to both the m1 and m2 states . interestingly , this study also found that heme ( in the form of rbc or free heme ) polarizes m0 macrophages to the m1 state . we found that , in murine macrophages , both m1 and m2 polarization caused decreased expression of fpn1 and flvcr , though notably the decrease in flvcr expression occurred later and was less marked under m2 polarizing conditions . the hypothesis is that macrophages sequester iron in response to infection ( m1 ) and export iron and heme under m2 conditions in which tissue regeneration and proliferating cells have higher demand for heme and iron . future studies could explore flvcr and fpn1 expression in vivo under physiologic conditions of m1 ( acute infection ) and m2 polarization ( late - stage wound healing ) or investigate how tumor - associated macrophages regulate heme and iron . surprisingly , flvcr mrna levels in j774 macrophages did not change significantly in response to heme treatment . while free heme may not alter flvcr mrna expression in macrophages , it is possible that flvcr expression may change in response to macrophage erythrophagocytosis , especially in splenic macrophages specialized to take up senescent rbc . heme has been shown to regulate fpn1 transcription through binding the transcriptional factors btb and cnc homology 1 ( bach1 ) and nuclear factor erythroid 2 - like ( nrf2 ) , which associate with a conserved maf recognition element ( mare ) / antioxidant response element ( are ) in the fpn1 promoter . thus , while hmox1 and fpn1 in macrophages may respond to changes in intracellular heme and iron levels in addition to inflammatory / infectious signals , the primary role of flvcr in macrophages may be the regulation of heme in response to infection / inflammation . it is notable that the decrease in flvcr expression occurs rapidly within 10 hours after lps stimulation , while fpn1 expression had an initially small increase followed by a slower decrease in expression ( figures 2 ( a ) and 4 ) . whether this transient fpn1 increase prior to the subsequent downregulation is functionally important is not known . it is not known whether flvcr is also posttranslationally regulated , though one study using transfected cell lines found that flvcr had a long half - life ( 16 hours ) . it has been difficult to study the localization and regulation of flvcr protein in vivo or from ex vivo murine cells because there is no antibody available . once alternative strategies ( such as genetic knock - in of epitope tag sequences ) make in vivo and ex vivo of murine flvcr detection and localization feasible , it will be important to study the kinetics and trafficking of flvcr and fpn1 protein after lps treatment . the decrease in flvcr expression precedes the major increase in hmox1 expression , at which point flvcr expression has returned to baseline . this suggests that the decrease in flvcr is functionally important in the first hours after infection , and as other mechanisms for systemic iron regulation ( hepcidin - mediated fpn1 degradation , increased ferritin expression ) are initiated , flvcr returns to baseline . one explanation is that early flvcr downregulation might be important for macrophage killing of intracellular pathogens . heme and iron - containing enzymes produce the reactive oxygen species and other compounds needed for intracellular killing of bacteria . macrophages that have just encountered and / or endocytosed bacteria may downregulate flvcr in order to increase heme available for cytolytic enzymes . a recent review highlighted the macrophage paradox , that is the finding that many pathogens preferentially replicate inside macrophages in spite of their specialized killing function , and different bacteria have different intracellular niches within macrophages . given that heme and ironare also trafficked and regulated differently in intracellular compartments , there are likely several layers of regulation of heme and iron regulatory proteins at transcriptional , posttranscriptional , translational , and posttranslational ( including trafficking ) levels required to meet the challenges presented by specific pathogens . this is supported by the recent finding that the survival of listeria monocytogenes localized to different intracellular compartments in macrophages was differentially altered by fpn1 expression . moreover , macrophages are not a uniform population , but rather there are several subtypes and macrophage differentiation states which serve specific functions in different tissues and depending on the conditions . macrophages that are specialized for erythrophagocytosis may regulate heme and iron regulatory proteins in response to heme and iron levels rather than inflammatory signals as we observed here . our finding that macrophages dynamically regulate flvcr expression in response to tlr signaling points to a new potential role for flvcr and heme export in macrophages during infection and inflammation . future studies aimed at elucidating the transcriptional and posttranscriptional regulation of flvcr in response to tlr and inflammatory signaling will improve our understanding of the complex interplay cell and tissue - localized demands for heme and iron and systemic heme / iron homeostasis .\noutput:\n" }, { "from": "agent", "value": "pathogenic bacteria have evolved multiple mechanisms to capture iron or iron - containing heme from host tissues or blood . in response , organisms have developed defense mechanisms to keep iron from pathogens . very little of the body 's iron store is available as free heme ; rather nearly all body iron is complexed with heme or other proteins . the feline leukemia virus , subgroup c ( felv - c ) receptor , flvcr , exports heme from cells . it was unknown whether flvcr regulates heme - iron availability after infection , but given that other heme regulatory proteins are upregulated in macrophages in response to bacterial infection , we hypothesized that macrophages dynamically regulate flvcr . we stimulated murine primary macrophages or macrophage cell lines with lps and found that flvcr is rapidly downregulated in a tlr4 / md2 - dependent manner ; tlr1 / 2 and tlr3 stimulation also decreased flvcr expression . we identified several candidate tlr - activated transcription factors that can bind to the flvcr promoter . macrophages must balance the need to sequester iron from systemic circulating or intracellular pathogens with the macrophage requirement for heme and iron to produce reactive oxygen species . our findings underscore the complexity of this regulation and point to a new role for flvcr and heme export in macrophages responses to infection and inflammation ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the term biofilm refers to assemblage of microbial cells , that is , irreversibly associated with a surface and enclosed in a matrix of primarily polysaccharide material . the growth of biofilm is considered to be a result of complex processes involving transport of organic and inorganic molecules and microbial cells to the surface , adsorption of molecules to the surface , and initial attachment of microbial cells followed by their irreversible adhesion , facilitated by production of extracellular polymeric substances , often referred to as glycocalyx or slime . organisms in dental unit water line biofilm are predominantly derived from the incoming mains water . once a new duwl system is connected to the mains water supply , a biofilm will form within eight hours . biofilm formation in dental unit water lines takes place even when it is not used for treatment of patients . the nature of duwls is such that they will develop a biofilm , and water flowing down the biofilm coated waterlines will contribute to microbial load in the water as it exits the tubing . frequent periods of water stagnation in duwls and the properties of the plastics used in duwls construction can promote the attachment and colonization of biofilm forming microorganisms . to keep the biofilm and the contamination of the duwls under control , or rather to reduce the risk of infection both for the patients and for the health staff , use of water - line flushing , independent water reservoir systems , distilled or pasteurized water , ultrasonic , ultraviolet light , inline micropore filtration , and periodic or continuous chemical disinfection has been suggested . the efficacy of disinfection is affected by a number of factors , including the prior cleaning of the object , the organic load present , the type and level of microbial contamination , the concentration of and exposure time to the germicide , the nature of the object , and the temperature and ph of the disinfection process . a few disinfectants will kill endospores after prolonged exposure times ( i.e. , 6 to 10 hours ) and are called chemical sterilants . dental practice has no exception and interest in the role of biofilms within dental units as a possible source of cross infection is intensifying . it is difficult to quantitate the risks associated with aerosolised bacteria for the majority of patients seen in general practice . however , it seems prudent to eliminate this source of infection during treatment of compromised patients . in search of a practical solution to reduce microbial contamination of duwls , the present study is conducted to test the efficacy of aloe vera solution to decrease the number of bacteria in duwls . to compare the efficacy of aloe vera , 5 % sodium hypochlorite ( naocl ) , and 10 % hydrogen peroxide ( h2o2 ) , each at different concentrations in controlling microbial contamination of dental unit water systems . to compare the efficacy of aloe vera , 5 % naocl , and 10 % hydrogen peroxide as disinfectants for dental unit waterlines.to assess the effectiveness of all the three disinfectants used at different concentrations in reducing the bacterial contamination of dental unit water . to compare the efficacy of aloe vera , 5 % naocl , and 10 % hydrogen peroxide as disinfectants for dental unit waterlines . to assess the effectiveness of all the three disinfectants used at different concentrations in reducing the bacterial contamination of dental unit water . thirty dental units were selected for the study that was used most often for the dental treatments in jaipur dental college , jaipur . water samples were collected from 15 dental units each from the department of conservative and endodontics and the department of pediatric dentistry . none of the selected units had ever been treated for removal of biofilm or reduction of planktonic bacteria . water samples between 10 and 50 ml were collected from the outlet of air / water syringe and high speed hand piece . samples were collected on monday morning before the beginning of the working day . before sample collection , the end of each hand piece and two - way syringe was disinfected with 70 % alcohol to avoid other sources of contamination . water splashing was minimized when filling the sample container and any contact between the hand piece and the container was avoided . a volume of 1050 ml of water was collected in sterile containers containing 0.1 gm 100 mlof sodium thiosulphate ( na2s2o35h2o ) to remove residual chlorine . the total viable count was estimated to assess the microbial contamination in the dental unit water line . the total viable count was then done to assess the microbial contamination in the dental unit water line . the study was designed to determine the efficacy of different disinfectants at various concentrations on duwls . thus each group of 10 dental chairs was treated with a particular disinfectant for a period of one week . cross disinfection was also avoided by treating a single dental chair with a similar disinfectant each time . disinfection is a process that eliminates many or all pathogenic microorganisms on inanimate objects with the exception of bacterial endospores . three disinfectants were diluted with distilled water to achieve 1 : 100 , 1 : 10 , 1 : 1 dilution and their effect in reducing the microbial contamination in the dental unit waterlines was studied . aloe vera ( sample a ) : the aloe vera juice was subjected to microbiological analysis before the start of the study to rule out the chances of contamination and to ensure the efficacy of the disinfectant . sample a was diluted with distilled water to achieve concentrations of 1 : 100 , 1 : 10 and 1 : 1 .10 % hydrogen peroxide ( sample b ) was also diluted at 1 : 100 , 1 : 10 and 1 : 1.5 % sodium hypochlorite ( sample c ) was similarly prepared to achieve 1 : 100 , 1 : 10 and 1 : 1 dilution . aloe vera ( sample a ) : commercially available aloe vera juice was used in the present study . the aloe vera juice was subjected to microbiological analysis before the start of the study to rule out the chances of contamination and to ensure the efficacy of the disinfectant . sample a was diluted with distilled water to achieve concentrations of 1 : 100 , 1 : 10 and 1 : 1 .10 % hydrogen peroxide ( sample b ) was also diluted at 1 : 100 , 1 : 10 and 1 : 1 .5 % sodium hypochlorite ( sample c ) was similarly prepared to achieve 1 : 100 , 1 : 10 and 1 : 1 dilution . the three disinfectant samples a , b , and c were added to the reservoir bottle of the 30 dental chairs from which baseline samples were obtained . weekly disinfecting regimen was followed by adding 200 to 250 ml of disinfectant in the reservoir bottle that supplied the dental unit and the solution was run through the system for two minutes . the disinfectants were added on the weekend just before the commencement of that day 's work and the unit was then turned off and the disinfectant was left in situ . water samples of 1050 ml from each treated unit 's air / water syringe were collected in separate sterile containers under aseptic conditions and labelled before treating the first patient of the day and quantified for total viable counts . it is a quantitative bacteriological analysis which enumerates total viable population capable of growing under a given set of conditions . the plate count expresses the number of all colony forming bacteria in 1 ml of water . it provides information about the amount and type of organic matter in the water which may be useful indicating the efficiency of the processes used for water treatment or the suitability of water . the study included collection of water samples from each unit beginning with baseline collection and after duwl exposure to disinfectant . when the different concentrations are compared , disinfectant property showed a direct relationship with the strength of the solution . the data was entered into a database using microsoft excel 2007 spreadsheet software , and the data was analyzed using common database and statistical software . the baseline total viable count for the thirty dental units of water line were ranging from 44 to 201 cfu / ml . the mean tvc of the three disinfectants irrespective of the dilutions of disinfectants were obtained ( table 1 ) . immediately after disinfection with sodium hypochlorite , hydrogen peroxide , and aloe vera , the output water from the disinfected dental chair units showed a high reduction in bacterial density ( figure 1 ) . when relevance of change in dilution was analyzed , it was found that increase in strength reduces the total viable count ( table 3 and figure 2 ) . no significant difference was observed when the three disinfectants were compared ( f = 5.96 , p 0.01 ) ( figure 3 ) . the difference was confirmed through one - way anova where by increasing the concentration of aloe vera its disinfectant properties also increased ( f = 2.9 , p 0.05 ) ( table 2 ) . the biofilm on the inner surface of the tubing of dental units provides a continuous reservoir of microorganisms . with the increasing number of immunocompromised and medically compromised individuals receiving regular dental treatment , contaminated dental unit output water poses a serious risk of infection . not only patients but also dentists and dental professionals are at the risk of being infected with opportunistic pathogens such as pseudomonas or legionella species by means of cross infection or following aerosol formation from water emanating from duwls . in thisregard , effective practical methods for controlling microbial contamination of duwls need to be developed . removal of these substances from water delivered into patient 's mouth may reduce the potential for posttreatment inflammatory episodes . the purpose of this study was to determine the extent of bacterial contamination of duwls in jaipur dental college and to compare the effect of aloe - vera - based disinfectant , 10 % hydrogen peroxide , and 5 % sodium hypochlorite in reducing the bacterial density . the tubing containing water is an ideal habitat for a host of microorganisms , leading to biofilm formation . the water travels through the tubing only for a few hours every working day and is enriched with organics and gets contaminated during operation . this ensures the growth of bacteria in the system , especially at the surfaces leading to the establishment of a stable source of inoculum for sterile water . the ideal properties for an agent required to treat duwl include low toxicity , low cost , ease of treatment , compatibility with a wide range of materials , and broad spectrum antimicrobial efficacy , especially against biofilms . a disinfecting process should ( i ) kill bacteria in the water phase , ( ii ) kill biofilm - embedded cells , ( iii ) remove biofilm from the surface ( as a killed biofilm can be a source of endotoxin and also allows rapid recolonization of a new and viable biofilm , which may occlude the tubing ) , ( iv ) be easily performed and offer continuous protection , thereby eliminating the root cause of poor dental unit water quality , and ( v ) provide continued efficacy during periods of nonuse , such as overnight and weekends . the disinfectant exhibiting these attributes would be easier to explain to patients and easier for practitioners to manage than the remedial treatment processes . considering the ideal properties of the disinfectant , herbal - based disinfectant like aloe veraaloe vera being a natural ingredient is said to be nontoxic and biodegradable . in the present study , the three disinfectants selected were found to be compatible with the duwls of the dental chair units used in the study . there was significant reduction in the mean cfu count when duwls were treated with disinfectants each for a period of one week . the results were in compliance with mcentegart and clark who proved the benefit of disinfectants for eliminating the cfu in routine use . however , the disinfectants should be evaluated for their effect on different pathogens and the duration of their effectiveness . it consists of essential oil of e. camaldulensis , characterized by the presence of high concentrations of 1,8 - cineole with well - documented antimicrobial activity . the efficacy of aloe vera liquid as an antibacterial agent is shown to have a wide range of effectiveness against gram - positive ( gram + ve ) and gram - negative ( gram ve ) bacteria due to an extract of the inner gel of the plant aloe barbadensis miller or aloe vera ( l. ) . the antimicrobial agents of aloe vera gel were reported to effectively kill or greatly reduce or eliminate the growth of streptococcus aureus , klebsiella pneumonia , streptococcus pyogenes , pseudomonas aeruginosa , e. coli , and helicobacter pyroli . whole leaf components are proposed to have direct antibacterial properties including anthraquinones and saponins , while polysaccharides have been attributed within direct bacterial activity through the stimulation of phagocytic leucocytes to destroy bacteria . the site and number of hydroxyl groups on the phenol group are thought to have relation with their toxicity to microorganisms and the increase in hydroxylation . the phenolic group present in aloe vera extracts acts by denaturing the proteins and cell membranes . they act as disinfectants and are effective in the presence of organic matter and remain active even long after application . streptococcus pyogenes and streptococcus faecalis are two microorganisms that have been inhibited by aloe vera gel . aloe gel is bacteriostatic or bactericidal against a variety of common wound - infecting bacteria in vitro : staphylococcus aureus , streptococcus pyogenes , serratia marcescens , klebsiella pneumoniae , pseudomonas aeruginosa , e. coli , salmonella typhosa , and mycobacterium tuberculosis . according to the study by agarry et al . , aloe vera gel and the leaf have inhibitory effect on s. aureus with zone of inhibition 18.0 and 4.0 mm , respectively . among the bacteria and fungi testedaloe gel is also used to promote wound healing due to the presence of some components like anthraquinones and hormones , which possess antibacterial , antifungal , and antiviral activities . aloe vera gel reportedly was bactericidal against pseudomonas aeruginosa which is also among one of the microorganisms isolated from the duwl . all the reported findings about the antimicrobial properties of aloe vera support the evidence of using aloe vera as a disinfectant in the present study . the study was designed in such a way that the strength of disinfectant was subsequently increased after every week in the same dental chair . treating a dental chair with single disinfectant would prevent error due to carry - over effect . aloe vera was proved to have superior disinfecting properties as compared to 5 % naocl and 10 % h2o2 when used at various dilutions . the strength of each disinfectant was increased every week , starting with the lowest ( 1 : 00 ) and achieving the highest dilution ( 1 : 1 ) . all the three disinfectants showed significant reduction in mean cfu / ml at various dilutions . out of all , aloe vera was most effective at higher concentration ( 1 : 1 ) . chemical compounds such as chlorhexidine gluconate , chlorhexidine acetate , sodium hypochlorite , povidone iodine , and listerine have been advocated for use in duwl . the conventional disinfectants like sodium hypochlorite proves to be a problem as they are highly corrosive and the taste and smell are unacceptable . aloe vera is suggested to be a potent antimicrobial agent as it was helpful in reducing the microbial contamination of dental unit water lines . it was also observed in the present research that with increasing the concentration the effect of disinfectant also increased . chemical disinfectants can be replaced by aloe - vera - based disinfectants.aloe vera is proved to be a cost - effective disinfecting agent.use of chemicals will cause clogging and corrosion of dental tubings and airotors which can be prevented by using aloe - vera - based disinfecting agent . use of chemicals will cause clogging and corrosion of dental tubings and airotors which can be prevented by using aloe - vera - based disinfecting agent . routine sterilization procedures , that is , steam under pressure ( autoclaving ) , dry heat , or heat / chemical vapor between - patient use is recommended for all high - speed dental hand pieces , low - speed hand piece components used intraorally , and reusable prophylaxis angles . internal surfaces of high - speed hand pieces , low - speed hand piece components , and prophylaxis angles often get contaminated during various dental procedures . this may result in cross contamination between patients.retraction valves in dental unit water lines may cause aspiration of patient material back into the hand piece and water lines ; anti retraction valves should be installed to prevent fluid aspiration and to reduce the risk of transferring potentially infective material.routine maintenance of antiretraction valves is necessary to ensure effectiveness ; the dental unit manufacturer should be consulted to establish an appropriate maintenance routine.high - speed hand pieces should be run to discharge water and air for a minimum of 2030 seconds after use on each patient . this procedure is intended to aid in physically flushing out patient material that may have entered the turbine and air or water lines . routine sterilization procedures , that is , steam under pressure ( autoclaving ) , dry heat , or heat / chemical vapor between - patient use is recommended for all high - speed dental hand pieces , low - speed hand piece components used intraorally , and reusable prophylaxis angles . internal surfaces of high - speed hand pieces , low - speed hand piece components , and prophylaxis angles often get contaminated during various dental procedures . retraction valves in dental unit water lines may cause aspiration of patient material back into the hand piece and water lines ; anti retraction valves should be installed to prevent fluid aspiration and to reduce the risk of transferring potentially infective material . routine maintenance of antiretraction valves is necessary to ensure effectiveness ; the dental unit manufacturer should be consulted to establish an appropriate maintenance routine . high - speed hand pieces should be run to discharge water and air for a minimum of 2030 seconds after use on each patient . this procedure is intended to aid in physically flushing out patient material that may have entered the turbine and air or water lines . every effort should be made to eliminate not only planktonic bacteria but also the biofilm within the water lines . this prevents the risk of cross - infection amongst treated patients and the dental staff who are regularly exposed to contaminated water and aerosols generated from using dental hand pieces . the development of herbal biocide in the form of aloe vera will prove to be a revolution in disinfecting dental unit water lines . further research is advocated to test the efficacy and shelf life of aloe vera not only in disinfecting the dental unit water but also to be applied in other areas for use as hospital disinfecting solution . the quality of water in a dental unit is of considerable importance because patients and dental staff are regularly exposed to water and aerosol generated from the dental unit . the aim of this study was to evaluate the use of herbal - based disinfectant in reducing contamination of dental unit water line .\noutput:\n" }, { "from": "agent", "value": "context . dental unit waterlines may be heavily contaminated with microorganisms and are a potential source of infection for both practicing staff and immunocompromised patients particularly . contamination of dental unit water lines could be inhibited with the use of disinfectants . the present study investigates the effect of aloe - vera - based disinfectant in reducing the microbial growth in dental unit water lines ( duwls ) . aims . to compare the efficacy of aloe vera , hydrogen peroxide ( h2o2 ) , and 5 % sodium hypochlorite ( naocl ) in controlling microbial contamination of duwls . materials and methods . after obtaining baseline water samples , the dental unit waterlines were treated with aloe vera , 10 % hydrogen peroxide , and 5 % sodium hypochlorite . each of the three disinfectants was used in increasing concentrations and their inhibiting effect was compared . water samples were analyzed for microbiological quality by the total viable count ( tvc ) method . statistical analysis used . spss 16 . results . there was significant reduction in mean cfu / ml when treated with disinfectants each for a period of one week . aloe - vera solution was found to be the most effective in reducing the microbial colonies . conclusions . improving the water quality from dental unit water lines is of considerable importance ; chemical - based disinfectants can be replaced with herbal disinfectants for treating microbial contamination in dental unit waterlines ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: numerous studies have revealed the immense diversity of microorganisms and have lent insight into their distributions within and across ecosystems ( ward et al . , 1990 ; vres , 2000 ; floyd et al . , 2005 ) . a number of recent studies have demonstrated that microorganisms have distinct patterns of distribution ( microbial biodiversity over space and time ) reminiscent of those of macroorganisms ( hughes martiny et al . , 2006 ) . biogeography concepts can be used to understand why organisms are distributed as they are within and across ecosystems and why stable , mixed communities exist ( green et al . , 2008 ) . on large regional scales , biogeographic patterns of microorganisms are more heavily influenced by edaphic parameters than by the factors that typically dictate the well documented biogeography of plants and animals , such as latitude and mean annual temperature ( fierer and jackson , 2006 ) . however , on the local scale , microbial biogeography is influenced by both edaphic and biotic parameters such as vegetation type , carbon availability , nutrient availability , and soil moisture . these patterns have been observed in terrestrial , wetland , and aquatic ecosystems ( crump et al . , 2004 ; dolan , 2005 ; fierer and jackson , 2006 ) . salt marsh ecosystems are excellent locations for the investigation of biogeographical patterns due to the small number of dominant macrophytes and to predictable environmental effectors such as tidal inundation and salinity . niche differentiation patterns are well - established as gradients of these effectors and develop in response to tidal flooding and bioturbation in salt marsh ecosystems . microbial communities express niche differentiation based on environmental gradients , often responding strongly to one or more specific environmental effectors in the ecosystem ( crump et al . for example , microbial diversity in estuarine tidal creeks is strongly influenced by salinity ( hollibaugh et al . , 2000 ; selje and simon , 2003 ; crump et al . , 2004 ) , which reflects both the direct impact of salinity on microbial communities and the influences of advective inputs of marine and freshwater microorganisms . niche - based theories of ecology help to explain the partitioning of limiting resources between competing species and the differentiation of niche space across all species within a community ( leibold and mcpeek , 2008 ) . particularly with reference to functional assemblages ( i.e. , assemblages of organisms carrying out specific ecological activities ) , such theories can give insight into the distribution of organisms throughout ecosystems and their ability to contribute significantly to ecosystem function in differing niche dimensions . this review will examine recent findings from north american salt marsh ecosystems , focusing specifically on the diverse assemblage of free - living diazotrophic ( nitrogen fixing ) organisms found there . the salt marsh diazotroph assemblage includes organisms that are quite specific for a given marsh microenvironment as well as for specific marsh plant hosts . this assemblage is also sufficiently stable in composition ( determined through field manipulation experiments discussed below in the section niche specialization ) to make analysis of geographic patterns feasible . coastal salt marshes are characteristically dominated by herbs , low shrubs and grasses bordering saline water bodies and are subjected to periodic flooding as a result of fluctuations ( tidal or non - tidal ) in the sea / ocean ( adam , 1990 ) . the marshes depend on the tidal cycle to maintain water regimes , flush peat and sediment with water and dissolved nutrients , and to maintain salinity gradients ( gardner , 1973 ; hemond and fifield , 1982 ; adam , 1990 ) . tidally dominated salt marshes are transitional between the mainly submerged sea grass communities and fully exposed terrestrial zones , and have received extensive study due to their importance as nursery grounds for commercially important fisheries species and as sources of carbon and nitrogen to nearshore waters ( long and long , 1983 ; schubauer and hopkinson , 1984 ; dame and kenny , 1986 ; dame et al . , 1986 ; morris and haskin , 1990 ; morris et al . , 1990 ; the coastal salt marshes of the south - eastern united states are typically dominated by halophyte perennial graminoids which have extensive underground rhizome systems ( odum , 1988 ) . the number of plant species that are numerically significant in coastal salt marshes is small ( schubauer and hopkinson , 1984 ) and a clear zonation of plant species that is based on edaphic environmental conditions , interspecies competition and minor differences in elevation is routinely observed ( bertness and ellison , 1987 ; adam , 1990 ; pennings and callaway , 1992 ) . key abiotic factors that influence plant zonation include sediment porewater salinity , soluble sulfide concentration , ph and redox potential ( bertness , 1991 ) . microbial activities have also been thought to influence the development of plant zonation , as expressed through their ability to affect the concentrations of nutrients and other solutes , particularly sulfide ( king et al . , 1982 ) . the low marsh , which is regularly flooded and where salinities are higher , is dominated by halophyte grasses such as spartina alterniflora and spartina patens . the high marsh typically has lower salinities , undergoes irregular flooding ( with frequency of flooding based on tidal heights and the elevation gradient ) , is closer to the terrestrial zone typically fringing the marsh , and is dominated by rushes and grasses having lower salt tolerance , such as juncus roemerianus . areas of disturbance in the marsh , such as those experiencing long - term waterlogged conditions or unusually high rates of evapotranspiration , are often dominated by successional species such as salicornia virginica ( pennings and callaway , 1992 ; levine et al . , 1998 ) . these plant zones are easily recognized in the field and some are monotypic with respect to the plant present . crab haul creek basin , north inlet , south carolina hosts a typical tidally dominated salt marsh with obvious plant zonation , fresh water input primarily from local rainfall , and nitrogen limitation . north inlet is a high salinity , relatively pristine estuary ( blood and vernberg , 1992 ) which serves as a benchmark system in the united states national estuarine research reserve . the crab haul creek basin has a relatively minor elevation gradient , just over 1 m from mean high tide to the highest points within the basin , with semi - diurnal tides averaging 1.5 m ( kjerfve , 1986 ) . this relatively flat landscape results in the edaphic parameter gradients that have influenced the plant zonation patterns observed in this system ( figures 1 and 2 ) . porewater salinity and sulfide concentration gradients , in particular , drive the development of macrophyte zonation along this elevation gradient . monotypic stands of short and tall growth forms of s. alterniflora occur in the low marsh , the successional species s. virginica in the waterlogged region of the midmarsh ( as well as in a mixed stand with the short growth form s. alterniflora ) , and j. roemerianus in the high marsh and in patches of slightly higher elevation within the low marsh zone of short growth form s. alterniflora . this pattern of plant zonation has been stable for decades ( e.g. , dame and kenny , 1986 ; morris and haskin , 1990 ) . differences in site elevation above mean sea level ( amsl ) and distance of each sampling location from the forest edge . site designations : juncus roemerianus stand ( js ) ; salicornia virginica ( sv ) ; mixed plant zone of co - occurring s. virginica and short form spartina alterniflora ( ss ) ; short form s. alterniflora ( s ) ; patch of j. roemerianus in the s zone ( jp ) ; and tall form s. alterniflora ( t ) . reproduced with kind permission from davis et al . ( 2011 ) , figure 1 . typical marsh zonation including vegetation zonation and gradients of influential abiotic parameters as observed in crab haul creek basin , north inlet . productivity in salt marshes has important impacts on coastal processes , and salt marshes are among the most productive ecosystems known ( keefe , 1972 ; turner , 1976 ; morris and haskin , 1990 ) . the average annual production ranges from 167 to 938 g m year , however this value varies greatly with temporal and local conditions ( kirwan et al . , salt marshes are often nitrogen - limited as combined nitrogen compounds ( nitrate , nitrite and ammonia ) can be rapidly depleted and sources of new nitrogen , such as n2 fixation , must be utilized ( howarth et al . , 1988 ) . phosphorus can also be a limiting factor for productivity of salt marshes and a seasonal switch is sometimes observed between nitrogen limitation and phosphorus limitation ( valiela and teal , 1974 ; howarth et al . , 1988 ; van wijnen and bakker , 1999 ) . estuaries that are not subject to high levels of anthropogenic nutrient inputs are particularly susceptible to the effects of nutrient limitation . nitrogen limitation has been demonstrated in these relatively pristine systems through nutrient addition experiments ( valiela and teal , 1974 ; marinucci et al . , 1983 ; hopkinson and schubauer , 1984 ; morris , 1991 ; dai and wiegert , 1997 ; van wijnen and bakker , 1999 ; bagwell and lovell , 2000a ; piceno and lovell , 2000a , b ) and through ecosystem - level mass balance considerations ( hopkinson and schubauer , 1984 ; hopkinson , 1988 ; morris , 1995 ) . biological nitrogen fixation in salt marshes is thought to be more important than in most other ecosystems due to its significant contribution of n to the nitrogen budget in these systems ( capone and carpenter , 1982 ) . only organisms of the domains bacteria and archaea are capable of the reduction of gaseous dinitrogen to ammonia ( nitrogen fixation or diazotrophy ; postgate , 1998 ) . ammonium levels in the sediment porewater are much higher than in salt marsh surface waters , demonstrating that the sediments are a net source of nitrogen for the system ( mendelssohn , 1979 ; morris and dacey , 1984 ; sundareshwar et al . , 2003 ) . the diazotrophs in the sediments of salt marshes are thus the main source of the considerable contribution of fixed nitrogen from salt marshes to the global nitrogen cycle . this was confirmed by n2 enrichment studies using microcosms of sediment from a california estuary where nitrogen fixation was the primary method of n transfer to vegetation and other primary producers ( moseman - valtierra et al . , 2010 ) . diazotrophs associated with salt marsh grasses are present in high numbers , are most active on the roots of these plants ( patriquin , 1978 ; mcclung et al . , 1983 ; whiting et al . , 1986 ; yoch and whiting , 1986 ) andare supported by root exudates , as well as by products of plant decomposition ( whiting et al . , 1986 ; diazotrophs associated with salt marsh macrophytes , particularly the cordgrasses ( spartina spp . ) , have been studied extensively and the remarkable diversity of the salt marsh diazotroph assemblages documented ( bagwell et al . , 1998 , 2001 , 2002 ; , 2000 , 2001a , b ; piceno and lovell , 2000a , b ; bergholz et al . , 2001 ; , 2009 , 2010 ; gamble et al . , 2010 ; cramer et al . , 2011 ; davis et al . , 2011 ) bacterial diazotroph assemblages associated with salt marsh grasses are primarily composed of organisms taxonomically related to the - , - , - , - , and - proteobacteria ( bagwell et al . , 1998 , 2001 , 2002 ; piceno et al . , 1999 ; bagwell and lovell , 2000a ; lovell et al . , 2000 , 2001a , b ; piceno and lovell , 2000a , b ; burke et al . , 2002 , 2003 ; brown et al . , 2003 ; moisander et al . , 2005 ; archaeal diazotrophs have not been extensively studied in most ecosystems ( zehr et al . , 2003 ) and have yet to be examined in salt marshes . salt marsh diazotroph assemblages consist of mainly novel , uncultivated organisms whose physiologies have not yet been determined . this is a common observation of diazotroph assemblages across natural ecosystems and the diversity of these assemblages in combination with their potentially very different physiologies has inspired many studies ( zehr et al . culture - dependent studies have also revealed diverse culturable assemblages , largely composed of proteobacteria ( bagwell et al . , 1998 , 2001 ; bagwell and lovell , 2000a ; bergholz et al . these assemblages are capable of utilizing a host of carbon compounds found in plant root exudates as determined in studies on isolates from washed roots ( bagwell et al . , 2001 ; bergholz et al . ,2001 ) , and of surviving substantial ranges of environmental conditions such as ph and salinity ( cramer et al . , 2011 ) . the development of nitrogenase gene specific polymerase chain reaction ( pcr ) primers has allowed the investigation of salt marsh diazotroph assemblages via culture - independent methods ( zehr and mcreynolds , 1989 ; ueda et al . , 1995 ; olson et al . , 1998 ; , 1999 ; widmer et al . , 1999 ; lovell et al . , 2000 ; welsh et al . , 2007 ) . briefly , the nitrogenase enzyme is composed of two multi - subunit metalloproteins ( reviewed in postgate , 1998 ; zehr et al . , 2003 ) . component i contains the active site for n2 reduction and is composed of two heterodimers encoded by the nifd and nifk genes . component ii couples atp hydrolysis to inter - protein electron transfer and is composed of two identical subunits encoded by the nifh gene . primers specific for the nifh gene have been used extensively in culture - independent studies of diazotroph assemblages across many ecosystems resulting in a robust database of gene sequences from uncultivated microorganisms ( zehr et al . , 2003 ) . primers specific for nifd ( ueda et al . , 1995 ) have also been developed but have not been used as broadly or as frequently as the nifh - specific primers ( zehr et al . , 2003 ) . the diazotroph assemblages associated with salt marsh macrophytes have been investigated through pcr - amplification using nifh - specific primers and the nifh amplicons have in turn been analyzed using methods such as denaturing gradient gel electrophoresis ( dgge ; bagwell et al . , 1998 , 2001 , 2002 ; piceno et al . , 1999 ; bagwell and lovell , 2000a ; lovell et al . , 2000 , 2001a , b ; 2003 ; welsh et al . , 2007 , 2010 ; gamble et al . , 2010 ; davis et al . ,2011 ) , restriction fragment length polymorphism ( rflp ; burke et al . , 2002 , 2003 ) , and terminal restriction fragment length polymorphism ( t - rflp ; moseman - valtierra et al . , 2009 , 2010 ) . pcr - amplification of reverse - transcribed mrna extracts has also been used to a lesser extent ( brown et al . , 2003 ) . in the north inlet estuary , diazotrophs have been investigated via culture - dependent methods as well as dgge ( bagwell et al . , 1998 , 2001 , 2002 ; , 2000 , 2001a , b ; piceno and lovell , 2000a , b ; brown et al . , 2003 ; gamble et al . , 2010 ; davis et al . , 2011 ) , reverse sample genome probing ( bagwell and lovell , 2000a ) , clone library construction and screening ( lovell et al . , 2008 ) and sequencing of reverse - transcribed mrna extracts ( brown et al . , 2003 ) . the composition of the diazotroph assemblages of this ecosystem are similar to those recovered from other salt marsh ecosystems ( e.g. , moisander et al . , 2005 ) and other estuaries ( e.g. , affourtit et al . , 2001 ; due to the number of studies that have been done in this area , detailed phylogenetic and statistical analyses can be conducted on the nifh sequence data that have been obtained . assemblages from the north inlet estuary have proven to be stable , ubiquitous , functionally versatile , distributed in predictable patterns across the marsh landscape and are characterized by their content of novel and undescribed taxa ( gamble et al . , 2010 ; davis et al . , 2011 ) . culture - dependent and culture - independent analyses of diazotroph assemblages associated with the rhizospheres of salt marsh macrophytes of north inlet have demonstrated the occurrence of plant host specific organisms . the colonization of plant species by specific microbial populations has been repeatedly observed in terrestrial ecosystems ( reviewed in berg and smalla , 2009 ) . soil quality and soil type heavily influences the root colonizing microorganisms , however it has been proven repeatedly that plant species also exerts a direct influence ( berg and smalla , 2009 ) . the biogeography of soil microbial communities on a large scale ( i.e. , continental ) is controlled primarily by soil abiotic parameters , particularly soil ph ( fierer and jackson , 2006 ) , and it is assumed that this premise holds true for salt marsh sediment microbial communities . however , as previously mentioned , parameters such as vegetation type , carbon and nutrient availability , and soil moisture have a more direct influence on the diversity of the local microbial community ( fierer and jackson , 2006 ) . plant type and the root exudates that individual plant species produce affect the relative abundance and diversity of indigenous microbial communities at the root and in the rhizosphere ( berg and smalla , 2009 ) resulting in plant host specific phylotypes . larocque et al . ( 2004 ) examined diazotrophs isolated from j. roemerianus rhizoplanes from two habitats differing in abiotic parameters . the two monotypic juncus stands were in different marsh zones having different salinities ( 29 and 40 parts per thousand ) , different porewater chemistries and experiencing different extents and durations of tidal inundation ( larocque et al . , 2004 ) . the higher salinity juncus habitat is regularly inundated during daily tidal cycles , whereas the lower salinity stand is in the high marsh and not as frequently inundated . diazotrophs from both habitats were analyzed in parallel using the same protocols ( including nifh pcr - amplification ) . the presence of nifh was confirmed in each isolate and isolates were grouped based on their carbon substrate utilization patterns . three major substrate utilization clusters were identified and each cluster contained isolates from both monotypic stands . dgge analysis of rhizoplane ( sediment free roots ) and rhizosphere ( sediments influenced by the roots ) nifh amplicons from both juncus stands confirmed the presence of host specific diazotrophsdiazotrophs that were present in both assemblages despite differences in salinity , sulfide , and ph . the use of both culture - dependent and independent methods in this study reduced the impact of biases that could have been introduced had only data from a single method been examined . ( 2001 ) isolated diazotrophs from the rhizoplanes of s. patens growing in two physically different habitats of north inlet estuary , along with diazotrophs from other macrophytes . the diazotrophs were grouped based on substrate utilization and strains from s. patens formed two distinct clusters each containing strains from both habitats . of the 16 physiologically different groups , only one strain isolated from s. patens was similar to diazotroph strains isolated from other macrophytes in the same salt marsh ecosystem . diazotroph strains from s. virginica were different from strains from other plants growing in other marsh zones , but were more similar to strains from host plants growing in the same marsh zone ( bagwell et al . , 2001 ) . as described above and in figure 2 , marsh zones are defined by edaphic parameters ( bertness and ellison , 1987 ; adam , 1990 ; pennings and callaway , 1992 ) . diazotrophs isolated from plant hosts in the same zone are presumed to be heavily influenced by the edaphic parameters of the marsh zone . nifh dgge analysis of diazotroph assemblages recovered from the rhizosphere and rhizoplane of host plants in north inlet also confirm the plant host specificity observed in the culture - dependent studies ( gamble et al . assemblages from s. alterniflora growing in two differing tidal drainage systems within north inlet estuary showed seasonal variability but no significant site - influenced variability ( gamble et al . , 2010 ) . the host plants were the same in both locations ( short and tall growth forms of s. alterniflora ) and the subtle changes in edaphic parameters with changes in seasons shaped the seasonally responsive segments of the diazotroph assemblages in these two locations . assemblages from the rhizospheres of plant hosts in the crab haul creek basin that exhibit zonation due to elevation differences , contained host specific diazotrophs as well as diazotrophs having broad distributions across the landscape ( davis et al . , 2011 ) . as described above , plant zones contain specific macrophytes due to the differences in marsh environments . a clear response of diazotroph assemblages to plant host zonation and seasonal changes in edaphic parameters was observed from principal component analysis ( pca ) of the recovered nifh amplicons ( gamble et al . , 2010 ; davis et al . , 2011 ) . ( 2011 ) confirmed the seasonal responses ( figure 3 ) and plant host specificity ( figure 4 ) observed by gamble et al . principal components analysis results for dates june ( ss , jp , s , and t ) and september 2000 ( sv , ss , s , and t ) . circles denote significance ( p 0.001 ) for clustering . for june 2000axis 1 represents 28.4 % of the variance and axis 2 represents 14.7 % of the variance . for september 2000axis 1 represents 31.5 % of the variance and axis 2 represents 11.5 % of the variance . principal components analysis results for vegetation zones juncus roemerianus stand and tall form spartina alterniflora on all dates . . for j. roemerianus stand axis 1 represents 31.2 % of the variance and axis 2 represents 20.8 % of the variance . for tall form s. alterniflora axis 1represents 25.8 % of the variance and axis 2 represents 15.5 % of the variance . reproduced with kind permission from davis et al . ( 2011 ) , supplementary figure 1a . to confirm the results from pca analysis , mothur ( schloss et al . , 2009 ) was used to conduct parsimony tests on neighbor - joining trees created using nifh sequences ( 400420 bp ) . these sequences were recovered from dgge banding patterns of rhizoplane and rhizosphere samples from all plant zones except the mixed zone of co - occurring s. virginica and short form s. alterniflora ( davis , 2010 ) . included in the phylogenetic analysis were plant zones ( with designations ) : j. roemerianus stand ( js ) , s. virginica ( sv ) , short form s. alterniflora ( ss ) , patch of j. roemerianus in the ss zone ( jp ) , and tall form s. alterniflora ( ts ) . using a significance threshold of p 0.01 it was confirmed that diazotroph assemblages in the same marsh zone ( based on edaphic parameters ) had similar structures ( table 1 ) . phylogenetic analyses of the sequences recovered from these assemblages also revealed clusters of plant host specific sequences that were considered identical ( sensu venter et al . , 2004 ; see also lovell et al . , 2008 ) throughout the nifh phylogenetic trees ( figure 5 ; table a2 in appendix , 19 clusters in the high marsh ; figures 6 and 7 ; table a4 in appendix , 39 clusters in the low marsh ) . results from parsimony tests ( mothur ) of neighbor - joining trees containing diazotroph sequences recovered from band stabs of dgge gels of pcr - amplified nifh amplicons from rhizoplane ( roots ) or rhizosphere ( sediments ) of different plant zones . ** * significance threshold ( using bonferroni corrections ) = 0.05 / 5 = 0.01 . all pairs yielding a parsimony significance 0.01 have significantly different structures from each other . key : jpx , j. roemerianus patch in short growth form s. alterniflora ; ssx , short growth form s. alterniflora ; xxr , rhizoplane ; xxs , rhizosphere . phylogenetic analysis of all nifh sequences from dgge bands of rhizoplane ( r ) and rhizosphere ( s ) samples from the high marsh plant zones ( nucleotide sequences , neighbor - joining , jukes cantor correction , complete deletion of gaps and missing data , 1000 bootstrap replicates ) . js , juncus roemerianus stand ; sv , salicornia virginica . phylogenetic analysis of all nifh sequences from dgge bands of rhizoplane ( r ) and rhizosphere ( s ) samples from the low marsh plant zones ( nucleotide sequences , neighbor - joining , jukes cantor correction , complete deletion of gaps and missing data , 1000 bootstrap replicates ) . abbreviations : jp , j. roemerianus patch ; ss , short form s. alterniflora ; ts , tall form s. alterniflora . continuation of figure 6 phylogenetic analysis of all nifh sequences recovered from the low marsh plant zones ( nucleotide sequences , neighbor - joining , jukes cantor correction , complete deletion of gaps and missing data , 1000 bootstrap replicates ) . abbreviations : jp , j. roemerianus patch ; ss , short form s. alterniflora ; ts , tall form s. alterniflora . multiple analyses of datasets obtained in several different studies provide strong evidence of plant host specific diazotroph assemblages associated with the rhizospheres of salt marsh plants . these organisms have been detected through both culture - dependent and culture - independent methods , in different sites throughout north inlet estuary , and over the course of more than a decade . it is very clear that salt marsh diazotrophs have a distinct biogeography driven by both biotic ( host plant ) and abiotic environmental parameters ( i.e. , salinity , tidal inundation , elevation , etc . ) . the results of these studies also indicate substantial resilience of some members of the diazotroph assemblages that are capable of withstanding wide ranges of environmental conditions and are present in multiple marsh zones . studies of diazotroph assemblages associated with the salt marsh plants in north inlet have demonstrated a diverse yet stable assemblage . bagwell and lovell ( 2000b ) conducted a series of field fertilization experiments and through reverse sample genome probing revealed a highly resilient , niche specialized diazotroph assemblage . the assemblage responded to environmental manipulations through increases and decreases in quantities of specific taxa , but not through loss of taxa ( bagwell and lovell , 2000b ) . dgge analysis of diazotroph assemblages in long - and short - term fertilization experiments ( fertilized with 16.3 g n m nh4no3 and 18.0 g p m p2o5 ) confirmed the stability of these assemblages ( piceno and lovell , 2000a , b ) . the results of these experiments indicate that salt marsh diazotrophs are quite competitive with non - diazotrophs and are able to maintain their populations despite the energy expense of nitrogen fixation . the resilience of diazotrophs associated with salt marsh plants has also been observed during periods of extreme environmental conditions ( davis , 2010 ) . in stark contrast to the diversity of diazotrophs associated with the rhizospheres of salt marsh plants , nifh sequences recovered from standing dead s. alterniflora biomass from north inlet and sapelo island ( ga , usa ) salt marshes revealed a diazotroph assemblage with markedly lower diversity ( lovell et al . , 2001b ) . these assemblages can produce significant levels of diazotrophy ( based on rates of nitrogen fixation ) despite the highly mineralized and frequently dry microenvironments they occupy ( newell et al . the analysis methods ( including nifh - specific pcr ) , which were also utilized in other studies , revealed that approximately 90 % of nifh sequences from these assemblages were similar to those from - proteobacteria . this demonstrates that the methods of nifh sequence recovery employed in these studies are sound , as the - proteobacteria are poorly represented in most salt marsh rhizosphere diazotroph assemblages ( lovell et al . , 2000 , 2008 ; gamble et al . , 2010 ; davis et al . , 2011 ) . for example , figures 57 show the small number of nifh sequences that are similar to those from - proteobacteria ( * - labeled clusters in tables a1 and a4 in appendix ) in comparison to the large number of recovered sequences related to those from the - proteobacteria . the majority of the - proteobacteria - like salt marsh sequences have been recovered from the high marsh , particularly in the j. roemerianus plant zone . in addition , approximately half of the - proteobacteria - like sequences that were recovered from the low marsh were from the patch of j. roemerianus growing in the short form s. alterniflora zone . ( 2010 ) revealed that changes in edaphic parameters associated with plant senescence , tidal intrusion , and nutrient cycling produced different responses from the seasonally ( growing season / summer vs. plant senescence / winter ) responsive groups within the diazotroph assemblages ( gamble et al . , 2010 ) . a seasonally responsive - proteobacteria clade was detected during the spartina growing season while , an anaerobic clade was only detected during plant senescence . some clades were also recovered throughout all seasons , indicating a resilient portion of the assemblage . these diazotrophs are capable of competing for resources and maintaining populations over seasonal changes in both biotic and abiotic environmental variables . ( 2011 ) demonstrated broadly distributed ( and mostly novel ) , frequently detected ( fd ) diazotroph sequences that did not respond detectably to seasonal changes ( davis et al . , these sequences were not detected in studies employing the same methods to examine diazotrophic assemblages associated with standing dead spartina ( lovell et al . sequences were also identified ( via statistical tests in pca ) as contributing significantly to the structure of the diazotroph assemblages ( lv sequences from bands producing long eigenvectors in euclidean bi - plot analysis of pca results ; for full explanation see davis et al . , phylogenetic analysis revealed several groups of fd and lv sequences that were virtually identical ( sensu venter et al . , 2004 ; see also lovell et al . , 2008 ) to each other and to previously recovered seasonally non - responsive ( detected throughout all seasons ) sequences from gamble et al . they have been recovered from multiple sites in north inlet estuary and differ from those recovered from other ecosystems . most importantly , these organisms have maintained ubiquity and strong influence on ecosystem function in an ecosystem characterized by distinct plant zones resulting from varying edaphic parameters . it has been determined in terrestrial ecosystems that free - living diazotrophs are functionally significant ( brgmann et al . , 2004 ; hsu and buckley , 2009 ) . it is reasonable to assume , based on the results of these studies , that these organisms are equally important in salt marsh ecosystems . phylogenetic analysis of sequences recovered from high marsh and low marsh zones ( figures 57 ) also confirm the presence of diazotrophs specific to marsh zones . throughout the phylogramsare clades containing virtually identical sequences recovered from host plants in the same marsh zone ( plant host labeled clusters in bolded font in figures 57 , and sequences listed in tables a2 and a4 in appendix ) , indicating niche specificity of these diazotrophs for the edaphic parameters present in these zones . these data have given insight into the distributions of diazotroph populations throughout the nitrogen - limited salt marsh ecosystem of north inlet , sc , usa . these diazotrophs are specialized for the niches within this ecosystem , whether the niches are defined by the microenvironment of the plant host , or by marsh zone , or by both . they maintain populations that are readily detectable by methods employed in multiple studies ( particularly nifh based pcr and dgge fingerprinting ) and influence ecosystem function as well as diazotroph assemblage structure . studies of this salt marsh ecosystem have revealed that the structure of a functional microbial assemblage can be predicted , based on specific environmental parameters . plant hosts and edaphic factors that vary in response to elevation are the key parameters that predict the biogeography of these organisms . on a continental scale , the biogeography of microbial communities in terrestrial ecosystems is predicted by abiotic parameters , particularly soil ph , rather than by geographic distance or vegetation type ( fierer and jackson , 2006 ) . however , on a local scale , environmental parameters and vegetation type more heavily influence the diversity of microbial populations . these patterns have been observed in this estuarine system and can be used to predict biogeographical patterns of diazotroph assemblages associated with salt marsh grass rhizospheres . diazotroph assemblages of salt marsh ecosystems are also capable of resisting relatively large changes in environmental parameters to maintain detectable and functionally important populations ( davis , 2010 ) and can be understood in the context of biogeographical concepts that have been applied to macroorganisms . strong evidence of plant host specificity and niche specialization in these assemblages has been compiled in this review ; however the methods used to obtain the data to support these hypotheses are not perfect . limitations of dgge include the co - migration of dna fragments which will result in a loss of information ( gelsomino et al . , 1999 ; also , the detection of nifh gene sequences by pcr does not confirm the expression of this gene . methods of quantification such as quantitative reverse transcriptase - pcr would be useful as this would identify the dominant diazotrophic phylotypes that actively fix nitrogen and could help to quantify the sizes of their populations . continuing difficulties in the cultivation of these organisms results in a very limited understanding of their physiology , with much of that understanding inferred from known physiologies of related organisms . finally , the evolutionary distances separating most salt marsh diazotrophs from their nearest characterized relatives limits even inference of ecologically significant characteristics of many of these organisms . a great deal remains to be done in identifying the taxa that contribute substantially to diazotrophy in salt marsh ecosystems , though a small start has been made ( brown et al . greater knowledge of these organisms may allow us to refine our cultivation strategies and finally isolate the key organisms into pure culture for characterization . perhaps metagenomic approaches could be employed , but the great diversity of distinct strains within even well studied lineages may limit the gains from these methods as chimeric genomic fragments may be encountered . clearly , many challenges remain to be overcome . based on current climate models , coastal salt marshes are in danger of being completely submerged by the end of the century ( nicholls et al . , 2007 ; craft et al . , 2009currently , it is expected that the ecogeomorphic feedbacks of these dynamic coastal ecosystems [ i.e. , rapid vegetation growth during years of low and high sea level ( morris et al . , 2002 ) ; sediment trapping , organic matter accretion and limiting erosion ( fagherazzi et al . , 2004 ) ] that have allowed the survival of intertidal wetlands over time will continue to do so . however , the ever increasing number of completely submerged wetlands indicates that the current rate of sea level rise may exceed the abilities of ecogeomorphic feedbacks to preserve tidal ecosystems , particularly salt marshes ( kirwan et al . , 2010 ) . continuous submersion of coastal salt marshes will result in losses of vegetation ( penland et al . , 2001 ; hartig et al . , 2002 ; kearnery et al . , 2002 ; kirwan et al . , 2010 ) and consequently loss of microorganisms restricted to a particular plant host or microenvironment ( berg and smalla , 2009 ) . loss of microorganisms critical to ecosystem function would clearly be detrimental to the ecosystem that is dependent on their activity and interactions with macrophytes ( primary producers ) . these events will eventually interrupt food webs and littoral biogeochemical cycles affecting the quality of estuarine water due to eutrophication and increasing the export of particulates ( kearnery et al . , 2002 ) . the ability to predict biogeographical distributions of microorganisms as critical to ecosystem function as diazotrophs are to salt marshes will be advantageous to ecosystem modelers , especially those involved in determining the effects of global climate change . these data clearly show that the distribution of diazotrophs is non - random and is driven directly or indirectly by edaphic parameters in their habitat . the assemblages contain microorganisms that appear to be restricted in their distributions , as well as broadly distributed microorganisms . each group is clearly engaged in ecosystem function as evidenced by their resilience and stability within the assemblages . however , even with this apparent ability to prosper over wide ranges of environmental parameters , there are limits to their survival . the flooding of coastal wetlands as sea level continues to rise could result in large losses from these assemblages . the biogeographical patterns observed in north inlet estuary can be applied to tidally dominated coastal wetlands when the edaphic parameters of the system in question are taken into consideration . the authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest .\noutput:\n" }, { "from": "agent", "value": "salt marshes located on the east coast of temperate north america are highly productive , typically nitrogen - limited , and support diverse assemblages of free - living nitrogen fixing ( diazotrophic ) bacteria . this article reviews and analyzes data from north inlet estuary ( sc , usa ) , addressing diazotroph assemblage structure and the influence of plant host and environmental conditions on the assemblage . the north inlet estuary is a salt marsh ecosystem in which anthropogenic influences are minimal and the distributions of diazotrophs are governed by the natural biota and dynamics of the system . denaturing gradient gel electrophoresis fingerprinting and phylogenetic analyses of recovered sequences demonstrated that the distributions of some diazotrophs reflect plant host specificity and that diazotroph assemblages distributed across marsh gradients are also heavily influenced by edaphic conditions . broadly distributed diazotrophs that are capable of maintaining populations under all environmental conditions spanning such gradients are also present in these assemblages . statistical analyses indicate that the structures of diazotroph assemblages in different vegetation zones are significantly ( p < 0.01 ) different . new data presented here demonstrate the heterogeneity of salt marsh rhizosphere microenvironments , and corroborate previous findings from different plant hosts growing at several locations within this estuary . the data from these collected works support the hypothesis that the biogeography of microorganisms is non - random and these biogeographic patterns are predictable ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: provision of a bowl of water for handwashing in preschools is an intervention by childcare facilities in ghana , to maintain hygienic practices and prevent transmission of microbes . in the year 2005 , the ghana school feeding programme ( gsfp ) was implemented as one of the most important social interventions by the government , to help boost public basic school enrolments . the programme offers one meal each day for all government preschoolers and primary school children . this provision is to reduce hunger and malnutrition , increase school enrolment and attendance , and stimulate local food production . bowl water ( water in a basin / bowl ) has been adapted to serve this purpose whenever the flow of running tap water is interrupted . it is an effective , feasible , and cost - effective means of preventing gastroenteric infection worldwide . recently , there has been growing awareness of its importance not only as a diarrhoeal disease preventive measure , but also as part of a wider public health effort to reduce the disease burden of acute respiratory infections worldwide . the importance of handwashing has also been underlined in a recent review of measures to control the spread of pandemic influenza . the two leading causes of disease burden globally , respiratory infections and diarrhoeal diseases , are responsible for half of all childhood deaths each year . therefore , good and adequate handwashing practice is a prerequisite to disease control and child 's survival . with reference to an appropriate handwashing procedure , communal handwashing from a bowl of water is not the best practice . a handwashing facility , even with soap , on a communal basis , where the same water is used by more than one person , does not constitute an adequate handwashing facility . this practice , especially when the water in the bowl is not changed frequently , could increase the exchange of microbes among the children when the goal is to get rid of them . therefore , this study aimed at determining the microbial content of bowl water used for handwashing in preschools within accra metropolis . it will also help appreciate whether , in the absence of flowing tap water , washing from a bowl of water could serve as an alternative way of getting rid of most microbes among children . preschools within accra , the capital of ghana , that either are under the ghana school feeding programme or are private schools that provide meals for children were selected for the current study . to maintain anonymous identity of the schools and confidentiality , the schools were coded as sa , sb , sc , sd , se , and sf . sterile plastic bottles were used to aseptically collect 1000 ml each of water samples used for handwashing and rinsing . three water samples were taken from each school ; one sample was taken from their main source , such as water storage tanks , commonly calledpoly tank , tap , and well , and labelled as source . soapy water and a third sample was taken from the basin containing water for rinsing and labelled as rinse . after a brief interview using a questionnaire , swabs were obtained from three randomly selected pupils from each school , before they washed their hands and after handwashing . the collected samples ( both the water and the swabs ) were transported on ice packs , to the laboratories at the departments of medical microbiology and medical laboratory sciences , all of the school of biomedical and allied health sciences , university of ghana , for examination . one hundred millilitres ( 100 ml ) of each water sample was centrifuged at 5000 rpm for 10 minutes . the supernatant was discarded and the remaining sediments were resuspended and examined by the direct wet mount and concentration techniques . briefly , a drop of the sediment was placed on two clean grease - free microscope slides . to one , a drop of iodine was added and both were covered with coverslips . each slide was then examined under a light microscope for the presence of life forms of protozoans and helminths . formol - ether concentration method was employed on the rest of the sediments . two out of the three slides were stained , one with iodine and the other with modified z - n stain , and the third was examined directly as wet mount using standard procedures . the water samples were well mixed and using disposable sterile loops ( 2 mm inside diameter ) each of the samples was inoculated onto macconkey agar ( ma ) and blood agar ( ba ) ( oxoid ltd . , the number of colonies seen was counted using a colony counter and recorded as colony forming unit per gram ( cfu / g ) for swabs and colony forming unit per millilitre ( cfu / ml ) for water samples . bacteria colonies were further subcultured onto ma and ba , to obtain pure cultures and primary identification done using colonial morphology . further identification was done based on a number of procedures including microscopy , gram staining , oxidation - fermentation tests , and other biochemical tests such as urease test , catalase test , citrate utilization test , indole test , and triple sugar iron test . similarly , the water samples and swabs were inoculated on sabouraud agar ( oxoid ltd . , susceptibility test for identified bacteria was determined using a modified form of the kirby bauer method . the antimicrobials tested with their disk concentrations in micrograms ( g ) were gentamicin ( 15 ) , amikacin ( 30 ) , tetracycline ( 30 ) , cotrimoxazole ( 25 ) , cefotaxime ( 30 ) , meropenem ( 10 ) , ampicillin ( 10 ) , ceftriaxone ( 30 ) , chloramphenicol ( 30 ) , cefuroxime ( 30 ) , levofloxacin ( 5 ) , and ciprofloxacin ( 5 ) ( oxoid ltd . , basingstoke , uk ) . briefly , on the procedure for antibiotic susceptibility testing , the test organism was emulsified in peptone water until the suspension was comparable with 0.5 mcfarland 's standard . a sterile cotton swab was dipped into the suspension and drained by pressing the swab against the inside of the bottle . the swab was then used to streak the entire surface of a mueller - hinton agar plate ( oxoid ltd . , the moisture was allowed to be absorbed for at least 15 minutes and sterile forceps were used to apply the antibiotic discs to the surface of the agar plates . the plate was kept at 4c for 46 hours , so that the antibiotic can diffuse on the agar media after which it was incubated at 37c for 1824 hours . zone diameters around the antibiotic discs were measured and later classified as susceptible or resistant based on the clinical laboratory standards institute ( clsi ) criteria . the water samples were tested for rotavirus using the prospect rotavirus elisa kit ( oxoid ltd . the process was carried out using the protocol designed by the manufacturer ( oxoid ltd . , uk ) . to ensure quality and accurate results , positive and negative controls were run for each test . three water samples and six swabs were obtained from each preschool making a total of 54 samples for the investigation . five ( 83 % ) of the preschools were privately owned while only one was government owned ( table 1 ) . the schools had different stages , ranging from preschool to junior high school ( jhs ) ( table 1 ) . cryptosporidium parvum and cyclospora cayetanensis were both found in the rinsing water of school sb and the soapy water of school sd . meanwhile , cryptosporidium parvum was also found in the main water source of school sc ( figure 1 ) . bacteriological investigations identified eight ( 8 ) different bacteria in the different water types ( table 2 ) . the bacteria isolates were in the following proportions : staphylococcus species ( 40.9 % ) , escherichia coli ( 13.6 % ) , citrobacter species ( 13.6 % ) , klebsiella species ( 4.6 % ) , proteus mirabilis ( 2.3 % ) , klebsiella pneumoniae ( 9.1 % ) , salmonella species ( 9.1 % ) , and klebsiella oxytoca ( 6.8 % ) . salmonella species was isolated from four different preschools , while escherichia coli , citrobacter species , and klebsiella pneumoniae were identified in three different schools . klebsiella oxytoca and klebsiella species were identified in two preschools and proteus mirabilis was isolated from only one preschool . examination of the swabs showed that staphylococcus species was present before handwashing and after handwashing . escherichia coli , citrobacter species , salmonella species , klebsiella pneumoniae , and klebsiella oxytoca were only isolated from swabs obtained after handwashing ( table 2 ) . notably , just a few colonies were observed for most of the bacterial isolates , for the different sources of water and hand swabs . the ranges of colony forming units of the isolates from various samples are as follows : staphylococcus spp . ( 1.0103.210 ) , e. coli ( 1.1101.710 ) , citrobacter spp . ( 1.4104.210 ) , k. pneumonia ( 1.5107.010 ) , k. oxytoca ( 2.0104.210 ) , klebsiella spp . ( 1.0103.310 ) , and p. mirabilis ( 1.0101.510 ) . apart from staphylococcus spp . and p. mirabilis , all the remaining bacteria recorded cfu below 10 ( table 3 ) . all the organisms tested ( 6/6 , 100 % ) were resistant to cotrimoxazole , ampicillin , and ciprofloxacin while they were susceptible ( 100 % ) to amikacin and levofloxacin . notably , for gentamicin , resistance was seen among salmonella species , klebsiella pneumoniae , and klebsiella oxytoca . all bacteria , except for proteus mirabilis and escherichia coli , were resistant to cefuroxime . similarly , resistance to chloramphenicol was observed in all the bacteria tested except for citrobacter speciesand escherichia coli . meanwhile , the only organism susceptible to tetracycline was escherichia coli . from the fungal studies , aspergillusniger was identified from hand swabs of school children from schools sb and sc before and after handwashing . the same fungal species was also found in the soapy water of school sb ( figure 3 ) . the rotavirus screening did not detect the presence of the virus in any of the water samples collected from the schools , as well as the swabs obtained from the hands of the children ( table 2 ) . bacteria isolates from the current study include salmonella species , citrobacter species , escherichia coli , proteus mirabilis , klebsiella pneumoniae , and klebsiella oxytoca . most of these organisms have also been isolated from a work done by tetteh - quarcoo et al . , when they investigated microbial carriage of cockroaches within the same geographical location as this study . this shows likelihood of these bacteria species circulating within the metropolis . a recent study conducted by ayeh - kumi et al . , on tiger nuts which were claimed to have been washed and sold in locations including that of the current study , also found bacterial isolates , including klebsiella oxytoca , suggesting the association of this particular bacterium with water used within the metropolis . most of the bacteria isolated in this study are pathogenic or potentially pathogenic and are therefore of public health significance , especially when in connection with preschool children . for example , klebsiella pneumo niae causes pneumonia , urinary tract infections , and wound infections . studies have shown that individuals with recurrent infections and those with structural abnormalities of the urinary tract have an increased frequency of infection caused by bacteria such as klebsiella oxytoca . the isolation of escherichia coli shows that washing with bowl - water is a possible source of transmitting this bacterium , which causes acute diarrhoea , especially in children . although escherichia coli is part of the normal flora of the intestinal tract , certain strains can cause moderate to severe gastroenteritis in adults and children . salmonella species and escherichia coli were isolated from even the source where the water used for handwashing was fetched . this is not surprising , since even sachet water , regarded as more purified , has been found to contain high levels of bacteria . almost all the bacteria isolated in this study are mostly responsible for enteric diseases in young children . all the same , the bacteriological methods used in this study provided not much quantification of bacterial load , unlike a study by hoque et al . infections from this organism occur when staphylococci enter the body through breaks , cuts , and abrasions in the skin or mucous membranes . hence , children who have openings such as cuts and abrasions of the skin have a high risk of getting infection caused by this organism when they use such handwashing facilities . isolation of citrobacter species is a notable observation , since citrobacter infections can be community acquired . citrobacter species also cause meningitis , septicaemia , and pulmonary infections in neonates and young children . most of these organisms were enteric bacteria which possibly found their way through accidentally , due to poor hygiene , suggestive of faecal contamination . observation from the antibiotic resistance testing of the current study conforms with the observation by tetteh - quarcoo et al . and reemphasizes the assertion that some antibiotics such as cotrimoxazole , ampicillin , and ciprofloxacin have been on the ghanaian market for a long time and therefore might have been subjected to indiscriminate use or abuse leading to the high levels of resistance recorded . although ciprofloxacin and levofloxacin are both from the same class of antibiotics ( fluoroquinolones ) , there was a notable difference in their performance against the bacteria isolates tested . this observation could be due to the probable indiscriminate use of ciprofloxacin in ghana , since it is readily available compared to levofloxacin . citrobacter species was found to be resistant to five out of the 12 antibiotics tested . in spite of this , shih et al . found that the combination of a beta - lactam and an aminoglycoside had better therapeutic results than a single agent alone for citrobacter bacteremia ; hence , children who acquire infection through handwashing can be treated using this recommendation . escherichia coli , citrobacter species , salmonella species , klebsiella pneumoniae , and klebsiella oxytoca were only isolated from swabs obtained after handwashing . another study also isolated staphylococcus species , escherichia coli , and klebsiella from the hands of preschool nurses . most of the isolates found on the hand swabs were from the after handwashing samples and therefore it is suggested that the children might have picked the bacteria during handwashing process . all the same , it is noteworthy that just a few colonies were counted for most of the bacteria isolates . this implies that although pathogenic bacteria were among the agents isolated , infection from these organisms might mostly be manifested in immunocompromised children who use this handwashing process . cryptosporidium parvum and cyclospora cayetanensis were present in some of the water samples used for handwashing in the preschools . these organisms are potential pathogens associated with water related diarrhoea outbreaks in healthy people and have devastating presentations in the immunocompromised individuals , particularly children . , when they carried out a study to determine the microbial quality of water on the streets of kumasi . hence , the finding of these parasites in the bowl water used for handwashing by preschool children is of public health importance . the current study identified aspergillus niger from the hands of school children before and after handwashing and also from soapy water used for handwashing . this emphasizes the ubiquitous nature of this mould and its association with water . in a study , different species of fungi were recovered from dead sea water , many of which belonged to nonhalophilic terrestrial species , known for their diverse distribution . examples of these species include aspergillus niger and cladosporium cladosporioides . in spite of their widespread occurrence , little attention has been given to the presence of fungi and their significance in preschool environments . the observation of aspergillus niger from water samples used for handwashing suggests that the communal handwashing facility could be considered a possible transmission route forthis fungal species . although aspergillus species cause significant pulmonary infections , aspergillus niger has rarely been reported as a cause of invasive pulmonary aspergillosis . therefore , identifying only this species in the study lowers the possibility of significant pulmonary infections in the school children , acquired through the handwashing process . in relation to rotavirus , almost half of the diarrhoeal disease hospitalization cases of children under 5 years of age are caused by rotavirus ; hence , this virus was included in the microbes under investigation in the current study . the absence of this virus in the bowl water and hands of school children is a positive and a comforting finding . in spite of this , the absence of detection of rotavirus may be a reflection of the sample size used in the current study or the season when the samples were collected . it is therefore important not to infer that all handwashing bowls are free of rotavirus . in the absence of running tap water in most locations , provision of bowl water for handwashing in preschools has been a common practice within the accra metropolis . the current study demonstrated the presence of microbes of faecal and zoonotic origin in some of the swabs and water samples examined ( except for rotavirus ) . this can be of public health concern as some of the organisms identified can cause diseases especially in immunocompromised individuals and young children . although handwashing has the ability to get rid of some microbes , this communal handwashing practice using water in a bowl could be considered a possible transmission route and may be of public concern . even though pathogenic bacteria were isolated , the colony forming units for most of them were low . in spite of the low cfu and nondetectable rotavirus content of the water samples in the current study , adapting an improvised running water system will be an improvement . therefore , adapting a system like the tippy - tap which is already practiced in some schools in ghana and has proven to deliver promising results since its introduction in some parts of uganda is highly recommended .\noutput:\n" }, { "from": "agent", "value": "objective . this study aimed at determining the microbial content of bowl water used for communal handwashing in preschools within the accra metropolis . method . six ( 6 ) preschools in the accra metropolis were involved in the study . water samples and swabs from the hands of the preschool children were collected . the samples were analysed and tested for bacteria , fungi , parasites , and rotavirus . results . eight different bacteria , two different parasites , and a fungus were isolated while no rotavirus was detected . unlike the rest of the microbes , bacterial isolates were found among samples from all the schools , with staphylococcus species being the most prevalent ( 40.9 % ) . out of the three schools that had parasites in their water , two of them had cryptosporidium parvum . the fungus isolated from two out of the six schools was aspergillus niger . all bacteria isolated were found to be resistant to cotrimoxazole , ciprofloxacin , and ampicillin and susceptible to amikacin and levofloxacin . conclusion . although handwashing has the ability to get rid of microbes , communal handwashing practices using water in bowls could be considered a possible transmission route and may be of public concern ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: there are controversies among surgeons regarding deep vein thrombosis ( dvt ) prophylaxis in laparoscopic cholecystectomy . many surgeons have the same opinion for prophylaxis because of an increased intraperitoneal pressure caused by the laparoscopic surgery leading to an induced pneumoperitoneum . in addition , this condition reduces lower limb venous blood flow significantly ( 1 ) , which is an extra risk factor for deep vein thrombosis . . however , some surgeons disagree based on clinical signs and symptoms which found it as a low risk procedure . the purpose of this study was to determine the incidence of clinically detectable dvt in patients undergoing laparoscopic cholecystectomy without a standard dvt prophylaxis regimen before surgery . in a prospective cross - sectional study , 100 candidates for laparoscopic cholecystectomy were studied . duplex scanning was performed by a group of experienced dedicated sonographers on the first day after operation . clinical follow up was done in the following two weeks after surgery for signs and symptoms of dvt . the quantitative data were expressed as mean standard deviation ( sd ) , and frequency used for analysis of the qualitative data . ten male and 90 female patients with mean age of 48.68 ( 4.14 ) years were studied . all of the duplex scans were negative for dvt except in a 73 - year old female who had partial thrombosis in the right femoral and popliteal veins . she did not have any dvt sign or symptom and received no treatment ; hense she was discharged in the second day of operation in a well condition . in the further 10 and 30 days clinical follow - up , no sign or symptom of deep vein thrombosis or pulmonary emboli was found . one to 2 weeks after operation there was not any sign or symptom of dvt in other patients . three deaths due to pulmonary embolismhave been reported in a retrospective survey of 77604 patients undergoing laparoscopic cholecystectomy ( 2 ) . in another study , among 100 consecutive patients who intended to undergo cholecystectomy , two patients showed postoperative dvt including 1 patient after 59 laparoscopic and 41 mini - laparotomy cholecystectomy each , respectively . therefore , despite the theoretical risk of thromboembolic disease due to laparoscopic pneumoperitoneum , the frequency of dvt after either laparoscopic cholecystectomy or mini - laparotomy cholecystectomy was low . the low risk of thromboembolism occurs if adequate thromboprophylaxis regimen which is subcutaneous heparin 5000 units tds and intermittent pneumatic compression were administrated in the patients especially in the high risk ones ( 3 ) . patel et al . reported 20 patients underwent elective or urgent laparoscopic cholecystectomy , in which all patients were given graduated compression stockings to wear and 16 received electrical stimulation of the calf during the operation . only 16 patients received pharmacological thromboprophylaxis before the operation , but all patients received the drug after the operation . eleven out of 19 patients completing all the required scans ( venous duplex scan before the operation and on day 1 , 7 and 30 after the operation ) developed venous thrombosis ( incidence , 55 % ) ; none of the dvts were suspected clinically ( 4 ) . in a series of 438 laparoscopic cholecystectomies , thromboembolism has occurred in three : one dvt , one non - fatal pulmonary embolism , and one fatal pulmonary embolism . all three thrombotic cases were confirmed by phlebography or ventilation - perfusion scanning or after death ( 5 ) . it is also reported that 114 patients were randomized into two groups , in which 58 and 56 patients underwent laparoscopic and open cholecystectomy , respectively . postoperative dvt developed in four ( 6.9 % ) and nine ( 16.07 % ) patients in the first and second groups , respectively ( 6 ) . all the patients had received thromboembolism prophylaxis and dvt was detected by bilateral phlebography 7 - 11 days after surgery ( 7 ) . it is import antfor a clinical practioner to consider the signs and symptoms further to paraclinic results . hense in addition to para clinic assessment of dvt by duplex scanning on the first day after operation , we set up a clinical follow up in the following two weeks after surgery for signs and symptoms of dvt . eighteen patients received some form of perioperative dvt prophylaxis , while 569 patients did not . in the course of 4 weeks clinical follow - up , none of the 587 patients had symptoms of dvt or pulmonary embolism ( 8 ) . in one report , no postoperative thrombi was diagnosed with duplex scanning during unspecified laparoscopic procedures in 61 patients and none of them received prophylaxis ( 9 ) . it is important to consider some risk factors like body mass index and duration of surgery in further researches . in this study , laparoscopic cholecystectomy may be considered as a low - risk procedure for thrombosis , and therefore routine use of prophylaxis is probably not justified for all patients . however , more clinical trials or further studies are crucial and recommended for an exact approval of this idea .\noutput:\n" }, { "from": "agent", "value": "backgroundsthere are controversies among surgeons about prophylaxis of deep vein thrombosis ( dvt ) in laparoscopic cholecystectomy . the aim of this study was the assessment of patients condition after laparoscopic cholecystectomy without any prophylactic measure.methods100 cases of laparoscopic cholecystectomy without dvt prophylaxis were followed by duplex scanning in the first postoperative day and by physical examination and patient history at the first to second postoperative week however no clinical sign was found for dvt.resultsonly one case of partially thrombosis ( 1 % ) was found by duplex scanning which was managed conservatively.conclusionlaparoscopic cholecystectomy may consider as a low - risk procedure and routine prophylaxis may not be justified in the absence of other risk factor ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the majority of studies published to date have reported the role of metformin in preventing the occurrence of cancer in general and of some cancers in particular . to describe the different variations of this bias , we use only some of these studies as a model ; the list of studies that incurred the same biases is provided in table 1 ( 1537 ) . time - related biases in observational studies investigating the effects of metformin on cancer incidence and as a cancer treatment the first published epidemiological study to verify this hypothesis involved a cohort of patients of 10,309 new users of oral hypoglycemic agents ( ohas ) identified from the saskatchewan health databases ( 15 ) . they were followed through 1999 for death due to cancer , which occurred in 407 patients . exposure was classified as sulfonylureas only or metformin , with the latter including users of only metformin and those who also used sulfonylureas at some point in time during follow - up . a cox proportional hazards model was used to estimate the hazard ratio ( hr ) , adjusted for age , sex , insulin use , and a chronic disease score . the adjusted hr of cancer mortality for sulfonylurea versus metformin was 1.3 ( 95 % ci 1.11.6 ) , which , when reversed , gives the hr for metformin relative to sulfonylurea as 0.8 ( 0.60.9 ) , suggesting a protective effect of metformin . immortal time bias is introduced in this study from its definition of exposure and related analysis . the 3,340 subjects who entered the cohort while using sulfonylureas and remained on these throughout the entire follow - up and the 1,229 who used only metformin from day 1 throughout follow - up pose no problem to the definition of exposure . the bias is introduced by classifying some of the remaining 5,740 who used sulfonylureas and metformin at various times during follow - up as metformin users . although those whose cohort entry prescription was metformin are classified correctly in the metformin - exposed group , those whose cohort entry prescription was a sulfonylurea are not ( fig .1 ) . indeed , the time between the sulfonylurea prescription at entry into the cohort and the first metformin prescription during follow - up is called immortal ( thick gray line in fig .1 ) because the patient must be alive to have received their first metformin prescription ( 1 ) . moreover , this immortal person - time should be classified as sulfonylurea - exposed until the start of metformin , at which point the remaining person - time can be classified as metformin - exposed . in this study , the authors misclassified this immortal person - time as metformin - exposed , which will lead to immortal time bias . illustration of immortal time bias using a description of patients exposed to metformin and sulfonylureas who died of cancer according to the definition used in the cohort study by bowker et al . the top patient initiated and continued treatment with a sulfonylurea and subsequently switched to or added metformin but is classified as a metformin user during the entire follow - up . the time between entry into the cohort and the first metformin prescription thus is immortal ( thick line ) because the subject must survive to receive this first metformin prescription and is misclassified as exposed to metformin when in fact it is exposed to sulfonylurea , leading to immortal time bias . because the data necessary to assess the magnitude of the bias are not provided in the article , for the sake of illustration we assume that the mean delay between cohort entry and the first metformin prescription was 1 year among the 5,740 combined users . this would result in 5,740 immortal person - years of sulfonylurea exposure misclassified as metformin exposure . the reported rates of cancer death for metformin ( 245/39 ,026 = 6.3 per 1,000 person - years ) and for sulfonylureas ( 162/16 ,700 = 9.7 per 1,000 person - years ) , which were based on misclassified denominators , produced a crude rate ratio of 0.65 . by properly reclassifying exposure ( per our assumption ) , the rates would become 245 / ( 39,0265,740 ) = 7.4 per 1,000 person - years for metformin and 162 / ( 16,700 + 5,740 ) = 7.2 per 1,000 person - years for sulfonylureas , resulting in a corrected crude rate ratio of 1.0 . there are more sophisticated ways to estimate the rate ratio while properly accounting for such time - varying exposures , such as cox proportional hazards models with time - dependent factors . an alternative approach simply is to use an intent - to - treat approach ( as is done in rcts ) that classifies exposure according to the first oha prescription type , irrespective of switching to or adding the other agent , with , of course , the limitations of interpretation inherent to this approach . in a subsequent publicationreanalyzing the same data , the authors recognized the presence of immortal time bias , claiming we extended our analyses by classifying time - varying exposure of metformin , sulfonylureas and insulin therapy ( 16 ) . the reported an adjusted hr of 0.80 ( 95 % ci 0.650.98 ; p = 0.03 ) for metformin use relative to sulfonylurea monotherapy and the corresponding rates of cancer mortality ( 6.3 vs. 9.7 per 1,000 person - years ) remained identical to those reported previously , which were subject to immortal time bias . this perfect equality of rates is numerically impossible and thus casts doubt on whether the time - varying statistical model was applied correctly to metformin exposure to properly reclassify the misclassified exposure in this second publication . immortal time bias also was evident in a study using taiwanese national health insurance data in 2000 ( 18 ) . it included 12,005 patients with type 2 diabetes who received at least two prescriptions of metformin during 20002007 ; these patients were compared with 4,597 patients who did not use metformin but had other ohas and 8,643 who did not use any oha during this period . cancer events occurring 1 year after entry into the cohort until the end of 2007 were identified . using the cox proportional hazards model to adjust for covariates , the use of metformin was associated with lower incidence of cancer with hrs of any cancer of 0.12 ( 95 % ci 0.080.19 ) , of colorectal cancer ( 0.36 [ 0.130.98 ] ) , liver cancer ( 0.06 [ 0.020.16 ] ) , and pancreatic cancer ( 0.15 [ 0.030.79 ] ) . indeed , the 12,005 subjects defined as exposed to metformin during 20002007 had to have at least two prescriptions for metformin during this period . the bias is introduced because the time between the first and second metformin prescriptions during follow - up is immortal , that is , the patient must be cancer - free to have received the second metformin prescription , which could have been dispensed much later . moreover , this person - time should be classified as unexposed until the second metformin prescription , at which point the remaining person - time should be classified as metformin - exposed . thus , the analysis misclassified all this person - time as metformin exposure , which led to immortal time bias . in contrast , the comparison group of patients who did not use any oha did not have such a condition of a second prescription . another example of this bias is the study using the hong kong diabetes registry to form a cohort of 2,658 patients diagnosed with type 2 diabetes who did not use metformin when enrolled in the study between 1996 and 2005 or in the 2.5 years before enrollment , with follow - up until 2005 ( 22 ) . during a median 5.5 years of follow - upa cox proportional hazards model was used to estimate the hr of cancer , which was adjusted for several covariates . the use of metformin during follow - up was associated with significant reductions in cancer incidence , with hrs of 0.51 ( 95 % ci 0.310.82 ) among patients with hdl cholesterol 1.0 mmol / l and 0.30 ( 0.130.70 ) among patients with hdl cholesterolimmortal time bias also is present in this study because none of the patients were using metformin at the time of entry into the cohort or during the 2.5 years before but were classified in the analysis as metformin users if they received a prescription for metformin during the follow - up . the bias then is introduced by classifying the time between entry into the cohort and the first metformin prescription as metformin - exposed . this person - time is immortal and should have been classified as unexposed until the start of metformin , at which point the remaining person - time should be classified as metformin - exposed . misclassifying all this person - time as metformin - exposed leads to immortal time bias . this bias also is present in a recent study investigating the association between metformin and the incidence of lung cancer ( 23 ) . in that study , the authors used administrative databases from the taiwanese national health insurance program to extract a cohort of 19,624 patients who were treated with antidiabetic agents between 2000 and 2005 . in cox proportional hazards models , the use of metformin was associated with a 45 % risk reduction of lung cancer ( hr 0.55 [ 95 % ci 0.370.82 ] ) . similar results were observed for thiazolidinediones and - glucosidase inhibitors ( 0.55 [ 0.320.94 ] and 0.61 [ 0.380.98 ] , respectively ) , whereas null results were observed for insulin and sulfonylureas ( 1.00 [ 0.681.45 ] and 1.27 [ 0.752.15 ] , respectively ) . as with the studies described earlier , immortal time bias was introduced by misclassifying unexposed person - time as exposed person - time . based on the data presented in the study , the 16,616 patients who ever used metformin generated 93,987 person - years of exposure , an average of 5.7 years per patient . however , the latter included immortal person - time ( i.e. , time between entry into the cohort and the first metformin prescription , during which no event could have occurred ) . assuming an average 1 - year delay between entry into the cohort and the first metformin prescription , a total of 16,616 immortal person - years would have been misclassified as exposed . as shown in table 2 , by correctly reclassifying this person - time , the rate of the unexposed group would become 33 / ( 14,266 + 16,616 ) = 10.7 per 10,000 person - years instead of 23.2 per 10,000 person - years , whereas the rate in the metformin - exposed group would become 96 / ( 93,98716,616 ) = 12.4 per 10,000 person - years instead of 10.2 per 10,000 person - years , resulting in a corrected crude rate ratio of 1.16 . based on similar calculations , a delay of only 9.6 months between entry into the cohort and the first metformin prescription would have been necessary to bring the crude rate ratio to the null value . thus , it is important to recognize that in the context of a highly prevalent exposure such as metformin , even small misclassifications of just a few months can result in greatly biased rate ratios . comparison between biased time - fixed and corrected time - dependent data analyses for the cohort study of metformin and lung cancer incidence ( 23 ) as summarized in table 1 , immortal time bias affected nine observational studies evaluating the association between metformin and cancer incidence or mortality . because of important misclassifications of exposure , the risk reductions observed in these studies were greatly exaggerated in favor of metformin . furthermore , the variations in the reported risk reductions , ranging between 20 and 94 % ( table 1 ) , are a direct reflection of the different magnitude of misclassification of immortal time in the studies , leading to bias of different magnitudes . a study design that has been used extensively is the nested case - control analysis conducted , in this first study , within a cohort of 22,621 women newly treated with ohas between 1994 and 2005 who were identified using the u.k . general practice research database ( 32 ) . during follow - up , 309 women developed breast cancer and were matched to 1,153 controls selected from the cohort on age , general practice , and index date . overall , the use of metformin was not associated with a decreased risk of breast cancer ( odds ratio [ or ] 1.03 [ 95 % ci 0.761.39 ] ) . however , for patients who were prescribed at least 40 prescriptions , metformin was associated with a significant risk reduction ( 0.44 [ 0.240.82 ] ) . in this study , the authors used risk - set sampling , making metformin exposure time - dependent and thus avoiding immortal time bias . however , the cases and controls were not matched on duration of follow - up or , more specifically , on duration of exposure opportunity time , which can lead to time - window bias ( 2 ) . matching on duration of follow - up ensures the same opportunity time of being exposed for cases and matched controls . in this study , the null finding for overall use of metformin likely indicates that cases and matched controls had , on average , similar follow - up times . however , it is possible that in certain subgroups , such as in those who received at least 40 prescriptions , the follow - up may have been different between cases and controls . as such , it is possible that controls had a longer follow - up period than cases and hence a greater opportunity to receive additional prescriptions . the opposite could have occurred as well , and therefore the direction of this bias highly depends on the distribution of follow - up among the randomly selected controls . indeed , in a subsequent study using similar methods to investigate the effects of metformin on the incidence of colorectal cancer , the same authors reported an increased risk among patients who received at least 50 prescriptions ( or 1.43 [ 95 % ci 1.081.90 ] ) ( 36 ) . this time - window bias also likely was present in other studies by the same authors who used this same approach to investigate the effect of metformin use on the risk of ovarian and pancreatic cancers ( 34,35 ) . another example of time - window bias is a study investigating the association between antidiabetic drugs and the risk of hepatocellular carcinoma ( 31 ) . this was a single - center , hospital - based , case - control study from texas , involving 420 cases of hepatocellular carcinoma and 1,104 hospital controls identified between 2000 and 2008 . the use of metformin and thiazolidinediones was associated with a decreased risk of hepatocellular carcinoma ( or 0.3 [ 95 % ci 0.20.6 ] and 0.3 [ 0.10.7 ] , respectively ) . it is interesting that cases were more likely than controls to be controlled with diet ( 13.1 vs. 2.3 % , respectively ) . a priori , diet - controlled diabetes would have been expected to be associated with the lowest risk of cancer because it is used early in the natural history of the disease primarily in patients with a new diagnosed of type 2 diabetes ( based on the assumption that disease severity is associated with an increased risk of cancer ) . however , it is surprising that diet - controlled diabetes was associated strongly with an increased risk of hepatocellular carcinoma ( 7.8 [ 1.540.0 ] ) . whereas duration of diabetes was generally similar between the cases and controls , this finding reveals that duration of treated diabetes was largely differential between cases and controls . indeed , the much lower prevalence of diet - controlled diabetes among the controls suggests that these patients had a longer treatment history than the cases . as such , on the basis of their longer treatment history , controls had a greater opportunity to use metformin and other antidiabetic drugs . this differential treatment time window between cases and controls likely led to the apparent increased risk of hepatocellular carcinoma with diet - controlled diabetes and consequently to an apparent decreased risk with metformin and thiazolidinediones . as discussed earlier and summarized in table 1 , time - window bias can lead to spurious associations even when proper time - dependent analyses are performed . in some studies , there was an attempt to either adjust or match on duration of diabetes ( 28,31 ) . although controlling for this important variable certainly minimizes confounding by disease severity , it does not correct for the differential lengths of the treatment time windows in the cases and controls . furthermore , it is difficult to predict the direction of the time - window bias because it depends on the distribution of treatment duration in the randomly selected controls compared with the cases . it is fortunate that this bias can easily be avoided at the design stage by properly accounting for duration of treatment in the cases and controls ( 2 ) . some studies that have used cohorts of patients treated with antidiabetic drugs have compared the exposure time of metformin use with exposure time of other antidiabetic treatments , including sulfonylureas and insulin . several methodological aspects have to be considered when a first - line therapy such as metformin is compared with second - or third - line therapies ( fig . first , patients are unlikely to be at the same stage of diabetes , which can induce confounding by disease duration : longer duration of diabetes may be associated with higher cancer incidence , independent of age . in such a case , the proper comparison would require matching on disease duration so that the cohort would be formed as in fig . 2 ( bottom ) rather than the time - lagged comparison suggested by fig . second , if the first treatment used is associated with an increased incidence of cancer , albeit after a long period of exposure , it is likely that the cancer will occur during exposure to the second - line agent , in which case attribution of the cancer to either treatment is challenging thus the importance of considering latency time windows . depiction of a time - lagging bias when comparing a first - line diabetic drug ( metformin ) used at an earlier stage of diabetes with second - or third - line drugs used or added at a later stage ( sulfonylurea ) ( top ) and a cohort design that controls for time - lagging bias by comparing two patients at the same stage of diabetes ( bottom ) . the arrows represent the time point where cohort follow - up starts in conducting comparisons : top represents a time - lagged comparison , whereas bottom arrow represents a comparison that accounts for stage of diabetes . ( a high - quality color representation of this figure is available in the online issue . ) a study that was affected by confounding by disease stage is one that used the health information network , a u.k . the study population was then subdivided into four cohorts : cohort 1 included new users of metformin monotherapy ; cohort 2 comprised new users of sulfonylurea monotherapy ; cohort 3 included those who switched from monotherapy with metformin or sulfonylurea to a combination of both drugs ; and cohort 4 included those who switched from ohas to insulin . incidence rates of cancer ( specifically breast , pancreas , colorectal , and prostate cancers ) were calculated within each of the aforementioned cohorts , and cox proportional hazards models were used to compare cohorts 2 , 3 , and 4 with cohort 1 ( metformin monotherapy ) . after a mean follow - up of 2 years , the hrs ( 95 % cis ) were 1.4 ( 1.21.5 ) for sulfonylurea monotherapy , 1.1 ( 1.01.2 ) for the metformin - sulfonylurea combination , and 1.4 ( 1.31.6 ) for insulin . among patients treated with insulin , the concomitant use of metformin was associated with a statistically significant risk reduction ( 0.54 [ 0.430.66 ] ) . however , this strong inverse association was likely due to immortal time bias because exposure to metformin was assessed at any time during follow - up and thus included person - time during which patients were not yet exposed to this therapy ( table 1 ) . furthermore , as noted by others , the survival curves of the different cohorts presented by the authors diverged as early as during the first year of treatment , thus arguing against a causal effect , which is biologically inconsistent with the long latencies of cancers ( 38 ) . aside from reverse causality and confounding , which are certainly important considerations , such early divergence in the survival curvesfirst , comparing the different cohorts , which consisted of second - and third - line treatments , with metformin monotherapy , a first - line treatment , inherently introduces biases related to disease duration and progression that may not be dealt with adequately during analysis . second , the consideration of cancers diagnosed early after entry into the cohort is problematic , especially for patients with a history of oha use ( i.e. , cohorts 3 and 4 ) , because it ignores the fact that previous exposure might have affected future cancer risk . indeed , patients may remain at risk for an extended period of time long after discontinuation of treatment . for example , former smokers with a history of smoking one pack per day for a period of 1 year have a nearly threefold increased risk of lung cancer after 30 years of cessation ( 39 ) . one approach to minimize this bias is to apply time - lag periods to exclude cancers diagnosed within a specified time period after entry into the cohort . this method works reasonably well , especially if there is clustering of cancers early during the treatment , as was observed in this study ( 17 ) . a study that introduced a variation of bias due to time - lagging of comparison cohorts was that based on the diabetes audit and research in tayside study cohort of patients diagnosed with type 2 diabetes in tayside , scotland ( 37 ) . all 4,085 eligible new users of metformin between 1994 and 2003 were matched individually with 4,085 nonusers on year of diabetes diagnosis ; each pair was assigned the date of entry into the cohort as the date of the first metformin prescription of the user . of the subjects who were cancer free at cohort entry , 771 developed cancer during follow - up . a cox proportional hazards model was used to estimate the hr of cancer , adjusted for several covariates . the adjusted hr of cancer associated with metformin use was 0.63 ( 95 % ci 0.530.75 ) , suggesting a strong protective effect of metformin . although this study avoided biases associated with prevalent exposures by using a new - user cohort of patients treated with metformin , this approach was not used for the comparison group , which was not based on a specific comparison drug . because the comparison metformin nonuser does not have a prescription date to define time zero , it was assigned the date of the first metformin prescription of its matched user , a date called the index date . in choosing among potential nonusers for a given user , a variation of bias from time lagsindeed , if the potential matched nonuser had a diagnosis of cancer or had died prior to the index date , it was discarded . however , it was potentially available for a different metformin user this process was repeated until suitable comparators were identified . nonusers should be alive and cancer free at entry into the cohort just like the matched users , but the net effect of selecting the nonusers with replacement is twofold . first , the final nonuser group had zero subjects excluded because of cancer before the index date , in contrast with the 239 excluded from the metformin group . second , the nonusers who should have been excluded ( and not reused ) because of a previous cancer were included as nonusers matched to other users . as a result , cancers that should have been an exclusion criterion were transferred to the follow - up period after the index date and counted as outcome events , thus artificially increasing the rate of cancer in the nonuser group . this phenomenon is noticeable in the kaplan - meier curves that suggest a clustering of cancers in the first 2 years of follow - up of the nonuser group . thus , by forming the nonuser group , the authors artificially induced a cohort that was immortal and cancer free before the index date but had more deaths and cancers after entry into the cohort . as a result of this transfer , the nonuser group had 474 cancers diagnosed during follow - up compared with 297 in the metformin group . if the exclusion of 239 cancers before the first metformin prescription is applied to the nonuser group , the 474 would be reduced to 177 . the first published epidemiological study to verify this hypothesis involved a cohort of patients of 10,309 new users of oral hypoglycemic agents ( ohas ) identified from the saskatchewan health databases ( 15 ) . they were followed through 1999 for death due to cancer , which occurred in 407 patients . exposure was classified as sulfonylureas only or metformin , with the latter including users of only metformin and those who also used sulfonylureas at some point in time during follow - up . a cox proportional hazards model was used to estimate the hazard ratio ( hr ) , adjusted for age , sex , insulin use , and a chronic disease score . the adjusted hr of cancer mortality for sulfonylurea versus metformin was 1.3 ( 95 % ci 1.11.6 ) , which , when reversed , gives the hr for metformin relative to sulfonylurea as 0.8 ( 0.60.9 ) , suggesting a protective effect of metformin . immortal time bias is introduced in this study from its definition of exposure and related analysis . the 3,340 subjects who entered the cohort while using sulfonylureas and remained on these throughout the entire follow - up and the 1,229 who used only metformin from day 1 throughout follow - up pose no problem to the definition of exposure . the bias is introduced by classifying some of the remaining 5,740 who used sulfonylureas and metformin at various times during follow - up as metformin users . although those whose cohort entry prescription was metformin are classified correctly in the metformin - exposed group , those whose cohort entry prescription was a sulfonylurea are not ( fig .1 ) . indeed , the time between the sulfonylurea prescription at entry into the cohort and the first metformin prescription during follow - up is called immortal ( thick gray line in fig .1 ) because the patient must be alive to have received their first metformin prescription ( 1 ) . moreover , this immortal person - time should be classified as sulfonylurea - exposed until the start of metformin , at which point the remaining person - time can be classified as metformin - exposed . in this study , the authors misclassified this immortal person - time as metformin - exposed , which will lead to immortal time bias . illustration of immortal time bias using a description of patients exposed to metformin and sulfonylureas who died of cancer according to the definition used in the cohort study by bowker et al . the top patient initiated and continued treatment with a sulfonylurea and subsequently switched to or added metformin but is classified as a metformin user during the entire follow - up . the time between entry into the cohort and the first metformin prescription thus is immortal ( thick line ) because the subject must survive to receive this first metformin prescription and is misclassified as exposed to metformin when in fact it is exposed to sulfonylurea , leading to immortal time bias . because the data necessary to assess the magnitude of the bias are not provided in the article , for the sake of illustration we assume that the mean delay between cohort entry and the first metformin prescription was 1 year among the 5,740 combined usersthis would result in 5,740 immortal person - years of sulfonylurea exposure misclassified as metformin exposure . the reported rates of cancer death for metformin ( 245/39 ,026 = 6.3 per 1,000 person - years ) and for sulfonylureas ( 162/16 ,700 = 9.7 per 1,000 person - years ) , which were based on misclassified denominators , produced a crude rate ratio of 0.65 . by properly reclassifying exposure ( per our assumption ) , the rates would become 245 / ( 39,0265,740 ) = 7.4 per 1,000 person - years for metformin and 162 / ( 16,700 + 5,740 ) = 7.2 per 1,000 person - years for sulfonylureas , resulting in a corrected crude rate ratio of 1.0 . there are more sophisticated ways to estimate the rate ratio while properly accounting for such time - varying exposures , such as cox proportional hazards models with time - dependent factors . an alternative approach simply is to use an intent - to - treat approach ( as is done in rcts ) that classifies exposure according to the first oha prescription type , irrespective of switching to or adding the other agent , with , of course , the limitations of interpretation inherent to this approach . in a subsequent publication reanalyzing the same data , the authors recognized the presence of immortal time bias , claiming we extended our analyses by classifying time - varying exposure of metformin , sulfonylureas and insulin therapythe reported an adjusted hr of 0.80 ( 95 % ci 0.650.98 ; p = 0.03 ) for metformin use relative to sulfonylurea monotherapy and the corresponding rates of cancer mortality ( 6.3 vs. 9.7 per 1,000 person - years ) remained identical to those reported previously , which were subject to immortal time bias . this perfect equality of rates is numerically impossible and thus casts doubt on whether the time - varying statistical model was applied correctly to metformin exposure to properly reclassify the misclassified exposure in this second publication . immortal time bias also was evident in a study using taiwanese national health insurance data in 2000 ( 18 ) . it included 12,005 patients with type 2 diabetes who received at least two prescriptions of metformin during 20002007 ; these patients were compared with 4,597 patients who did not use metformin but had other ohas and 8,643 who did not use any oha during this period . cancer events occurring 1 year after entry into the cohort until the end of 2007 were identified . using the cox proportional hazards model to adjust for covariates , the use of metformin was associated with lower incidence of cancer with hrs of any cancer of 0.12 ( 95 % ci 0.080.19 ) , of colorectal cancer ( 0.36 [ 0.130.98 ] ) , liver cancer ( 0.06 [ 0.020.16 ] ) , and pancreatic cancer ( 0.15 [ 0.030.79 ] ) . indeed , the 12,005 subjects defined as exposed to metformin during 20002007 had to have at least two prescriptions for metformin during this period . the bias is introduced because the time between the first and second metformin prescriptions during follow - up is immortal , that is , the patient must be cancer - free to have received the second metformin prescription , which could have been dispensed much later . moreover , this person - time should be classified as unexposed until the second metformin prescription , at which point the remaining person - time should be classified as metformin - exposed . thus , the analysis misclassified all this person - time as metformin exposure , which led to immortal time bias . in contrast , the comparison group of patients who did not use any oha did not have such a condition of a second prescription . another example of this bias is the study using the hong kong diabetes registry to form a cohort of 2,658 patients diagnosed with type 2 diabetes who did not use metformin when enrolled in the study between 1996 and 2005 or in the 2.5 years before enrollment , with follow - up until 2005 ( 22 ) . during a median 5.5 years of follow - upa cox proportional hazards model was used to estimate the hr of cancer , which was adjusted for several covariates . the use of metformin during follow - up was associated with significant reductions in cancer incidence , with hrs of 0.51 ( 95 % ci 0.310.82 ) among patients with hdl cholesterol 1.0 mmol / l and 0.30 ( 0.130.70 ) among patients with hdl cholesterolimmortal time bias also is present in this study because none of the patients were using metformin at the time of entry into the cohort or during the 2.5 years before but were classified in the analysis as metformin users if they received a prescription for metformin during the follow - up . the bias then is introduced by classifying the time between entry into the cohort and the first metformin prescription as metformin - exposed . this person - time is immortal and should have been classified as unexposed until the start of metformin , at which point the remaining person - time should be classified as metformin - exposed . misclassifying all this person - time as metformin - exposed leads to immortal time bias . this bias also is present in a recent study investigating the association between metformin and the incidence of lung cancer ( 23 ) . in that study , the authors used administrative databases from the taiwanese national health insurance program to extract a cohort of 19,624 patients who were treated with antidiabetic agents between 2000 and 2005 . in cox proportional hazards models , the use of metformin was associated with a 45 % risk reduction of lung cancer ( hr 0.55 [ 95 % ci 0.370.82 ] ) . similar results were observed for thiazolidinediones and - glucosidase inhibitors ( 0.55 [ 0.320.94 ] and 0.61 [ 0.380.98 ] , respectively ) , whereas null results were observed for insulin and sulfonylureas ( 1.00 [ 0.681.45 ] and 1.27 [ 0.752.15 ] , respectively ) . as with the studies described earlier , immortal time bias was introduced by misclassifying unexposed person - time as exposed person - time . based on the data presented in the study , the 16,616 patients who ever used metformin generated 93,987 person - years of exposure , an average of 5.7 years per patient . however , the latter included immortal person - time ( i.e. , time between entry into the cohort and the first metformin prescription , during which no event could have occurred ) . assuming an average 1 - year delay between entry into the cohort and the first metformin prescription , a total of 16,616 immortal person - years would have been misclassified as exposed . as shown in table 2 , by correctly reclassifying this person - time , the rate of the unexposed group would become 33 / ( 14,266 + 16,616 ) = 10.7 per 10,000 person - years instead of 23.2 per 10,000 person - years , whereas the rate in the metformin - exposed group would become 96 / ( 93,98716,616 ) = 12.4 per 10,000 person - years instead of 10.2 per 10,000 person - years , resulting in a corrected crude rate ratio of 1.16 . based on similar calculations , a delay of only 9.6 months between entry into the cohort and the first metformin prescription would have been necessary to bring the crude rate ratio to the null value . thus , it is important to recognize that in the context of a highly prevalent exposure such as metformin , even small misclassifications of just a few months can result in greatly biased rate ratios . comparison between biased time - fixed and corrected time - dependent data analyses for the cohort study of metformin and lung cancer incidence ( 23 ) as summarized in table 1 , immortal time bias affected nine observational studies evaluating the association between metformin and cancer incidence or mortality . because of important misclassifications of exposure , the risk reductions observed in these studies were greatly exaggerated in favor of metformin . furthermore , the variations in the reported risk reductions , ranging between 20 and 94 % ( table 1 ) , are a direct reflection of the different magnitude of misclassification of immortal time in the studies , leading to bias of different magnitudes . a study design that has been used extensively is the nested case - control analysis conducted , in this first study , within a cohort of 22,621 women newly treated with ohas between 1994 and 2005 who were identified using the u.k .309 women developed breast cancer and were matched to 1,153 controls selected from the cohort on age , general practice , and index date . overall , the use of metformin was not associated with a decreased risk of breast cancer ( odds ratio [ or ] 1.03 [ 95 % ci 0.761.39 ] ) . however , for patients who were prescribed at least 40 prescriptions , metformin was associated with a significant risk reduction ( 0.44 [ 0.240.82 ] ) . in this study , the authors used risk - set sampling , making metformin exposure time - dependent and thus avoiding immortal time bias . however , the cases and controls were not matched on duration of follow - up or , more specifically , on duration of exposure opportunity time , which can lead to time - window bias ( 2 ) . matching on duration of follow - up ensures the same opportunity time of being exposed for cases and matched controls . in this study , the null finding for overall use of metformin likely indicates that cases and matched controls had , on average , similar follow - up times . however , it is possible that in certain subgroups , such as in those who received at least 40 prescriptions , the follow - up may have been different between cases and controls . as such , it is possible that controls had a longer follow - up period than cases and hence a greater opportunity to receive additional prescriptions . the opposite could have occurred as well , and therefore the direction of this bias highly depends on the distribution of follow - up among the randomly selected controls . indeed , in a subsequent study using similar methods to investigate the effects of metformin on the incidence of colorectal cancer , the same authors reported an increased risk among patients who received at least 50 prescriptions ( or 1.43 [ 95 % ci 1.081.90 ] ) ( 36 ) . this time - window bias also likely was present in other studies by the same authors who used this same approach to investigate the effect of metformin use on the risk of ovarian and pancreatic cancers ( 34,35 ) . another example of time - window bias is a study investigating the association between antidiabetic drugs and the risk of hepatocellular carcinoma ( 31 ) . this was a single - center , hospital - based , case - control study from texas , involving 420 cases of hepatocellular carcinoma and 1,104 hospital controls identified between 2000 and 2008 . the use of metformin and thiazolidinediones was associated with a decreased risk of hepatocellular carcinoma ( or 0.3 [ 95 % ci 0.20.6 ] and 0.3 [ 0.10.7 ] , respectively ) . it is interesting that cases were more likely than controls to be controlled with diet ( 13.1 vs. 2.3 % , respectively ) . a priori , diet - controlled diabetes would have been expected to be associated with the lowest risk of cancer because it is used early in the natural history of the disease primarily in patients with a new diagnosed of type 2 diabetes ( based on the assumption that disease severity is associated with an increased risk of cancer ) . however , it is surprising that diet - controlled diabetes was associated strongly with an increased risk of hepatocellular carcinoma ( 7.8 [ 1.540.0 ] ) . whereas duration of diabetes was generally similar between the cases and controls , this finding reveals that duration of treated diabetes was largely differential between cases and controls . indeed , the much lower prevalence of diet - controlled diabetes among the controls suggests that these patients had a longer treatment history than the cases . as such , on the basis of their longer treatment history , controls had a greater opportunity to use metformin and other antidiabetic drugs . this differential treatment time window between cases and controls likely led to the apparent increased risk of hepatocellular carcinoma with diet - controlled diabetes and consequently to an apparent decreased risk with metformin and thiazolidinediones . as discussed earlier and summarized in table 1 , time - window bias can lead to spurious associations even when proper time - dependent analyses are performed . in some studies , there was an attempt to either adjust or match on duration of diabetes ( 28,31 ) . although controlling for this important variable certainly minimizes confounding by disease severity , it does not correct for the differential lengths of the treatment time windows in the cases and controls . furthermore , it is difficult to predict the direction of the time - window bias because it depends on the distribution of treatment duration in the randomly selected controls compared with the cases . it is fortunate that this bias can easily be avoided at the design stage by properly accounting for duration of treatment in the cases and controls ( 2 ) . some studies that have used cohorts of patients treated with antidiabetic drugs have compared the exposure time of metformin use with exposure time of other antidiabetic treatments , including sulfonylureas and insulin . several methodological aspects have to be considered when a first - line therapy such as metformin is compared with second - or third - line therapies ( fig . first , patients are unlikely to be at the same stage of diabetes , which can induce confounding by disease duration : longer duration of diabetes may be associated with higher cancer incidence , independent of age . in such a case , the proper comparison would require matching on disease duration so that the cohort would be formed as in fig . 2 ( bottom ) rather than the time - lagged comparison suggested by fig . second , if the first treatment used is associated with an increased incidence of cancer , albeit after a long period of exposure , it is likely that the cancer will occur during exposure to the second - line agent , in which case attribution of the cancer to either treatment is challenging thus the importance of considering latency time windows . depiction of a time - lagging bias when comparing a first - line diabetic drug ( metformin ) used at an earlier stage of diabetes with second - or third - line drugs used or added at a later stage ( sulfonylurea ) ( top ) and a cohort design that controls for time - lagging bias by comparing two patients at the same stage of diabetes ( bottom ) . the arrows represent the time point where cohort follow - up starts in conducting comparisons : top represents a time - lagged comparison , whereas bottom arrow represents a comparison that accounts for stage of diabetes . ( a high - quality color representation of this figure is available in the online issue . ) a study that was affected by confounding by disease stage is one that used the health information network , a u.k . general practice database ( 17 ) . in this study , the authors identified 62,809 users of ohas or insulin between 2000 and 2007 . the study population was then subdivided into four cohorts : cohort 1 included new users of metformin monotherapy ; cohort 2 comprised new users of sulfonylurea monotherapy ; cohort 3 included those who switched from monotherapy with metformin or sulfonylurea to a combination of both drugs ; and cohort 4 included those who switched from ohas to insulin . incidence rates of cancer ( specifically breast , pancreas , colorectal , and prostate cancers ) were calculated within each of the aforementioned cohorts , and cox proportional hazards models were used to compare cohorts 2 , 3 , and 4 with cohort 1 ( metformin monotherapy ) . after a mean follow - up of 2 years , the hrs ( 95 % cis ) were 1.4 ( 1.21.5 ) for sulfonylurea monotherapy , 1.1 ( 1.01.2 ) for the metformin - sulfonylurea combination , and 1.4 ( 1.31.6 ) for insulin . among patients treated with insulin , the concomitant use of metformin was associated with a statistically significant risk reduction ( 0.54 [ 0.430.66 ] ) . however , this strong inverse association was likely due to immortal time bias because exposure to metformin was assessed at any time during follow - up and thus included person - time during which patients were not yet exposed to this therapy ( table 1 ) . furthermore , as noted by others , the survival curves of the different cohorts presented by the authors diverged as early as during the first year of treatment , thus arguing against a causal effect , which is biologically inconsistent with the long latencies of cancers ( 38 ) . aside from reverse causality and confounding , which are certainly important considerations , such early divergence in the survival curvesfirst , comparing the different cohorts , which consisted of second - and third - line treatments , with metformin monotherapy , a first - line treatment , inherently introduces biases related to disease duration and progression that may not be dealt with adequately during analysis . second , the consideration of cancers diagnosed early after entry into the cohort is problematic , especially for patients with a history of oha use ( i.e. , cohorts 3 and 4 ) , because it ignores the fact that previous exposure might have affected future cancer risk . indeed , patients may remain at risk for an extended period of time long after discontinuation of treatment . for example , former smokers with a history of smoking one pack per day for a period of 1 year have a nearly threefold increased risk of lung cancer after 30 years of cessation ( 39 ) . one approach to minimize this bias is to apply time - lag periods to exclude cancers diagnosed within a specified time period after entry into the cohort . this method works reasonably well , especially if there is clustering of cancers early during the treatment , as was observed in this study ( 17 ) . a study that introduced a variation of bias due to time - lagging of comparison cohorts was that based on the diabetes audit and research in tayside study cohort of patients diagnosed with type 2 diabetes in tayside , scotland ( 37 ) . all 4,085 eligible new users of metformin between 1994 and 2003 were matched individually with 4,085 nonusers on year of diabetes diagnosis ; each pair was assigned the date of entry into the cohort as the date of the first metformin prescription of the user . of the subjects who were cancer free at cohort entry , 771 developed cancer during follow - up . a cox proportional hazards model was used to estimate the hr of cancer , adjusted for several covariates . the adjusted hr of cancer associated with metformin use was 0.63 ( 95 % ci 0.530.75 ) , suggesting a strong protective effect of metformin . although this study avoided biases associated with prevalent exposures by using a new - user cohort of patients treated with metformin , this approach was not used for the comparison group , which was not based on a specific comparison drug . because the comparison metformin nonuser does not have a prescription date to define time zero , it was assigned the date of the first metformin prescription of its matched user , a date called the index date . in choosing among potential nonusers for a given user , a variation of bias from time lagsindeed , if the potential matched nonuser had a diagnosis of cancer or had died prior to the index date , it was discarded . however , it was potentially available for a different metformin user this process was repeated until suitable comparators were identified . nonusers should be alive and cancer free at entry into the cohort just like the matched users , but the net effect of selecting the nonusers with replacement is twofold . first , the final nonuser group had zero subjects excluded because of cancer before the index date , in contrast with the 239 excluded from the metformin group . second , the nonusers who should have been excluded ( and not reused ) because of a previous cancer were included as nonusers matched to other users . as a result , cancers that should have been an exclusion criterion were transferred to the follow - up period after the index date and counted as outcome events , thus artificially increasing the rate of cancer in the nonuser group . this phenomenon is noticeable in the kaplan - meier curves that suggest a clustering of cancers in the first 2 years of follow - up of the nonuser group . thus , by forming the nonuser group , the authors artificially induced a cohort that was immortal and cancer free before the index date but had more deaths and cancers after entry into the cohort . as a result of this transfer , the nonuser group had 474 cancers diagnosed during follow - up compared with 297 in the metformin group . if the exclusion of 239 cancers before the first metformin prescription is applied to the nonuser group , the 474 would be reduced to 177 . several of these studies reported significant risk reductions for all - cause mortality , cancer - specific mortality , and cancer progression , ranging between 34 and 62 % ( 2427 ) . all of the studies reporting these important risk reductions suffered from immortal time bias ( summarized in table 1 ) . we describe below selected studies to illustrate this bias in the setting of cancer treatment . in the first study , the authors reviewed the records of 233 patients diagnosed with prostate cancer between 1999 and 2008 at a medical institution in texas ( 24 ) . they evaluated whether antidiabetic treatments were associated with all - cause mortality in this patient population . cox proportional hazards models were constructed , with ever - use of insulins and ohas entered as independent variables , and adjusted for potential confounders . their results indicate that metformin ( hr 0.55 [ 95 % ci 0.320.96 ] ) and thiazolidinediones ( 0.45 [ 0.210.97 ] ) were associated with a significant decrease in all - cause mortality . no statistically significant associations were observed with the other antidiabetic agents , although few patients were exposed in this small dataset . misclassifying as exposed the time between cohort entry and first prescription of metformin or a thiazolidinedione introduced immortal time bias , thus greatly exaggerating the benefits of these drugs on all - cause mortality . that exposure was defined as any time during the 10 - year follow - up period contributed to compound the effect of this misclassification . as explained earlier , the appropriate analysis would have treated exposures to the different antidiabetic agents as time - dependent variables . the authors of another study identified 595 patients who had been diagnosed with both colorectal cancer and diabetes mellitus and compared the 258 taking metformin any time during follow - up with the 337 nonusers ( 25 ) . after a median follow - up of 41 months , the adjusted hr of all - cause mortality with metformin use was 0.66 ( 95 % ci 0.450.98 ) , whereas for colorectal cancer , mortality was also 0.66 ( 0.480.92 ) . here again , these mortality reductions are the result of immortal time bias caused by misclassifying as exposed to metformin the time between cohort entry and first prescription , when in fact it is unexposed . immortal time bias also was present in a cohort study of 1,983 consecutive patients with her2 + breast cancer treated between 1 january 1998 and 30 september 2010 ( 26 ) . all - cause and cancer - specific deaths were identified . among the patients with diabetes , the hr of all - cause death associated with metformin was 0.52 ( 95 % ci 0.280.97 ) , whereas for breast cancerthese mortality reductions again are the result of immortal time bias caused by misclassifying as exposed the time between cancer diagnosis and first prescription of metformin given during follow - up , when in fact it is unexposed to metformin . we have shown that a large number of observational studies reporting significant reductions in the incidence of or mortality from cancer associated with metformin use are afflicted with time - related biases such as immortal time bias , time - window bias , and time - lag bias . by not classifying metformin exposure duringfollow - up or measuring metformin exposure over different time intervals properly , the resulting analyses produced apparent reductions in risk that were created artificially by the misclassification of metformin exposure . these biases , regrettably common in pharmacoepidemiology , have been described extensively in different therapeutic areas ( 1,2,4042 ) but do not seem to have sufficiently penetrated the fields of diabetes and cancer . although two of the studies recognized the possibility of immortal time bias , the technique of data analysis required to address it was clearly not appropriate ( 16,18 ) . other studies have been conducted with varying results ; some have found no association between metformin use and cancer incidence or prognosis ( 4348 ) , others have found lower rates of cancer with metformin ( 4957 ) , and one study found an increased risk ( 58 ) . although these studies were designed and analyzed with no obvious time - related biases , it is of course possible that other epidemiological biases such as selection , information , or confounding could have affected them . this article focused specifically on time - related biases , where metformin was associated with strong risk reductions , ranging from relative risks of 0.80 ( 20 % risk reduction ) to 0.06 ( 94 % risk reduction ) , likely due to flaws in their designs and methods of analysis . three recent studies that specifically used the time - dependent techniques needed to avoid both immortal time and time - window biases found no association between metformin use and cancer incidence ( 5961 ) . general practice research database and found a rate ratio of prostate cancer incidence of 1.23 ( 95 % ci 0.991.52 ) with metformin use . with more than 36 prescriptions the rate ratio was significantly elevated at 1.40 ( 1.031.89 ) . the second study used the kaiser permanente database and found no effect of metformin on the incidence of the 10 different cancers studied , with hrs ranging between 0.8 ( 0.61.1 ) for melanoma to 1.3 ( 1.01.6 ) for kidney / renal and pelvic cancers . finally , no effect of metformin was found on lung cancer incidence ( 61 ) . it is also important to recognize that most observational studies focused on the incidence of cancer as it relates to the effects of metformin on carcinogenesis , which is distinct from its effects on proliferation of established tumors . nevertheless , large rcts using patients with established tumors currently are being planned or already are in progress . one such study is the ma .32 being conducted by the national cancer institute of canada , a multicenter phase iii rct that includes almost 3,600 women with early breast cancer and is comparing metformin to placebo as adjuvant therapy on the primary end point of invasive , disease - free survival over a 5 - year follow - up ( 12,13 ) . the authors claim that we believe the science underlying such a trial is strong , the novelty of the intervention is high , and the potential for benefit is large ( 12 ) . although it is possible that the in vitro science is strong and metformin may lead to positive results , we have shown that the pharmacoepidemiological evidence from observational studies is weak at best . in conclusion , time - related biases are common in the field of diabetes and can be avoided using appropriate study designs and methods of analysis . in the case of the association between metformin and cancer , we believe that methodologically inaccurate studies , even if their results are replicated in different settings , should not be the driving force behind long and expensive trials . at this time , it may be important to question and reassess the scientific evidence of the potential beneficial effects of metformin on cancer . although the in vitro science seems to be strong , certainly all observational studies identified as potentially biased would need to be redone properly to correct for the bias . moreover , new observational studies using more rigorous designs and analyses that avoid these biases should urgently be undertaken before more randomized trials are initiated in vain .\noutput:\n" }, { "from": "agent", "value": "objectivetime - related biases in observational studies of drug effects have been described extensively in different therapeutic areas but less so in diabetes . immortal time bias , time - window bias , and time - lag bias all tend to greatly exaggerate the benefits observed with a drug.research design and methodsthese time - related biases are described and shown to be prominent in observational studies that have associated metformin with impressive reductions in the incidence of and mortality from cancer . as a consequence , metformin received much attention as a potential anticancer agent ; these observational studies sparked the conduction of randomized , controlled trials of metformin as cancer treatment . however , the spectacular effects reported in these studies are compatible with time - related biases.resultswe found that 13 observational studies suffered from immortal time bias ; 9 studies had not considered time - window bias , whereas other studies did not consider inherent time - lagging issues when comparing the first - line treatment metformin with second - or third - line treatments . these studies , subject to time - related biases that are avoidable with proper study design and data analysis , led to illusory extraordinarily significant effects , with reductions in cancer risk with metformin ranging from 20 to 94 % . three studies that avoided these biases reported no effect of metformin use on cancer incidence.conclusionsalthough observational studies are important to better understand the effects of drugs , their proper design and analysis is essential to avoid major time - related biases . with respect to metformin , the scientific evidence of its potential beneficial effects on cancer would need to be reassessed critically before embarking on further long and expensive trials ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: extracellular stimuli evoke very rapid transcription of an array of immediate early genes such as c - fos , egr1 / zif268 , arc / arg3 .1 and homer1a ( herdegen & leah , 1998 ) . among the immediate early genes , c - fos was discovered very early and has been studied in detail subsequently ( durchdewald et al . , 2009 ) . egr1 is similar to c - fos as transcription factor , but basal expression level is high compared to c - fos and the time course of expression is different ( zangenehpour & chaudhuri , 2002 ; veyrac et al . , 2014 ) . unlike c - fos and egr1 , arc is not a transcription factor , but the mrna and protein are localized in dendrites at sites of synaptic activity mediating synaptic plasticity ( \" effector \" immediateearly gene ) ( bramham et al . , 2008 ) . homer1a is similar to arc in localization and function , but slower in mrna expression than arc ( vazdarjanova et al . , 2002 ; hu et al . , 2010 ) in addition to the detection of mrna and protein , recently other molecular markers or functional tools could be attached to the fos gene to amplify the fos signal detection or to provide other manipulations including optogenetic and chemogenetic stimulations ( kawashima et al . , 2014 ) . however , all of these tools still depend on the experimental condition of c - fos expression . the purpose of this brief review is to provide very basic properties of fos signal as an activity marker . further information can be found from excellent reviews on fos and other immediate early genes ( lyons & west , 2011 ; nestler , 2015 ) . many external stimuli can induce c - fos by increasing neuronal activity ( morgan & curran , 1991 ; herdegen & leah , 1998 ) . however , intracellular calcium is the common molecule that mediates synaptic activity to c - fos gene expression ( ghosh et al . , 1994 ) . because of the diverse effects of calcium , basal neuronal intracellular calcium is kept very low by extrusion to the extracellular space and by uptake into calcium stores ( cohen & greenberg , 2008 ) . during neuronal activity , intracellular calcium concentration increases due to calcium influx mainly from two routes , a type of glutamate receptor ( nmda receptor , nmdar ) and l - type voltage - sensitive calcium channel ( vscc ) ( chaudhuri et al . nmdars can be activated by coincident presynaptic glutamate release and postsynaptic depolarization . as a glutamate receptor - channel complex , the nmdar is highly permeable to calcium ( lau & zukin , 2007 ) . the calcium influx through nmdars can modulate c - fos gene expression ( cohen & greenberg , 2008 ) . in support of this notion , activation of nmdars induces c - fos mrna and fos protein ( liste et al . , 1995 ; berretta et al . , 1997 ; parthasarathy & graybiel , 1997 ) . in contrast , nmdar antagonists block fos expression ( berretta et al . , 1992 ; ghosh et al . , 1994 ; berretta et al . , 1997 ; vanhoutte et al . , 1999 ) . in addition to nmdar , glutamate can also activate fast - acting ampa receptors and metabotropic glutamate receptors ( mglurs ) . ampa receptors can also allow calcium influx especially during early development , but in mature neurons the calcium influx through ampa receptors is limited in function ( derkach et al . , 2007 ) . still , ampars indirectly can contribute to the calcium influx by membrane depolarization to activate nmdars and vsccs . group i mglurs can increase calcium influx , but the effect on fos expression is not strong ( wang et al . the l - type vscc is involved with immediate early gene expression ( rajadhyaksha et al . . basal expression of c - fos is rapidly suppressed by exposure to l - type vscc antagonists and increased by a vscc agonist ( murphy et al . , 1991 ) . as an alternative source of intracellular calcium , calcium can be released from calcium stores after neuronal activity , but more studies are needed to understand its contribution to fos expression ( lyons & west , 2011 ) . after the local calcium increase around the pore of the channels , the specific functional consequences of calcium influx is determined by the signaling molecules physically associated with the nmdar and vscc ( cohen & greenberg , 2008 ) . the increased calcium can activate multiple kinase pathways including mapk , camkiv , camkii and pka . however , fos expression is mainly mediated by mapk pathway which is distinct from other pathways ( chaudhuri et al . , 2000 ) . compared with camkiv pathway , mapk pathway activation is relatively slow , requires strong external stimulation and higher calcium increase ( wu et al . , 2001 ; deisseroth & tsien , 2002 ) . this property can tune mapk pathway to large and continued neural activity ( murphy et al . , strong external stimuli preferentially activate the mapk pathway to result in fos expression while weak stimuli are less likely to be translated into fos signal . the mapk activates two transcription factors binding to the c - fos promoter in the nucleus ( lyons & west , 2011 ) . first , creb ( cyclin amp - response element - binding protein ) is phosphorylated via ribosomal s6 kinase . phosphorylated creb binds to the calcium response element ( or cyclic amp response element ) in the c - fos promotor . second , phosphorylated elk - 1 in association with serum response factor ( srf ) bind to the serum response element in the cfos promotor ( cruz et al . , 2014 ) . inside the nucleus , fos and jun make up the ap - 1 complex that acts as a transcription factor for \" late \" genes . at the basal level , low constitutive levels of c - fosis maintained . this is due to instability of c - fos mrna and auto - repression of c - fos transcription by the fos protein itself ( lucibello et al . the other possibility is the presence of active repression of the promoter because transcription factors and the rna polymerase ii complex are bound already before neural activity ( carrion et al . these molecular conditions suggest the optimal conditions for eliciting the best fos signal as a neural activity marker in vivo . before an experimentfor example , sensory deprivation can be given in the form of social isolation in a singlyhoused animals before stimulus presentation . the isolation duration can be 1 to 7 days . to maximize the signal , a novel stimulus is recommended . in the same line of thinking , repetitive stimulation is expected to reduce the signal . but this issue becomes complex because learning can both sensitize and desensitize the neural circuit depending on the nature of the stimulus to the organism . for example , in negative stimulations such as social defeat from other animals , multiple attacks over days can make the individual animals either depressed or resilient ( wang et al . , it is difficult to predict what the fos signal will be like and how to interpret the signal at the level of single cells . an interesting example was reported in the comparison of acute cocaine injection and a test injection after prior repeated cocaine injection in fos - gfp transgenic mice ( koya et al . , 2012 ) . in this mouse , fos - gfp fusion protein under c - fos promoter is expressed after strong neural activation ( barth et al . , 2004 ) . after repeated cocaine injection , test cocaine injection increased fos signal as gfp positive ( gfp ) cell count compared to acute cocaine injection after repeated saline . the increase of fos signal may reflect increased neural circuit activity . if this is true , increased synaptic strength and increased synaptic transmissions are predicted . in gfp negative cells ( gfp ) , the result is consistent with this prediction . synaptic strength was higher and excitatory postsynaptic current ( epsc ) frequency was increased in the case of repeated cocaine injections . however , in gfp positive cells , synaptic strength was lower than gfp cells and epsc frequency was lower than gfp cells . because the number of gfp cells are much more than gfp cells , in randomly selected cells the overall results reflected those of gfp cells . though gfp cells are small in number , they are not less important than gfp cells . this is an example where fos as neural activity marker represented overall activity correctly , but the prediction did not extend to a functionally important subset of neurons ( ensemble ) . it is intriguing to speculate whether similar results will be found in negative behaviors such as social defeat . multiple social defeat ( e.g. 10 episodes ) can lead to depression - like behavior in defeated animals ( krishnan & nestler , 2011 ) . in general , fos was decreased after repeated social defeat in multiple brain regions ( martinez et al . , 2002 ) . when the cue associated with social defeat was presented 1 day or 7 days later , the cue increased fos signal in medial prefrontal cortex ( bourne et al . , 2013 ) . in this case , the fos signal is used as an indicator of longterm memory . in another study c - fos mrna in medial prefrontal cortex did not change , but arc and zif268 mrna were decreased ( covington et al . , 2010 ) . the physiological properties of the fos positive cells in this negative valence is an interesting question . in learned helpless behavior training in fos - gfp transgenic mice , fos cells of helpless micefos cells show reduced glutamatergic transmission compared to fos cells ( wang et al . , 2014 ) . in this studythe change of one immediate early gene signal over the course of a repeated motor task was tested in arc - gfp mice ( cao et al . , 2015 ) . though not fos , this study can give a clue on fos signal change , too . in repeated rotarod learning over 3 days , overall gfp cell number and signal intensity decreased . at individual cell level , those cells with strong gfp expression on day 3 were those exhibiting strong expression previously on day 1 . cellular recordings from that specific class of cells were not done in this study , although testing the unique properties of those persistent cells is technically possible ( cossell et al . , 2015 ) . it is a question whether c - fos will behave similarly to arc , or if the pattern will be quite different . however , the directional change of fos signal as fos + cell number or intensity to repeated stimuli can be a cellular marker for learning or memory ( fig . in contrast , repeated stimuli of negative value ( e.g. social defeat ) decrease fos signal over time . one way is to capture those fos cells and compare the property fos vs fos cells . if the captured cells can be identified and tested after variable time intervals ( e.g. days , weeks or months ) , cellular basis of long term memory can be tested . repeated stimuli can increase or decrease fos signal according to the positive or negative value of the stimuli to the organism . capturing and studying of individual fos positive cells before and after the stimuli provides an opportunity to study learning or memory for specific valences . increased or decreased fos signal of cell number or signal intensitythe utility of c - fos as a neural activity marker is still in progress with many , new useful tools to be employed . first , in repeated stimuli presentation over multiple days , what does the fos signal represent ? second , beyond the role of activity marker , what is the inherent role of fos in behaving animals ( zhang et al . , 2009 ) ? what is the role of \" late \" genes that fos as a transcription factor serves to induce in the nervous system ? third , after neuronal activity , multiple immediate early genes are expressed including c - fos ( lyons & west , 2011 ) . what is the overlapping or unique role of the \" late \" genes from multiple immediate early genes as transcription factors ? many external stimuli can induce c - fos by increasing neuronal activity ( morgan & curran , 1991 ; herdegen & leah , 1998 ) . however , intracellular calcium is the common molecule that mediates synaptic activity to c - fos gene expression ( ghosh et al . , 1994 ) . because of the diverse effects of calcium , basal neuronal intracellular calcium is kept very low by extrusion to the extracellular space and by uptake into calcium stores ( cohen & greenberg , 2008 ) . during neuronal activity , intracellular calcium concentration increases due to calcium influx mainly from two routes , a type of glutamate receptor ( nmda receptor , nmdar ) and l - type voltage - sensitive calcium channel ( vscc ) ( chaudhuri et al . , 2000 ) . nmdars can be activated by coincident presynaptic glutamate release and postsynaptic depolarization . as a glutamate receptor - channel complex , the calcium influx through nmdars can modulate c - fos gene expression ( cohen & greenberg , 2008 ) . in support of this notion , activation of nmdars induces c - fos mrna and fos protein ( liste et al . , 1995 ; berretta et al . , 1997 ; parthasarathy & graybiel , 1997 ) . in contrast , nmdar antagonists block fos expression ( berretta et al . , 1992 ; ghosh et al . , 1994 ; berretta et al . , 1997 ; in addition to nmdar , glutamate can also activate fast - acting ampa receptors and metabotropic glutamate receptors ( mglurs ) . ampa receptors can also allow calcium influx especially during early development , but in mature neurons the calcium influx through ampa receptors is limited in function ( derkach et al . , 2007 ) . still , ampars indirectly can contribute to the calcium influx by membrane depolarization to activate nmdars and vsccs . group i mglurs can increase calcium influx , but the effect on fos expression is not strong ( wang et al . , 2007 ) . the l - type vscc is involved with immediate early gene expression ( rajadhyaksha et al . , 1999 ) . basal expression of c - fos is rapidly suppressed by exposure to l - type vscc antagonists and increased by a vscc agonist ( murphy et al . , 1991 ) . as an alternative source of intracellular calcium , calcium can be released from calcium stores after neuronal activity , but more studies are needed to understand its contribution to fos expression ( lyons & west , 2011 ) . after the local calcium increase around the pore of the channels , the specific functional consequences of calcium influx is determined by the signaling molecules physically associated with the nmdar and vscc ( cohen & greenberg , 2008 ) . the increased calcium can activate multiple kinase pathways including mapk , camkiv , camkii and pka . however , fos expression is mainly mediated by mapk pathway which is distinct from other pathways ( chaudhuri et al . , 2000 ) . compared with camkiv pathway , mapk pathway activation is relatively slow , requires strong external stimulation and higher calcium increase ( wu et al . , 2001 ; this property can tune mapk pathway to large and continued neural activity ( murphy et al . , strong external stimuli preferentially activate the mapk pathway to result in fos expression while weak stimuli are less likely to be translated into fos signal . the mapk activates two transcription factors binding to the c - fos promoter in the nucleus ( lyons & west , 2011 ) . first , creb ( cyclin amp - response element - binding protein ) is phosphorylated via ribosomal s6 kinase . phosphorylated creb binds to the calcium response element ( or cyclic amp response element ) in the c - fos promotor . second , phosphorylated elk - 1 in association with serum response factor ( srf ) bind to the serum response element in the cfos promotor ( cruz et al . , 2014 ) . inside the nucleus , fos and jun make up the ap - 1 complex that acts as a transcription factor for \" late \" genes . at the basal level , low constitutive levels of c - fos is maintained . this is due to instability of c - fos mrna and auto - repression of c - fos transcription by the fos protein itself ( lucibello et al . the other possibility is the presence of active repression of the promoter because transcription factors and the rna polymerase ii complex are bound already before neural activity ( carrion et al . , 1999 ; these molecular conditions suggest the optimal conditions for eliciting the best fos signal as a neural activity marker in vivo . before an experimentfor example , sensory deprivation can be given in the form of social isolation in a singlyhoused animals before stimulus presentation . the isolation duration can be 1 to 7 days . to maximize the signal , a novel stimulus is recommended . it will produce negligible result or less than optimal signal . in the same line of thinking , this issue becomes complex because learning can both sensitize and desensitize the neural circuit depending on the nature of the stimulus to the organism . for example , in negative stimulations such as social defeat from other animals , multiple attacks over days can make the individual animals either depressed or resilient ( wang et al . , 2014 ) . it is difficult to predict what the fos signal will be like and how to interpret the signal at the level of single cells . an interesting example was reported in the comparison of acute cocaine injection and a test injection after prior repeated cocaine injection in fos - gfp transgenic mice ( koya et al . , 2012 ) . in this mouse , fos - gfp fusion protein under c - fos promoter is expressed after strong neural activation ( barth et al . , 2004 ) . after repeated cocaine injection , test cocaine injection increased fos signal as gfp positive ( gfp ) cell count compared to acute cocaine injection after repeated saline . if this is true , increased synaptic strength and increased synaptic transmissions are predicted . in gfp negative cells ( gfp ) , the result is consistent with this prediction . synaptic strength was higher and excitatory postsynaptic current ( epsc ) frequency was increased in the case of repeated cocaine injections . however , in gfp positive cells , synaptic strength was lower than gfp cells and epsc frequency was lower than gfp cells . because the number of gfp cells are much more than gfp cells , in randomly selected cells the overall results reflected those of gfp cells . though gfp cells are small in number , they are not less important than gfp cells . this is an example where fos as neural activity marker represented overall activity correctly , but the prediction did not extend to a functionally important subset of neurons ( ensemble ) . it is intriguing to speculate whether similar results will be found in negative behaviors such as social defeat . multiple social defeat ( e.g. 10 episodes ) can lead to depression - like behavior in defeated animals ( krishnan & nestler , 2011 ) . in general , fos was decreased after repeated social defeat in multiple brain regions ( martinez et al . , 2002 ) . when the cue associated with social defeat was presented 1 day or 7 days later , the cue increased fos signal in medial prefrontal cortex ( bourne et al . , 2013 ) . in this case , the fos signal is used as an indicator of longterm memory . in another study c - fos mrna in medial prefrontal cortex did not change , but arc and zif268 mrna were decreased ( covington et al . , 2010 ) . the physiological properties of the fos positive cells in this negative valence is an interesting question . in learned helpless behavior training in fos - gfp transgenic mice , fos cells of helpless micefos cells show reduced glutamatergic transmission compared to fos cells ( wang et al . , 2014 ) . in this study , it was not tested if the fos signal changed over repeated training sessions . the change of one immediate early gene signal over the course of a repeated motor task was tested in arc - gfp mice ( cao et al . , 2015 ) . though not fos , this study can give a clue on fos signal change , too . in repeated rotarod learning over 3 days , overall gfp cell number and signal intensity decreased . at individual cell level , those cells with strong gfp expression on day 3 were those exhibiting strong expression previously on day 1 . cellular recordings from that specific class of cells were not done in this study , although testing the unique properties of those persistent cells is technically possible ( cossell et al . , 2015 ) . it is a question whether c - fos will behave similarly to arc , or if the pattern will be quite different . however , the directional change of fos signal as fos + cell number or intensity to repeated stimuli can be a cellular marker for learning or memory ( fig . in contrast , repeated stimuli of negative value ( e.g. social defeat ) decrease fos signal over time . one way is to capture those fos cells and compare the property fos vs fos cells . if the captured cells can be identified and tested after variable time intervals ( e.g. days , weeks or months ) , cellular basis of long term memory can be tested . repeated stimuli can increase or decrease fos signal according to the positive or negative value of the stimuli to the organism . capturing and studying of individual fos positive cells before and after the stimuli provides an opportunity to study learning or memory for specific valences . increased or decreased fos signal of cell number or signal intensity was indicated as darkness or lightness , respectively . the utility of c - fos as a neural activity marker is still in progress with many , new useful tools to be employed . first , in repeated stimuli presentation over multiple days , what does the fos signal represent ? second , beyond the role of activity marker , what is the inherent role of fos in behaving animals ( zhang et al . what is the role of \" late \" genes that fos as a transcription factor serves to induce in the nervous system ? third , after neuronal activity , multiple immediate early genes are expressed including c - fos ( lyons & west , 2011 ) . what is the overlapping or unique role of the \" late \" genes from multiple immediate early genes as transcription factors ?\noutput:\n" }, { "from": "agent", "value": "the immediate early gene c - fos has long been known as a molecular marker of neural activity . the neuron s activity is transformed into intracellular calcium influx through nmda receptors and l - type voltage sensitive calcium channels . for the transcription of c - fos , neural activity should be strong enough to activate mitogen - activated protein kinase ( mapk ) signaling pathway which shows low calcium sensitivity . upon translation , the auto - inhibition by fos protein regulates basal fos expression . the pattern of external stimuli and the valence of the stimulus to the animal change fos signal , thus the signal reflects learning and memory aspects . understanding the features of multiple components regulating fos signaling is necessary for the optimal generation and interpretation of fos signal ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: cataract prevalence increases dramatically with age , affecting ~ 40 % of all adults aged 70 years and increasing to 60 % of adults aged 75 years .1,2 as of 2010 , an estimated 24.4 million american adults had cataracts ; due to a substantial aging population , prevalence is expected to double to 50 million by 2050.1 as the world s population ages , the global prevalence of cataract is likely to increase in the same timeframe , placing an even greater clinical and economic burden on the health care system . with aging populations and a doubling of prevalence ,1 there is a need for more efficient and effective surgical techniques to provide cataract treatment with reduced resource utilization and costs .3 the cost of cataract surgery varies widely depending on location and setting . data collected from nine european countries showed that in 2005 , per surgery costs ranged from 318 in hungary to 1,087 in italy ( or ~ 3441,177 usd ) . in this study , the greatest cost variations were due to overhead and personnel / labor , including the amount of time required for each surgery .3 another research study ( 20022003 ) found the mean cost of cataract surgery in europe to be 1,261 ( or ~ 1,365 usd ) .4 in cataract surgery , the opacified lens is surgically removed and replaced with an artificial intraocular lens ( iol ) . the process of handling and manually loading the iol into an inserter increases surgery duration and presents a chance of contamination . additionally , although serious complications are uncommon in cataract surgery , this procedure is associated with the greatest number of surgical errors in ophthalmology , including the insertion of an incorrect iol .5 the majority of toxic anterior segment syndrome cases following cataract surgery are attributed to surgical instrument contamination resulting from improper or insufficient cleaning , or to products introduced into the eye during surgery .6 similarly , postoperative endophthalmitis most commonly occurs due to a bacterial infection following cataract surgery and iol implantation .7 although complications , such as toxic anterior segment syndrome and endophthalmitis , are infrequent , occurring in 0.07 % and 0.04 % of patients receiving cataract surgery respectively ,8,9 these complications can include severe pain , serious intraocular tissue damage , and dramatic vision loss or blindness , increasing health care utilization and costs .10 exposure of the lens to the surgical environment through a manual loading and insertion process can be a vector for introduction of bacteria that can lead to endophthalmitis . data from france estimate that hospitalization costs for endophthalmitis are ~ 6.36 million for 1,725 cases ( 3,688 per patient ) .11 in the us , charges and payments related to treating patients with endophthalmitis are ~ 2.5 times higher compared to controls .7 additionally , the risk of complications related to cataract surgery increases with age . one us study found that , compared with patients aged 6574 years , patients aged 7584 years had an 11 % higher risk of developing endophthalmitis following cataract surgery , while patients aged 85 years had a 53 % higher risk .12 it is likely that many of these negative outcomes could be avoided and cost burden alleviated with improved sterile surgical techniques . in other areas of ophthalmology , intraoperative efficiencies have been achieved with the use of disposable surgical tools . one study found that switching from conventional metal corneal lens rings to disposable sutureless silicone rings during a combined 23 g vitrectomy and cataract procedure resulted in average preparation time savings of 3.94 minutes per procedure .13 use of the disposable sutureless silicone rings also led to significant reductions in intraoperative corneal limbus bleeding and scarring . as the need for cataract surgery increases with the aging global population , surgeons require improved safety and efficiency in the operating room ( or ) .3 the tecnis 1 - piece iol with the tecnis itec preloaded delivery system ( abbott medical optics inc . , santa ana , ca , usa ) is a no - touch preloaded and disposable delivery system designed to allow a cataract surgeon to implant an iol safely without having to physically touch or manipulate the lens outside of the eye and has the potential to decrease total case time , eliminate iol handling , and improve throughput . this study was designed to evaluate the operational impact of converting from a manually loaded iol process to the single use , no - touch , tecnis 1 - piece iol with the tecnis itec preloaded delivery system in three facilities that perform cataract surgeries . this prospective , observational , multicenter study was conducted at three sites located in the us , france , and canada . each site scheduled cataract surgeries 12 d / wk , and each site predominately or exclusively performed routine cataract cases , with a majority ( 62 % 100 % ) being monofocal iol insertions . in canada , the site in france was moderate volume ( ~ 17 cases / d ) , and the site in the us was high volume ( ~ 25 cases / d ) , as shown in table 1 . the sites in france and canada were located within hospital facilities , whereas the us site was located in an ambulatory surgical center . prior to starting the study , the preloaded iol system had not been adopted in the canada and us sites , and the standard of care was for the surgeon to perform the surgery using a manually loaded lens delivery process . in contrast , the site in france already had experience using the preloaded system for routine cataract surgeries . for all study sites , the loading process includes preparing the ophthalmic viscosurgical device - filled cartridge and advancing the plunger to place the lens near the cartridge tip prior to the inserter being placed into the incision . each site setup was unique , with specific staffing models designed to support the surgeon and optimize workflows . the france center had two ors , with one scrub technician ( st ) and one circulating nurse ( n ) in each or for the full duration of each surgery day . two sterilization technicians ( cl ) cleaned the used equipment and disposables in a cleaning station adjacent to the two ors . lastly , the center in canada had one or with three nurses rotating between st , n , and surgical preparation nurse roles . the anesthetist remained in the or during surgery and was responsible for wheeling the patient in and out of the or . at this center , the cleaning station was located across the hallway from the surgery prep area . time - and - motion data , staff and surgery schedules , and cost accounting reports were collected across all three sites . staff schedules , surgery schedules , and cost accounting reports were collected in the 2 months prior and after introduction of the preloaded iol delivery system . in the us site , revenue and claimsthe preloaded iol delivery system utilized throughout the course of the study was the tecnis 1 - piece iol with the tecnis itec preloaded delivery system . the primary outcome was total case time , including or setup , surgery , and teardown time . or setup time was defined as the time between when the n or st opened the ophthalmology pack and when all surgical items were prepped and placed in the sterile field . in france and canada , surgery began with placement of the speculum by the surgeon and ended with the removal of the speculum or administration of povidoneiodine ( betadine ) . in the us , surgery began when the surgeon sat in the surgical chair and positioned the microscope . surgery ended when the surgeon finished checking the status of the eye and provided a verbal indication that surgery was complete . teardown time was defined as the time following surgery until the n or st finished applying disinfectant to the surgery table surfaces . to control for variability introduced by nonlens - related workflows , total case time excluded the time between the end of or setup and start of surgery . this time period varied widely across study sites and included the application of surgical drapes , administration of ophthalmic drops , and other patient - centric activities . secondary outcomes included surgeon lens time , surgeon delays , and the number of iol touches per case . surgeon lens time was defined as the length of time the surgeon spent loading , inserting , and positioning the lens in the eye . surgeon delays were defined as any issues that prevented the surgeon from beginning surgery , such as the staff not having the or setup complete or the patient was not prepped and ready for surgery . iol touches were defined as the number of times that the surgeon physically touched or manipulated the lens while manually loading the inserter . montreal , qc , canada ) , a time - and - motion work measurement mobile software application . data recorded for each case included time measurements of the respective tasks performed by the surgeon , st , n , and cl . the time taken by or staff to complete key lens - related case components ( or setup time , surgery time , and or teardown time ) was documented and analyzed . for the canadian and american sites , time - and - motion measurements were collected over two surgical days prior to and two surgical days after adoption of the preloaded iol delivery system . in france , because the preloaded system was already in use at the time of study commencement , time - and - motion data using both manual and preloaded iol delivery systems were collected simultaneously over a 4 - day period . all sites collected data from a minimum of 20 cases for each type of lens insertion system , for a minimum of 40 cases at each site . cases performed with the preloaded iol delivery system were referred to as preloaded cases , and cases performed with a manual iol system were referred to as manual cases . that there was no change to patient care ( eg , patients received standard of care ) , the irb did not require patient written informed consent . descriptive statistics included the median , minimum , and maximum duration of all time - and - motion metrics ( eg , total case , surgery , and surgeon lens times ) and iol touches by individual case at each site . descriptive statistics , including mean and sd , were also calculated for total case time . only mean was calculated for iol touches across sites . lens - related delays , nonlens - related delays , and surgeon delays were also recorded . lens - related delays were delays directly related to the lens , such as lens scratching and loading errors . nonlens - related delays were the delays unrelated to the iol system used for surgery , such as delays due to staff talking . surgeon delays were recorded separately in the france and us sites ( two ors ) and were not removed from time - and - motion measurements . to compare time - and - motion parameters between manual and preloaded cases , p - values were calculated using a wilcoxon rank sum test for the canadian center , which had a one - or setup . general linear models were used to compare outcomes at the sites in france and the us , both of which had a two - or setup . at the centers with two ors , this prospective , observational , multicenter study was conducted at three sites located in the us , france , and canada . each site scheduled cataract surgeries 12 d / wk , and each site predominately or exclusively performed routine cataract cases , with a majority ( 62 % 100 % ) being monofocal iol insertions . in canada , the site in france was moderate volume ( ~ 17 cases / d ) , and the site in the us was high volume ( ~ 25 cases / d ) , as shown in table 1 . the sites in france and canada were located within hospital facilities , whereas the us site was located in an ambulatory surgical center . prior to starting the study , the preloaded iol system had not been adopted in the canada and us sites , and the standard of care was for the surgeon to perform the surgery using a manually loaded lens delivery process . in contrast , the site in france already had experience using the preloaded system for routine cataract surgeries . for all study sites , the loading process includes preparing the ophthalmic viscosurgical device - filled cartridge and advancing the plunger to place the lens near the cartridge tip prior to the inserter being placed into the incision . each site setup was unique , with specific staffing models designed to support the surgeon and optimize workflows . the france center had two ors , with one scrub technician ( st ) and one circulating nurse ( n ) in each or for the full duration of each surgery day . two sterilization technicians ( cl ) cleaned the used equipment and disposables in a cleaning station adjacent to the two ors . lastly , the center in canada had one or with three nurses rotating between st , n , and surgical preparation nurse roles . the anesthetist remained in the or during surgery and was responsible for wheeling the patient in and out of the or . at this center , the cleaning station was located across the hallway from the surgery prep area . time - and - motion data , staff and surgery schedules , and cost accounting reports were collected across all three sites . staff schedules , surgery schedules , and cost accounting reports were collected in the 2 months prior and after introduction of the preloaded iol delivery system . in the us site , revenue and claimsthe preloaded iol delivery system utilized throughout the course of the study was the tecnis 1 - piece iol with the tecnis itec preloaded delivery system . the primary outcome was total case time , including or setup , surgery , and teardown time . or setup time was defined as the time between when the n or st opened the ophthalmology pack and when all surgical items were prepped and placed in the sterile field . in france and canada , surgery began with placement of the speculum by the surgeon and ended with the removal of the speculum or administration of povidoneiodine ( betadine ) . in the us , surgery began when the surgeon sat in the surgical chair and positioned the microscope . surgery ended when the surgeon finished checking the status of the eye and provided a verbal indication that surgery was complete . teardown time was defined as the time following surgery until the n or st finished applying disinfectant to the surgery table surfaces . to control for variability introduced by nonlens - related workflows , total case time excluded the time between the end of or setup and start of surgery . this time period varied widely across study sites and included the application of surgical drapes , administration of ophthalmic drops , and other patient - centric activities . secondary outcomes included surgeon lens time , surgeon delays , and the number of iol touches per case . surgeon lens time was defined as the length of time the surgeon spent loading , inserting , and positioning the lens in the eye . surgeon delays were defined as any issues that prevented the surgeon from beginning surgery , such as the staff not having the or setup complete or the patient was not prepped and ready for surgery . iol touches were defined as the number of times that the surgeon physically touched or manipulated the lens while manually loading the inserter . montreal , qc , canada ) , a time - and - motion work measurement mobile software application . data recorded for each case included time measurements of the respective tasks performed by the surgeon , st , n , and cl . the time taken by or staff to complete key lens - related case components ( or setup time , surgery time , and or teardown time ) was documented and analyzed . for the canadian and american sites , time - and - motion measurements were collected over two surgical days prior to and two surgical days after adoption of the preloaded iol delivery system . in france , because the preloaded system was already in use at the time of study commencement , time - and - motion data using both manual and preloaded iol delivery systems were collected simultaneously over a 4 - day period . all sites collected data from a minimum of 20 cases for each type of lens insertion system , for a minimum of 40 cases at each site . cases , and cases performed with a manual iol system were referred to as manual cases . given that there was no change to patient care ( eg , patients received standard of care ) , the irb did not require patient written informed consent . descriptive statistics included the median , minimum , and maximum duration of all time - and - motion metrics ( eg , total case , surgery , and surgeon lens times ) and iol touches by individual case at each site . descriptive statistics , including mean and sd , were also calculated for total case time . only mean was calculated for iol touches across sites . lens - related delays , nonlens - related delays , and surgeon delays were also recorded . lens - related delays were delays directly related to the lens , such as lens scratching and loading errors . nonlens - related delays were the delays unrelated to the iol system used for surgery , such as delays due to staff talking . surgeon delays were recorded separately in the france and us sites ( two ors ) and were not removed from time - and - motion measurements . to compare time - and - motion parameters between manual and preloaded cases , p - values were calculated using a wilcoxon rank sum test for the canadian center , which had a one - or setup . general linear models were used to compare outcomes at the sites in france and the us , both of which had a two - or setup . at the centers with two ors , the study included a total of 154 routine cataract cases , collected over twelve surgery days across all three sites . the site in canada included a total of 40 cases ( 20 preloaded and 20 manual ) , the site in france included 47 cases ( 20 preloaded and 27 manual ) , and the site in the us included 67 cases ( 37 preloaded and 30 manual ) . an adoption period of 17 months allowed all sites to perform a minimum of 100 monofocal cataract cases using the preloaded iol delivery system prior to data collection . at all three sites , use of the preloaded iol delivery system resulted in significant reductions in mean total case time . in canada , a 12.0 % reduction in mean total case time was observed , with a mean difference of 3.3 minutes per case ( p 0.001 ) ; in france , a 6.2 % reduction in mean total case time was observed , with a mean difference of 1.1 minutes per case ( p 0.05 ) ; and in the us , a 9.4 % reduction in mean total case time was observed , with a mean difference of 2.1 minutes per case ( p 0.001 ) . while total case time savings were observed across all sites and segments ( or setup , surgery , and or teardown ) , the reduction in time was not statistically significant for all measured time segments across all sites , as shown in table 2 . across all three sites , the preloaded iol delivery system resulted in significant reductions in surgeon lens times . the site in canada had a 43.7 % reduction in total surgeon lens time with the preloaded system , with a median difference of 0.8 minutes ( p 0.001 ) ; the site in france had a 31.9 % reduction with a median difference of 0.4 minutes ( p 0.001 ) ; and the site in the us had a 17.4 % reduction with a median difference of 0.4 minutes ( p 0.001 ) . surgeon delays were documented for the two sites that had a 2 - or setup ( france and the us ) , and both found reduced surgeon delays with the preloaded iol system . in the site in france , surgeon delays occurred in 30 % of cases utilizing a manually loaded process and 20 % of cases utilizing the preloaded system ( representing a 33 % reduction ) , as shown in table 3 . in france , the overall mean duration of surgeon delay was 13 % lower for preloaded iol cases , at 0.8 minutes , compared to 0.9 minutes with manual cases . in the us site , surgeon delays occurred in 27 % of cases utilizing a manually loaded process and 11 % of cases utilizing the preloaded system ( representing a 59 % reduction ) . the overall mean duration of surgeon delay at this site was 72 % lower for preloaded cases , at 0.3 minutes , compared to 1.1 minutes with manual cases . the number of iol touches was recorded only for manual cases , as the preloaded iol device eliminates the need for iol touches outside of the eye . for manual cases , the mean number of iol touches was four at the canada site and five at both the france and us sites , respectively . the study included a total of 154 routine cataract cases , collected over twelve surgery days across all three sites . the site in canada included a total of 40 cases ( 20 preloaded and 20 manual ) , the site in france included 47 cases ( 20 preloaded and 27 manual ) , and the site in the us included 67 cases ( 37 preloaded and 30 manual ) . an adoption period of 17 months allowed all sites to perform a minimum of 100 monofocal cataract cases using the preloaded iol delivery system prior to data collection . at all three sites , use of the preloaded iol delivery system resulted in significant reductions in mean total case time . in canada , a 12.0 % reduction in mean total case time was observed , with a mean difference of 3.3 minutes per case ( p 0.001 ) ; in france , a 6.2 % reduction in mean total case time was observed , with a mean difference of 1.1 minutes per case ( p 0.05 ) ; and in the us , a 9.4 % reduction in mean total case time was observed , with a mean difference of 2.1 minutes per case ( p 0.001 ) . while total case time savings were observed across all sites and segments ( or setup , surgery , and or teardown ) , the reduction in time was not statistically significant for all measured time segments across all sites , as shown in table 2 . across all three sites , the preloaded iol delivery system resulted in significant reductions in surgeon lens times . the site in canada had a 43.7 % reduction in total surgeon lens time with the preloaded system , with a median difference of 0.8 minutes ( p 0.001 ) ; the site in france had a 31.9 % reduction with a median difference of 0.4 minutes ( p 0.001 ) ; and the site in the us had a 17.4 % reduction with a median difference of 0.4 minutes ( p 0.001 ) . surgeon delays were documented for the two sites that had a 2 - or setup ( france and the us ) , and both found reduced surgeon delays with the preloaded iol system . in the site in france , surgeon delays occurred in 30 % of cases utilizing a manually loaded process and 20 % of cases utilizing the preloaded system ( representing a 33 % reduction ) , as shown in table 3 . in france , the overall mean duration of surgeon delay was 13 % lower for preloaded iol cases , at 0.8 minutes , compared to 0.9 minutes with manual cases . in the us site , surgeon delays occurred in 27 % of cases utilizing a manually loaded process and 11 % of cases utilizing the preloaded system ( representing a 59 % reduction ) . the overall mean duration of surgeon delay at this site was 72 % lower for preloaded cases , at 0.3 minutes , compared to 1.1 minutes with manual cases . the number of iol touches was recorded only for manual cases , as the preloaded iol device eliminates the need for iol touches outside of the eye . for manual cases , the mean number of iol touches was four at the canada site and five at both the france and us sites , respectively . this study was conducted to evaluate the operational impact of converting from a manually loaded iol delivery process to a preloaded iol delivery system for routine cataract surgeries . at all study sites , adoption of the preloaded system significantly reduced total case time and total surgeon lens time . additionally , the incidence and total duration of surgeon delays decreased with the preloaded system . the preloaded delivery system also eliminated the need for the surgeon to handle and manually load the iol prior to insertion , obviating the likelihood of lens contamination associated with direct handling of the iol . the case time efficiencies observed with the preloaded system were attributed to a reduction in serial lens handling and preparation activities . during or setup , the preloaded system eliminated the assembling of a lens inserter and cartridge , thereby reducing or setup time between 7.7 % and 17.0 % . while the preloaded device requires application of the ophthalmic viscosurgical device , the st was able to perform this activity in parallel with other surgical steps ( eg , phacoemulsification ) . the surgeon not having to manually load the iol contributed to a 3.7 % 8.7 % decrease in total surgery time . in addition , the disposable feature of the preloaded system eliminated the need for the inserter to be placed into the sterilization box and carried into the sterilization area , contributing to a reduction in the or teardown time of 4.1 % 12.5 % . the combination of these increased efficiencies resulted in an overall decrease in total case time of 6.2 % 12.0 % . reductions in total case time and total surgeon time ( eg , total surgery time and surgeon delays ) have different implications on case throughput depending on the or setup . in a one - or setup , switching from a manual iol - loading process to a preloaded system could allow the site to increase throughput if cumulative time savings achieved during or setup , surgery , and teardown are equal to or greater than the total time required to perform a single cataract case . in a two - or setup , the site is optimized to make best use of the surgeons time , and therefore , switching to a preloaded system could allow an improved throughput if total surgeon time savings are equal to or greater than the time required for the surgeon to start and finish the surgery . apart from surgery time savings , or setup and teardown efficiencies provided by a preloaded system only have throughput implications if they reduce the frequency or duration of surgeon delays . in canada ( one or ) , the preloaded system saved an average of 3.4 minutes per surgery case compared to manual loading . during the manual case 2 - month economic data collection period , the canada site averaged 10.2 cases per surgery day with a 100 % monofocal case mix . assuming no changes are made to surgery volume and case mix , a total of 33.7 minutes could be saved per surgery day by switching from manual lens - loading process to a preloaded system . adding back the time between the completion of or setup and surgery start ( 2.9 minutes ) to total case time ( 24.3 minutes ) results in a total preloaded case time of 27.2 minutes , which is less than the 33.7 minutes saved throughout the course of the surgery day . as a result , in a low - volume , single or cataract surgery center , switching from a manual iol - loading process to a preloaded iol systemsaves enough time to add at least one routine cataract case without having to increase staff or surgeon capacity , as shown in table 4 . in france and the us ( two - or sites ) , the preloaded system saved a median of 0.6 minutes and 0.4 minutes in surgery time per monofocal cataract case , respectively . during the manual case 2 - month data collection period , the french site averaged 17.4 cases per surgery day with a monofocal case mix of 61 % , and us site averaged 25.2 cases per surgery day with a 92 % monofocal case mix , resulting in 5.8 minutes and 9.3 minutes of surgery time savings per surgery day , respectively . in addition , the reduction in both frequency and duration of surgeon delays contributed an additional 1.2 minutes and 6.3 minutes in surgeon time savings per surgery day in france and us , respectively . the reduction in surgeon delays with a preloaded iol system is believed to be a result of surgery staff being more proactive when handling day - to - day operational variability ( eg , retrieving surgical supplies and dealing with uncooperative patients ) as a result of efficiencies gained in or setup and teardown . the total surgeon time savings with a preloaded lens system equates to 7.0 minutes and 15.5 minutes in the france and us sites , which is greater than the median 5.8 minutes and 10.4 minutes required to perform a surgery with a preloaded system , respectively . similar to the canadian site ( one or ) , the preloaded system saves enough surgeon time to add at least one routine cataract case in moderate - and high - volume two - or surgery centers without impacting surgeon capacity , as shown in table 5 . assuming that each site took advantage of the time - and - motion efficiencies , adding one routine cataract case per surgery day could result in substantial improvements in annual throughput , as shown in table 6 . assuming that the number of surgery days per month remains unchanged , the low - volume one - or canada site could increase annual throughput by 9.9 % or 36 cases , the moderate - volume two - or france site could increase annual throughput by 5.7 % or 90 cases , and the high - volume two - or us site could increase annual throughput by 4.0 % or 96 cases . while the results are promising , this study has some limitations . first , this was a pilot study , and while data were rigorously collected across three sites , it was not powered to demonstrate statistical significance . it was also difficult to prospectively assess the direct impact of case time savings on throughput and profitability due to an inability to control for external variable factors at each site ( eg , cataract case mix , seasonality in patient demand , and changes in scheduling ) . second , the estimated improvement in throughput assumes that sites have a broader focus on increasing efficiencies and that time savings achieved with the preloaded system are realized and operationalized by the staff at each site . this analysis does not account for the impact of higher case volume on staff satisfaction and employee morale . finally , the study findings are limited by the fact that participating surgeons standard practice was to load the lens into the inserter themselves ( for manual cases ) . while the observed total surgery time efficiencies may not be directly applicable to sites where surgery staff load the lens into the inserter , use of a preloaded system may result in efficiencies in or setup and or teardown . this pilot observational study showed that converting from a manually loaded iol delivery process to a preloaded iol delivery system for routine cataract surgeries reduces total case time , reduces surgeon lens time , and has the potential to increase case throughput . the preloaded system also eliminates the need for iol handling outside of the eye , thus reducing the potential for lens contamination and postsurgical complications . for facilities that are focused on improving efficiency , the time savings that can be achieved with the preloaded system may help increase efficiency and effective treatment as the demand for cataract surgery increases .\noutput:\n" }, { "from": "agent", "value": "purposethe aim of this study was to evaluate the operational impact of using preloaded intraocular lens ( iol ) delivery systems compared with manually loaded iol delivery processes during routine cataract surgeries.methodstime and motion data , staff and surgery schedules , and cost accounting reports were collected across three sites located in the us , france , and canada . time and motion data were collected for manually loaded iol processes and preloaded iol delivery systems over four surgery days . staff and surgery schedules and cost accounting reports were collected during the 2 months prior and after introduction of the preloaded iol delivery system.resultsthe study included a total of 154 routine cataract surgeries across all three sites . of these , 77 surgeries were performed using a preloaded iol delivery system , and the remaining 77 surgeries were performed using a manual iol delivery process . across all three sites , use of the preloaded iol delivery system significantly decreased mean total case time by 6.2 % 12.0 % ( p < 0.001 for data from canada and the us and p < 0.05 for data from france ) . use of the preloaded delivery system also decreased surgeon lens time , surgeon delays , and eliminated lens touches during iol preparation.conclusioncompared to a manual iol delivery process , use of a preloaded iol delivery system for cataract surgery reduced total case time , total surgeon lens time , surgeon delays , and eliminated iol touches . the time savings provided by the preloaded iol delivery system provide an opportunity for sites to improve routine cataract surgery throughput without impacting surgeon or staff capacity ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: patients with underlying conditions are at a higher risk of developing sepsis , a systematic response to infection , which has a high mortality rate . after the march 2011 fukushima daiichi nuclear power plant accident , there has been an influx of migrant decontamination workers ; however , little is known about their health status . a japanese 55 - year - old male decontamination worker , who had several underlying diseases , was transferred to our hospital in cardiopulmonary arrest . he had a history of diabetes mellitus and hypertension and a past history of tuberculosis . the poor control of underlying diseases seen in this patient could have been influenced by his recent job transfer and engagement in decontamination work and additionally related to his socioeconomic status ( ses ) . this case highlights the need for further research to elucidate the underlying diseases , working conditions , and ses of this population . sepsis is defined as a systemic response to a confirmed or suspected infection including pneumonia , intra - abdominal infection , and urinary tract infection , with the presence of systemic inflammatory response syndrome . although several antisepsis treatments have been established such as early goal - directed therapy , the risk of mortality due to severe sepsis and septic shock remains high . in terms of prophylaxis , it is imperative to control underlying diseases such as diabetes mellitus , alcoholism , and chronic obstructive pulmonary disease , which are known to enhance the incidence of sepsis . klebsiella pneumoniae is a rare sepsis - causing bacteria , but it is well known for its severe outcomes with high mortality . bacteremia caused by k. pneumoniae is seen more , and with a poorer prognosis , in patients with underlying diseases because of potential deterioration of the immune system . therefore , control of underlying diseases is highly important to reduce the mortality due to sepsis caused by k. pneumoniae . in the long - term radioactive decontamination work in fukushima , the march 2011 fukushima daiichi nuclear power plant accident caused widespread radioactive contamination , a health hazard for the residents of fukushima . to reduce the level of radiation exposure to the residents , decontamination work has been extensively implemented in affected areas . decontamination workers are engaged in physically difficult jobs that impose wearing protective equipment , carrying heavy loads , and working on elevated infrastructures such as roofs . health maintenance of these workers is important ; nevertheless , little information is available on their health and underlying diseases . we present here the case of a 55 - year - old male decontamination worker who was admitted to our hospital and eventually died from sepsis due to k. pneumoniae . further examination revealed that he had multiple underlying diseases , indicating that the risk of bacterial infection could be high among the presumed 15,000 - 20,000 decontamination workers in fukushima prefecture . the present case highlights the importance of health maintenance of decontamination workers and the need to identify the risks they may face . eight days before admission , he moved to minamisoma city to begin the decontamination work . oral intake gradually decreased , and a coworker attempted to bring him to the hospital on admission day . during transfer , he lost consciousness . he was immediately brought to a nearby fire station and was found to be in cardiopulmonary arrest . he had a history of insulin - dependent diabetes mellitus , recently indicated hypertension , and past history of tuberculosis . while details of his health condition before engagement in decontamination work were not available because of lack of hospital history , potentially owing to settling in an unfamiliar place , his health condition may have worsened after starting work . he originated from outside fukushima prefecture , lived alone in a dormitory , and had an income of 2.5 - 3 million yen per year [ mean japanese male income was 5.1 million yen in 2014 ] , and he did not complete high school . in minamisoma city , decontamination workers are managed as per the following working conditions : 8 hours of work per day , 5 days a week , with a 1 - hour break per day . workers must wear long - sleeved shirts , long pants , and paper masks to prevent external or internal radio - contamination . these conditions are strictly enforced by employers following governmental regulations for radiological protection for decontamination work . our patient drank more than 60 g of ethanol per day and had a 25 - year history of tobacco smoking one pack a day but had stopped for the treatment of tuberculosis at the age of 45 years . on arrival to the hospital , we found him in cardiopulmonary arrest : asystole and not breathing . three milligrams of adrenaline and 1 mg of atropine were intravenously administered with high - flow oxygen administered under intubation . twenty - seven minutes after arrival to the hospital , spontaneous circulation was restored . on examination in the emergency room , the body temperature was 37.6 c , blood pressure was 96/62 mmhg , pulse was 135 bpm , and oxygen saturation was 98 % while being administered oxygen ( 15 l ) from a ventilator . results of a laboratory examination of blood revealed the following : ph 6.62 , partial pressure of oxygen 57.5 mmhg , partial pressure of carbon dioxide 154 mmhg , white cell count 11900 cells / l , c - reactive protein levels 26.98 mg / dl , hba1c 13.8 % , blood glucose 584 mg / dl , urea nitrogen 76.4 mg / dl , creatinine 3.07 mg / dl , and positively for hepatitis c virus antibody . no evidence of active tuberculosis was found from the cultures of gastric juice and sputum and from interferon - gamma release assay . the patient was diagnosed with pneumonia - induced bacteremia and sepsis . despite post resuscitation care using a ventilator and vasopressorcontrol of underlying diseases , which may have adverse effects on the immune system , is significant in reducing the mortality risk inherent to sepsis . in the present case , the patient had history of diabetes mellitus , and his blood glucose control was extremely poor , with hba1c of 13.8 % . in addition , he had untreated hypertension and hepatitis c virus infection with a past medical history of tuberculosis . from these conditions , he should have been regarded as a high - risk candidate for developing severe bacterial infections before his development of sepsis . the poor control of underlying diseases seen in this patient could have been influenced by the patient 's recent job transfer in which he left his family behind to begin decontamination work in addition to his working environment . additionally , socioeconomic status ( ses ) , measurable by level of education , income , and occupation , of this patient was low . in general , most decontamination workers are migrant workers , and they live alone in unfamiliar areas . it has previously been reported that in low - ses patients , the incidence of hypertension , arteriosclerosis , cardiovascular disease , and strokeis high , and hospitalization caused by bacterial infection is more frequent than in higher ses patients . although it is impossible to draw a conclusion from only one case , individuals engaged in decontamination work appear more likely to have low ses and poorly controlled underlying diseases . it is unclear at this moment whether the observed bacteremia resulted from poor baseline health or poor working environment . given the short working duration as a decontamination worker and low ses , the bacteremia observed in this case may be associated with his underlying health rather than working environment . however , this case may not represent all decontamination workers , and further research is warranted in this area to understand the baseline characteristics of health in decontamination workers and the possible influence of their ses . in conclusion , our case was a 55 - year - old man with poorly controlled underlying diseases , who eventually died from sepsis due to k. pneumoniae . his recent job transfer and engagement in decontamination work could have caused the deterioration of underlying conditions . to improve the health of decontamination workers , there is a need for further research addressing the underlying diseases , working conditions , and ses of this population .\noutput:\n" }, { "from": "agent", "value": "objectives : patients with underlying conditions are at a higher risk of developing sepsis , a systematic response to infection , which has a high mortality rate . after the march 2011 fukushima daiichi nuclear power plant accident , there has been an influx of migrant decontamination workers ; however , little is known about their health status.case : a japanese 55 - year - old male decontamination worker , who had several underlying diseases , was transferred to our hospital in cardiopulmonary arrest . he had a history of diabetes mellitus and hypertension and a past history of tuberculosis . control of underlying conditions was poor , with hba1c of 13.8 % at presentation . he was diagnosed with pneumonia - induced bacteremia and sepsis due to klebsiella pneumoniae . although spontaneous circulation returned in emergency room , he died a day after admission.conclusion : the poor control of underlying diseases seen in this patient could have been influenced by his recent job transfer and engagement in decontamination work and additionally related to his socioeconomic status ( ses ) . this case highlights the need for further research to elucidate the underlying diseases , working conditions , and ses of this population ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: papillae are the visible bumps on the tongue s surface . there are four types of papillae : fungiform ( fp ) , foliate , circumvallate , and filiform . while filiform papillae are spread over the surface of the tongue , circumvallate are localized only on the back of the tongue , and foliate are found on the sides . fp , foliate , and circumvallate papillae are considered gustatory because they have the potential to contain taste buds while filiform do not . taste buds are clusters of cells responsible for detecting chemical tastants and transducing the stimuli into a gustatory signal in the brain . saliva and food molecules enter into the taste buds through openings called taste pores where taste molecules then have the potential of activating taste cells . interestingly , there are large individual differences in taste bud density , as first observed in a histological study of tongues from 18 cadavers ( miller , 1988 ) . taste buds themselves are not visible on the tongue 's surface , however , taste pores are visible when using proper magnification , lighting , and staining techniques which led miller & reedy ( 1990 ) to develop a method to identify taste pores and fungiform papillae using videomicroscopy in living human beings . a number of labs have modified their original videomicroscopy technique , using still photography and little or no magnification . however , since fungiform papillae are much easier to visualize than are pores using these latter techniques , labs turned to counting fungiform papillae in place of taste pores . in doing so , it is assumed that fungiform papilla density is a reasonable proxy measure for taste pore density , even though many fungiform papillae do not contain taste pores or taste buds ; not only are fp more visible and accessible than circumvallate and foliate papillae , but their image capture is less time consuming than taste pore analysis through the alternative method of videomicroscopy . in 1990 , miller & reedy used this technique to find that taste pore densities are correlated with fp densities which was further corroborated in bartoshuk et al . in addition to this anatomical relationship , miller & reedy also found that the 8 individuals in the upper half of the taste pore density distribution also rated sucrose , nacl , and propylthiouracil ( prop ) as significantly more intense than did the other 8 individuals . ( 1994 ) observed a correlation between suprathreshold prop taste intensity and fungiform papilla density , as well as taste pore density , in 42 subjects . this convenient method led to influential studies reporting that subjects whose tongues have many papillae elicit a stronger reaction to many tastants , including the bitter tastants phenylthiocarbamide ( ptc ) and prop . ptc and prop are well - researched tastants oft used due to the clear link between a person s taste sensitivity phenotype and their genotype . population studies have shown that people who have the homozygous recessive diplotype of the gene , tas2r38 , have a significantly lower sensitivity to prop than carriers of the dominant or heterozygous variant of the gene . this heritable phenomenon was first reported in 1932 when arthur l. fox announced his discovery of taste blindness to ptc . among people able to taste these bitter compounds , the intensity of taste reported can vary anywhere from slightly unpleasant to excruciatingly bitter . to account for variance that can not be explained by tas2r38 , the theory was put forth that it could be attributed to the density of fp on the tongue . as taste research progressed , the field was divided into two schools of thought around this theory concerning the role of fp and bitter taste sensitivity . although many studies corroborated the original claim that fp density is a factor in prop sensitivities , there has been a small , but important contingency that has found evidence to refute it , reporting an inability to replicate the role . ( 2001 ) warned that the trend is highly variable ; fp density does not uniformly account for differences in bitterness sensitivity across subjects , and was only demonstrable for subjects with at least a moderate sensitivity to prop . in addition to the use of the less rigorously defined miller & reedy method on how to quantify fp , it is important to note that with exception of the beaver dam offspring study conducted by fischer et al . , most of the above studies had small sample sizes which may also contribute to inconsistent findings on the role of fp in taste . briefly , in miller & reedy s seminal methodology paper ( 1990 ) , the authors stained tongues blue to quantify fp because fp remain pink while filiform papillae absorb the dye and turn blue . while the authors advised that before using this method for further analytical work , fp characteristics should be more strictly defined and concluded that the variation already noted in the literature might be attributable to different subject populations , different methods , and different investigators , their research has led to the commonly accepted characteristics that fp are round , large , pink or stained lighter , and elevated . taken at face value , these characteristics appear very straight forward . in the genetics of taste lab ( got lab or lab ) , the use of the method was complicated by the scorers individual attempts at qualifying and prioritizing the importance of the above characteristics when some , but not all , of the characteristics were present . these complications included small papillae that appeared pink in the midst of much larger papillae ; the entire tongue absorbing the blue dye thus eliminating classification based on color variation ; oblong papillae instead of round ; and tongues having no variation in elevation , all of which contributed to scorers reporting widely - varied fp counts of the same image . these variations in analysis led us to review the literature in order to pinpoint the subjectivity , identify any exceptions to the commonly accepted fp characteristics and ultimately devise a protocol to accurately and objectively define and score fp . first , fp shape is described in the literature as a rounded , mushroom - like structure . miller emphasized that the term fungiform is a misnomer and that many fp are not mushroom - shaped but can vary widely in size and morphology . distorted , where the fp diameter in one direction was at least two standard deviations longer than in another direction . furthermore , cheng & robinson found that when indicating fp by staining , they ranged from flat - topped to elongated in appearance . noting the above exceptions , the characterization of an fp being round and mushroom - shaped appears too narrow a definition . second , fp color is described as pink circles against a blue background after staining the tongue with blue dye . though staining lighter was the most consistent criterion of fp throughout the literature it was still not a uniform qualifier . cheng & robinson observed that fp were not always lightly stained , making identification difficult and uncertain . it appears then that tongues absorb dye differently and while the contrast is apparent on many tongues , some become entirely blue with no distinction while others immediately lose any trace of blue dye . the third characteristic , fp size , was fairly consistent among papers , ranging from 0.5 mm to 0.97 mm . in the literature miller noted that there were two size ranges of papillae on the dorsal anterior of the tongue . the papillae with larger diameters were primarily fungiform and conical papillae , while the papillae with a smaller diameter were mostly filiform . however , with the exception of the beaver dam offspring study , size did not appear to determine if a structure is a fp in the literature , but was provided for papillae already classified as fungiform \" . finally , elevation is listed as the fourth fp characteristic though miller pointed out that distinction between filiform and fungiform papillae is difficult when using this criteria near the margin of the tongue . he gave two examples of fp that varied greatly in elevation , one being 0.8 mm in height while another was less than 0.1 mm in height , but still had two taste pores that were clearly observed . these definitions and their reported exceptions show that the taste field has long recognized the inconsistency in characterizing fp and the shortcomings of the commonly - used protocol from miller & reedy . indeed , miller & reedy exhorted the field to further define the features of fp . we hypothesized that scorers were giving different weight to the characteristics and prioritizing their importance differently when papillae failed to meet every criterion , such as when a papilla was large and mushroom shaped , but stained blue . it was reasoned that investigators of the previously published studies likely did the same which , when combined with small sample sizes , may account for the varied results coming from use of this method . the got lab addressed this gap in fp methodology by developing a guideline that defines each characteristic using objective measurements and prioritizes the characteristics to indicate which takes precedence in analysis . this method is the denver papillae protocol ( dpp ) , a dichotomous key with clear and distinct characteristics of fp to ensure accurate and repeatable counts from digital photographs of the tongue . dpp is a proposed method to standardize the previously used miller & reedy method , thus removing individual interpretation and ensuring more consistent results when analyzing fp density . by doing so , dpp can be used to more confidently determine the role of fp in taste . the tongue images taken of the subjects were analyzed by the citizen scientists ( scorers ) of the lab who are the true subjects of this study . the lab s core of citizen scientists is comprised of members from the community ranging in age ( years ) from 16 to mid-80s . a summative evaluation report commissioned by the museum in 2012 describes citizen scientists as having a strong interest in science and with two - thirds having earned a college degree in a scientific discipline . candidate citizen scientists are currently recruited via word of mouth , must successfully complete an interview process with veteran volunteers at the museum , and undergo a trial period in the museum s permanent health exhibition , expedition health , before they have the opportunity to apply for a position in the lab . once accepted into the lab , citizen scientists undergo a 12 - week training to become certified to enroll human subjects . following this certification , they are able to take training modules on various techniques in the lab ( e.g. papillae counting , dna extraction ) and following additional certifications and regular quality control measures , these citizen scientists have the opportunity to actively participate in data analysis . citizen scientists volunteer their time and are not compensated for their contributions to the museum . the images scored in this study were collected as part of a larger taste study conducted in the genetics of taste lab at the denver museum of nature & science ( the museum ) . subjects of the larger study were museum visitors ( n = 1195 ) ranging in age from 18 - 93 . while subjects came from six of the seven continents , participants were primarily of european descent . the western institutional review board approved the protocol , informed written consent was given , and subjects volunteered their time and were not compensated for their participation in the study . image capture show subjects a photograph of how to pose themselves ( figure 1 ) and what the captured image will look like . this is the photograph shown to subjects in the got lab in order to correctly pose for their tongue photo.direct subjects to dry their tongue with a paper hand towel and leave tongue protruding from their mouths.apply approximately 3 ml of blue food dye at a 1:36 concentration to the apex of the tongue using a sterile , rayon applicator with a 1 - inch tip . have subjects return tongue to their mouth and swallow to remove excess dye.have subjects pose themselves as shown in figure 1 , with their chin on their hands and elbows propped on a table for stability . direct subjects to extend their tongue a comfortable distance and secure it gently between their teeth.adhere a 2.5 cm piece of filter paper with a 10 mm diameter circular cutout punched in it to the tip of the anterior of the left side of the tongue next to midline ( see figure 1 ) . take at least three close - up images of the tongue , capturing the entire 10 mm circular cutout to ensure visualization of all fp within that area . use the macro setting of a high - quality digital point and shoot camera attached to a tripod for stability . zoom in to the extent that the entire cutout is photographed while still within the camera s recommended zoom range . ensure that the plane of the camera lens is parallel to the plane of the tongue and that the cutout appears circular in the photo instead of oblong . show subjects a photograph of how to pose themselves ( figure 1 ) and what the captured image will look like . this is the photograph shown to subjects in the got lab in order to correctly pose for their tongue photo . direct subjects to dry their tongue with a paper hand towel and leave tongue protruding from their mouths . apply approximately 3 ml of blue food dye at a 1:36 concentration to the apex of the tongue using a sterile , rayon applicator with a 1 - inch tip . have subjects pose themselves as shown in figure 1 , with their chin on their hands and elbows propped on a table for stability . direct subjects to extend their tongue a comfortable distance and secure it gently between their teeth . adhere a 2.5 cm piece of filter paper with a 10 mm diameter circular cutout punched in it to the tip of the anterior of the left side of the tongue next to midline ( see figure 1 ) . take at least three close - up images of the tongue , capturing the entire 10 mm circular cutout to ensure visualization of all fp within that area . use the macro setting of a high - quality digital point and shoot camera attached to a tripod for stability . zoom in to the extent that the entire cutout is photographed while still within the camera s recommended zoom range . ensure that the plane of the camera lens is parallel to the plane of the tongue and that the cutout appears circular in the photo instead of oblong . zoom in to the extent that the entire cutout is photographed while still within the camera s recommended zoom range . ensure that the plane of the camera lens is parallel to the plane of the tongue and that the cutout appears circular in the photo instead of oblong . review photos to ensure they are high quality and useful for counting . image selection and preparationupload the photos to the computer.of the images taken of the same subject s tongue , select only one for further analysis based on clear definition between structures on the tongue at the highest zoom and the least distorted angle so the tongue is broad and flat toward the camera.open the selected raw image in the open source software , imagej . click on plugins and in the dropdown menu scroll to analyze and clickwhen the cell counter opens , click initialize to link the image to the cell counter . note : here , use imagej 1.45 sec with 32 - bit java 1.6.0_10 version . use a standard magnification of 50 % for consistency between scorers and for use in subsequent steps to score fp . move this image to the left side of the screen next to the cell counter . this image will be referred to as copy a ( see figure 2 , left side of screen ) . upload the photos to the computer . of the images taken of the same subject s tongue , select only one for further analysis based on clear definition between structures on the tongue at the highest zoom and the least distorted angle so the tongue is broad and flat toward the camera . click on plugins and in the dropdown menu scroll to analyze and clickwhen the cell counter opens , click initialize to link the image to the cell counter . note : here , use imagej 1.45 sec with 32 - bit java 1.6.0_10 version . use a standard magnification of 50 % for consistency between scorers and for use in subsequent steps to score fp . move this image to the left side of the screen next to the cell counter . this image will be referred to as copy a ( see figure 2 , left side of screen ) . use a standard magnification of 50 % for consistency between scorers and for use in subsequent steps to score fp . move this image to the left side of the screen next to the cell counter . this image will be referred to as copy a ( see figure 2 , left side of screen ) . open a second copy of the raw image ( copy b ) for measuring the diameters of the papillae being quantified . zoom in and out as needed to the preference of the individual scorer throughout the scoring process . move this copy to the right side of the screen so the two copies are not accidentally confused . . using copy b , zoom in as much as necessary to accurately draw a diameter across the 10 mm inner circle of the filter paper at any angle and click analyze and set scale . verify the scale is correct by measuring an alternate angle and ensure the diameter range is between 9.8 - 10.2 mm . figure 2 : copy a and copy b. copy a ( left ) is linked to the cell counter window and remains at 50 % magnification for consistency from scorer to scorer while copy b ( right ) may be zoomed to the preference of the individual . for each candidate papilla , use the following dichotomous key ( step 2.2 - 2.5 ) detailing the criteria to determine if it is a fp . refer to figure 3 for a visual of papillae that are classified as fp and for ones that are rejected at each step in the process . figure 3a is a tongue with several qualifying fp while 3b - 3e have circled areas that violate each rule . ( 3b ) area is amorphous ; ( 3c ) papillae are too small ; 3d ) papilla is blue compared to those surrounding it , ( 3e ) papilla is recessed compared to those around it . see if there is a commonly - recognized geometric shape ( oval , cuboidal , round ) . if there is a geometric shape ( see figure 3a ) , move to step 2.3 . if there is no geometric shape ( see figure 3b ) , go to the cell counter window and click type 1 . on copy a ( 50 % zoom ) , click the candidate papilla to mark it as amorphous and not a fp . clicking on types1 - 4 in this and subsequent steps allows scorers to know they have addressed all candidate papillae and categorizes which rule was violated when rejecting a structure which will aid in the discussion in step 2.7.2 . see if there is a commonly - recognized geometric shape ( oval , cuboidal , round ) . if there is a geometric shape ( see figure 3a ) , move to step 2.3 . if there is no geometric shape ( see figure 3b ) , go to the cell counter window and click type 1 . on copy a ( 50 % zoom ) , click the candidate papilla to mark it as amorphous and not a fp . clicking on types 1 - 4 in this and subsequent steps allows scorers to know they have addressed all candidate papillae and categorizes which rule was violated when rejecting a structure which will aid in the discussion in step 2.7.2 . color refer to copy a at 50 % zoom and determine if there is any color differentiation over the surface of the tongue . if not , do not use color as a determining factor ; move to step 2.4 . determine if the candidate papilla is lighter than the tissue or papillae surrounding it ( see figure 3a ) . if any part of the candidate papilla has remained pink or stained lighter , move to step 2.4 . if the candidate papilla is blue and the surrounding papillae are lighter ( see figure 3c ) , go to the cell counter window and click type 2 on the cell counter . on copya , click the candidate to mark as too blue and not a fp . refer to copy a at 50 % zoom andif not , do not use color as a determining factor ; move to step 2.4 . determine if the candidate papilla is lighter than the tissue or papillae surrounding it ( see figure 3a ) . if any part of the candidate papilla has remained pink or stained lighter , move to step 2.4 . if the candidate papilla is blue and the surrounding papillae are lighter ( see figure 3c ) , go to the cell counter window and click type 2 on the cell counter . on copysize using copy b , zoom in to the distance where one can comfortably see the outline of the candidate papilla.click on the line tool and measure across the longest dimension of the candidate papilla . clickif the measured length is 0.5 mm or greater ( see figure 3a ) , move to step 2.5 . if the measured length is 0.499 mm or less , measure once more to ensure accuracy . if it is still 0.499 mm or less ( see figure 3d ) , click type 3 on the cell counter window and on copy a , click the candidate papilla to mark it as too small and not a fp . using copy b , zoom in to the distance where one can comfortably see the outline of the candidate papilla . click on the line tool and measure across the longest dimension of the candidate papilla . clickif the measured length is 0.5 mm or greater ( see figure 3a ) , move to step 2.5 . if the measured length is 0.499 mm or less , measure once more to ensure accuracy . if it is still 0.499 mm or less ( see figure 3d ) , click type 3 on the cell counter window and on copy a , click the candidate papilla to mark it as too small and not a fp . recession using copy a , assess if the candidate papilla is either uniform height with the rest of the tongue or elevated . if the papilla is in a crevice , determine its height compared to the other structures in the crevice , not the surface of the tongue . if the papilla is lower than the papillae surrounding it ( see figure 3e ) , use type 4 and on copy a , click the candidate papilla to mark it as recessed and not a fp.if the candidate papilla is either of uniform height with the rest of the tongue or elevated ( see figure 3a ) , use type 5 to click it and mark that this is a fp . do not close the copies at this point as imagej does not save the scores on the cell counter nor the colored marks from types 1 - 5 on copy a. using copy a , assess if the candidate papilla is either uniform height with the rest of the tongue or elevated . if the papilla is in a crevice , determine its height compared to the other structures in the crevice , not the surface of the tongue . if the papilla is lower than the papillae surrounding it ( see figure 3e ) , use type 4 and on copy a , click the candidate papilla to mark it as recessed and not a fp . if the candidate papilla is either of uniform height with the rest of the tongue or elevated ( see figure 3a ) , use type 5 to click it and mark that this is a fp . do not close the copies at this point as imagej does not save the scores on the cell counter nor the colored marks from types 1 - 5 on copy a. saving copy a write down in notebook raw fp score.on the cell counter window , click export image . this will allow the opening of copy a in the future to retain the colored marks from types 1 - 5 . this will allow the opening of copy a in the future to retain the colored marks from types 1 - 5 . quality control score each photo by two individual scorers and compare.if the higher fp raw score is within 10 % of the lower fp raw score , average the two scores together for a consensus fp score . if the two fp raw scores differ by more than 10 % , pull both scored photos onto the screen . use counter types 1 - 4 to aid in discussion of discrepancies and confer on a final consensus score . if no consensus can be reached during the discussion , take a break from scoring . at a later point , score each photo by two individual scorers and compare . if the higher fp raw score is within 10 % of the lower fp raw score , average the two scores together for a consensus fp score . if the two fp raw scores differ by more than 10 % , pull both scored photos onto the screen . use counter types 1 - 4 to aid in discussion of discrepancies and confer on a final consensus score . if no consensus can be reached during the discussion , take a break from scoring . at a later point , use counter types 1 - 4 to aid in discussion of discrepancies and confer on a final consensus score . if no consensus can be reached during the discussion , take a break from scoring . at a later point , if a consensus still can not be reached , pull in a third scorer . ask them to score the image and dialogue with the other two . background on training have two scorers count a variety of images , scoring individually and conferring regularly to ensure that they were using the same criteria . only when individual counts were consistently within 10 % of each other for each the images when scored was the method ( finalized above ) considered acceptable and termed dpp.choose 15 official images and 15 training images ( supplemental figures 2 - 17 ) in sequential order to score . if an image was deemed uncountable during selection , skip the image and choose next sequential image . note : these images vary in quality and size as they were chosen while the lab was still mastering the correct photography technique . one of the selected images was deemed uncountable through this primary counting process but was left in to ensure that scorers were able to make that call when needed . therefore there are 16 images given to trainees though only 15 scored images.using dpp , have the above - mentioned scorers count the 15 training images and create a consensus score for each.give trainees the 15 official images and ask to score using miller & reedy to create a baseline . once step 3.2 was completed , have the scorers score the 15 official images again and record their scores . have two scorers count a variety of images , scoring individually and conferring regularly to ensure that they were using the same criteria . only when individual counts were consistently within 10 % of each other for each the images when scored was the method ( finalized above ) considered acceptable and termed dpp . choose 15 official images and 15 training images ( supplemental figures 2 - 17 ) in sequential order to score . if an image was deemed uncountable during selection , skip the image and choose next sequential image . note : these images vary in quality and size as they were chosen while the lab was still mastering the correct photography technique . one of the selected images was deemed uncountable through this primary counting process but was left in to ensure that scorers were able to make that call when needed . therefore there are 16 images given to trainees though only 15 scored images . using dpp , have the above - mentioned scorers count the 15 training images and create a consensus score for each . give trainees the 15 official images and ask to score using miller & reedy to create a baseline . once step 3.2 was completed , have the scorers score the 15 official images again and record their scores . training subsequent scorers on dpp give training scorers the first training image and demonstrate dpp for a few papillae on this image . allow trainees to continue practicing scoring for the rest of that photo and confer with the consensus number ( for the got lab s consensus number and type 1 - 5 markers , see supplementary figure 1 ) . for this photo discuss any discrepancies regardless of the 10 % to ensure understanding of dpp.give subsequent scorers the second training image and have them score using dpp.if the trainee raw fp score is within ten percent of the established consensus count from section 3.1.3 . , allow trainee to move onto the next image and repeat steps.if the score is outside the ten percent range , use the trainee s colored marks representing types 1 - 5 to understand and identify the inconsistency and then address discrepant understanding of dpp.give the trainee the opportunity to rescore the image and verify the new score once more . if successful , trainee moves onto the next image until all images are completed . give training scorers the first training image and demonstrate dpp for a few papillae on this image . allow trainees to continue practicing scoring for the rest of that photo and confer with the consensus number ( for the got lab s consensus number and type 1 - 5 markers , see supplementary figure 1 ) . for this photo discuss any discrepancies regardless of the 10 % to ensure understanding of dpp . if the trainee raw fp score is within ten percent of the established consensus count from section 3.1.3 . if the score is outside the ten percent range , use the trainee s colored marks representing types 1 - 5 to understand and identify the inconsistency and then address discrepant understanding of dpp . give the trainee the opportunity to rescore the image and verify the new score once more . if successful , trainee moves onto the next image until all images are completed . image capture show subjects a photograph of how to pose themselves ( figure 1 ) and what the captured image will look like . this is the photograph shown to subjects in the got lab in order to correctly pose for their tongue photo.direct subjects to dry their tongue with a paper hand towel and leave tongue protruding from their mouths.apply approximately 3 ml of blue food dye at a 1:36 concentration to the apex of the tongue using a sterile , rayon applicator with a 1 - inch tip . have subjects return tongue to their mouth and swallow to remove excess dye.have subjects pose themselves as shown in figure 1 , with their chin on their hands and elbows propped on a table for stability . direct subjects to extend their tongue a comfortable distance and secure it gently between their teeth.adhere a 2.5 cm piece of filter paper with a 10 mm diameter circular cutout punched in it to the tip of the anterior of the left side of the tongue next to midline ( see figure 1 ) . take at least three close - up images of the tongue , capturing the entire 10 mm circular cutout to ensure visualization of all fp within that area . use the macro setting of a high - quality digital point and shoot camera attached to a tripod for stability . zoom in to the extent that the entire cutout is photographed while still within the camera s recommended zoom range . ensure that the plane of the camera lens is parallel to the plane of the tongue and that the cutout appears circular in the photo instead of oblong . show subjects a photograph of how to pose themselves ( figure 1 ) and what the captured image will look like . this is the photograph shown to subjects in the got lab in order to correctly pose for their tongue photo . direct subjects to dry their tongue with a paper hand towel and leave tongue protruding from their mouths . apply approximately 3 ml of blue food dye at a 1:36 concentration to the apex of the tongue using a sterile , rayon applicator with a 1 - inch tip . have subjects pose themselves as shown in figure 1 , with their chin on their hands and elbows propped on a table for stability . direct subjects to extend their tongue a comfortable distance and secure it gently between their teeth . adhere a 2.5 cm piece of filter paper with a 10 mm diameter circular cutout punched in it to the tip of the anterior of the left side of the tongue next to midline ( see figure 1 ) . take at least three close - up images of the tongue , capturing the entire 10 mm circular cutout to ensure visualization of all fp within that area . use the macro setting of a high - quality digital point and shoot camera attached to a tripod for stability . zoom in to the extent that the entire cutout is photographed while still within the camera s recommended zoom range . ensure that the plane of the camera lens is parallel to the plane of the tongue and that the cutout appears circular in the photo instead of oblong . zoom in to the extent that the entire cutout is photographed while still within the camera s recommended zoom range . ensure that the plane of the camera lens is parallel to the plane of the tongue and that the cutout appears circular in the photo instead of oblong . review photos to ensure they are high quality and useful for counting . image selection and preparationupload the photos to the computer.of the images taken of the same subject s tongue , select only one for further analysis based on clear definition between structures on the tongue at the highest zoom and the least distorted angle so the tongue is broad and flat toward the camera.open the selected raw image in the open source software , imagej . click on plugins and in the dropdown menu scroll to analyze and clickwhen the cell counter opens , click initialize to link the image to the cell counter . note : here , use imagej 1.45 sec with 32 - bit java 1.6.0_10 version . use a standard magnification of 50 % for consistency between scorers and for use in subsequent steps to score fp . move this image to the left side of the screen next to the cell counter . this image will be referred to as copy a ( see figure 2 , left side of screen ) . upload the photos to the computer . of the images taken of the same subject s tongue , select only one for further analysis based on clear definition between structures on the tongue at the highest zoom and the least distorted angle so the tongue is broad and flat toward the camera . click on plugins and in the dropdown menu scroll to analyze and clickwhen the cell counter opens , click initialize to link the image to the cell counter . note : here , use imagej 1.45 sec with 32 - bit java 1.6.0_10 version . use a standard magnification of 50 % for consistency between scorers and for use in subsequent steps to score fp . move this image to the left side of the screen next to the cell counter . this image will be referred to as copy a ( see figure 2 , left side of screen ) . use a standard magnification of 50 % for consistency between scorers and for use in subsequent steps to score fp . move this image to the left side of the screen next to the cell counter . this image will be referred to as copy a ( see figure 2 , left side of screen ) . open a second copy of the raw image ( copy b ) for measuring the diameters of the papillae being quantified . zoom in and out as needed to the preference of the individual scorer throughout the scoring process . move this copy to the right side of the screen so the two copies are not accidentally confused . ( see figure 2 , right side of screen ) click on the line tool . using copy b , zoom in as much as necessary to accurately draw a diameter across the 10 mm inner circle of the filter paper at any angle and click analyze and set scale . verify the scale is correct by measuring an alternate angle and ensure the diameter range is between 9.8 - 10.2 mm . figure 2 : copy a and copy b. copy a ( left ) is linked to the cell counter window and remains at 50 % magnification for consistency from scorer to scorer while copy b ( right ) may be zoomed to the preference of the individual . for each candidate papilla , use the following dichotomous key ( step 2.2 - 2.5 ) detailing the criteria to determine if it is a fp . refer to figure 3 for a visual of papillae that are classified as fp and for ones that are rejected at each step in the process . figure 3a is a tongue with several qualifying fp while 3b - 3e have circled areas that violate each rule . ( 3b ) area is amorphous ; ( 3c ) papillae are too small ; 3d ) papilla is blue compared to those surrounding it , ( 3e ) papilla is recessed compared to those around it . see if there is a commonly - recognized geometric shape ( oval , cuboidal , round ) . if there is a geometric shape ( see figure 3a ) , move to step 2.3 . if there is no geometric shape ( see figure 3b ) , go to the cell counter window and click type 1 . on copy a ( 50 % zoom ) , click the candidate papilla to mark it as amorphous and not a fp . clicking on types1 - 4 in this and subsequent steps allows scorers to know they have addressed all candidate papillae and categorizes which rule was violated when rejecting a structure which will aid in the discussion in step 2.7.2 . see if there is a commonly - recognized geometric shape ( oval , cuboidal , round ) . if there is a geometric shape ( see figure 3a ) , move to step 2.3 . if there is no geometric shape ( see figure 3b ) , go to the cell counter window and click type 1 . on copy a ( 50 % zoom ) , click the candidate papilla to mark it as amorphous and not a fp . clicking on types1 - 4 in this and subsequent steps allows scorers to know they have addressed all candidate papillae and categorizes which rule was violated when rejecting a structure which will aid in the discussion in step 2.7.2 . color refer to copy a at 50 % zoom and determine if there is any color differentiation over the surface of the tongue . if not , do not use color as a determining factor ; move to step 2.4 . determine if the candidate papilla is lighter than the tissue or papillae surrounding it ( see figure 3a ) . if any part of the candidate papilla has remained pink or stained lighter , move to step 2.4 . if the candidate papilla is blue and the surrounding papillae are lighter ( see figure 3c ) , go to the cell counter window and click type 2 on the cell counter . on copya , click the candidate to mark as too blue and not a fp . refer to copy a at 50 % zoom andif not , do not use color as a determining factor ; move to step 2.4 . determine if the candidate papilla is lighter than the tissue or papillae surrounding it ( see figure 3a ) . if any part of the candidate papilla has remained pink or stained lighter , move to step 2.4 . if the candidate papilla is blue and the surrounding papillae are lighter ( see figure 3c ) , go to the cell counter window and click type 2 on the cell counter . on copysize using copy b , zoom in to the distance where one can comfortably see the outline of the candidate papilla.click on the line tool and measure across the longest dimension of the candidate papilla . clickif the measured length is 0.5 mm or greater ( see figure 3a ) , move to step 2.5 . if the measured length is 0.499 mm or less , measure once more to ensure accuracy . if it is still 0.499 mm or less ( see figure 3d ) , click type 3 on the cell counter window and on copy a , click the candidate papilla to mark it as too small and not a fp . using copy b , zoom in to the distance where one can comfortably see the outline of the candidate papilla . click on the line tool and measure across the longest dimension of the candidate papilla . if the measured length is 0.5 mm or greater ( see figure 3a ) , move to step 2.5 . if the measured length is 0.499 mm or less , measure once more to ensure accuracy . if it is still 0.499 mm or less ( see figure 3d ) , click type 3 on the cell counter window and on copy a , click the candidate papilla to mark it as too small and not a fp . recession using copy a , assess if the candidate papilla is either uniform height with the rest of the tongue or elevated . if the papilla is in a crevice , determine its height compared to the other structures in the crevice , not the surface of the tongue . if the papilla is lower than the papillae surrounding it ( see figure 3e ) , use type 4 and on copy a , click the candidate papilla to mark it as recessed and not a fp.if the candidate papilla is either of uniform height with the rest of the tongue or elevated ( see figure 3a ) , use type 5 to click it and mark that this is a fp . do not close the copies at this point as imagej does not save the scores on the cell counter nor the colored marks from types 1 - 5 on copy a. using copy a , assess if the candidate papilla is either uniform height with the rest of the tongue or elevated . if the papilla is in a crevice , determine its height compared to the other structures in the crevice , not the surface of the tongue . if the papilla is lower than the papillae surrounding it ( see figure 3e ) , use type 4 and on copy a , click the candidate papilla to mark it as recessed and not a fp . if the candidate papilla is either of uniform height with the rest of the tongue or elevated ( see figure 3a ) , use type 5 to click it and mark that this is a fp . do not close the copies at this point as imagej does not save the scores on the cell counter nor the colored marks from types 1 - 5 on copy a. saving copy a write down in notebook raw fp score.on the cell counter window , click export image . this will allow the opening of copy a in the future to retain the colored marks from types 1 - 5 . this will allow the opening of copy a in the future to retain the colored marks from types 1 - 5 . quality control score each photo by two individual scorers and compare.if the higher fp raw score is within 10 % of the lower fp raw score , average the two scores together for a consensus fp score . if the two fp raw scores differ by more than 10 % , pull both scored photos onto the screen . use counter types 1 - 4 to aid in discussion of discrepancies and confer on a final consensus score . if no consensus can be reached during the discussion , take a break from scoring . at a later point , score each photo by two individual scorers and compare . if the higher fp raw score is within 10 % of the lower fp raw score , average the two scores together for a consensus fp score . if the two fp raw scores differ by more than 10 % , pull both scored photos onto the screen . use counter types 1 - 4 to aid in discussion of discrepancies and confer on a final consensus score . if no consensus can be reached during the discussion , take a break from scoring . at a later point , use counter types 1 - 4 to aid in discussion of discrepancies and confer on a final consensus score . if no consensus can be reached during the discussion , take a break from scoring . at a later point , background on training have two scorers count a variety of images , scoring individually and conferring regularly to ensure that they were using the same criteria . only when individual counts were consistently within 10 % of each other for each the images when scored was the method ( finalized above ) considered acceptable and termed dpp.choose 15 official images and 15 training images ( supplemental figures 2 - 17 ) in sequential order to score . if an image was deemed uncountable during selection , skip the image and choose next sequential image . note : these images vary in quality and size as they were chosen while the lab was still mastering the correct photography technique . one of the selected images was deemed uncountable through this primary counting process but was left in to ensure that scorers were able to make that call when needed . therefore there are 16 images given to trainees though only 15 scored images.using dpp , have the above - mentioned scorers count the 15 training images and create a consensus score for each.give trainees the 15 official images and ask to score using miller & reedy to create a baseline . once step 3.2 was completed , have the scorers score the 15 official images again and record their scores . have two scorers count a variety of images , scoring individually and conferring regularly to ensure that they were using the same criteria . only when individual counts were consistently within 10 % of each other for each the images when scored was the method ( finalized above ) considered acceptable and termed dpp . choose 15 official images and 15 training images ( supplemental figures 2 - 17 ) in sequential order to score . if an image was deemed uncountable during selection , skip the image and choose next sequential image . note : these images vary in quality and size as they were chosen while the lab was still mastering the correct photography technique . one of the selected images was deemed uncountable through this primary counting process but was left in to ensure that scorers were able to make that call when needed . using dpp , have the above - mentioned scorers count the 15 training images and create a consensus score for each . give trainees the 15 official images and ask to score using miller & reedy to create a baseline . once step 3.2 was completed , have the scorers score the 15 official images again and record their scores . training subsequent scorers on dpp give training scorers the first training image and demonstrate dpp for a few papillae on this image . allow trainees to continue practicing scoring for the rest of that photo and confer with the consensus number ( for the got lab s consensus number and type 1 - 5 markers , see supplementary figure 1 ) . for this photo discuss any discrepancies regardless of the 10 % to ensure understanding of dpp.give subsequent scorers the second training image and have them score using dpp.if the trainee raw fp score is within ten percent of the established consensus count from section 3.1.3 . , allow trainee to move onto the next image and repeat steps.if the score is outside the ten percent range , use the trainee s colored marks representing types 1 - 5 to understand and identify the inconsistency and then address discrepant understanding of dpp.give the trainee the opportunity to rescore the image and verify the new score once more . if successful , trainee moves onto the next image until all images are completed . give training scorers the first training image and demonstrate dpp for a few papillae on this image . allow trainees to continue practicing scoring for the rest of that photo and confer with the consensus number ( for the got lab s consensus number and type 1 - 5 markers , see supplementary figure 1 ) . for this photo discuss any discrepancies regardless of the 10 % to ensure understanding of dpp . if the trainee raw fp score is within ten percent of the established consensus count from section 3.1.3 . , allow trainee to move onto the next image and repeat steps . if the score is outside the ten percent range , use the trainee s colored marks representing types 1 - 5 to understand and identify the inconsistency and then address discrepant understanding of dpp . give the trainee the opportunity to rescore the image and verify the new score once more . if successful , trainee moves onto the next image until all images are completed . here is a representative photograph scored by two individual scorers when using the commonly - used miller & reedy methodology for fp identification based on the field standards of round , large , pink or stained lighter , and elevated , and then the same photograph scored by two scorers using dpp . the counts shown are representative of the high variance observed using the original method compared to the lower variance using dpp . the image on the left is representative of two scorers counts using the miller & reedy method . red is scorer 1 , yellow is scorer 2 , green is scorers 1 & 2 . statistical reliability of dpp was previously studied using a mixed linear model to assess variability . briefly , to generate data to assess the role dpp plays in consistency of scores , fifteen images were scored twice . in the first batch of scores , the scorers were then trained to use dpp and the images were individually rescored without the final consensus step described in section 2.7 detailing quality control ( figure 5 ) . the fp score data set was then used in the mixed model to assess the combined differences due to protocol ( figure 6 ) , within - scorer variability and the interaction between the two . this model showed a significant difference in scoring when using the miller & reedy method compared to dpp ( p - value 1 x 10 ) with dpp leading to a higher count by 6.99 ( se = 0.99 ) ; 5.2 % of the variability in the score was due to training , 25.9 % due to scorer , and the remaining due to variability specific to the image . next , to generate data to determine within - scorer variability , a series of thirty images in random order were scored by 11 individuals . panels provide boxplots of reviewer scores for 15 images pre and post denver papillae protocol training . for each boxplot , using dpp , the variance within image counts across independent scorers and within - scorer s counts decreased significantly . while this method makes visual fp density analysis without videomicroscopy less subjective , it should be noted that this method only scores fp . dpp can not guarantee that structures classified as fp have taste pores and are therefore gustatory papillae nor that the counts are reflective of real taste bud density.the nature of this method is that it establishes reliability through consistency and precision ; however , it may be biasing results in a consistent direction . to test accuracy relative to other methods using a true measure of taste bud density ( e.g. , videomicroscopy ) would extend beyond the scope of this study.however , by characterizing the morphology of fp more stringently and creating a dichotomous key , this method addresses miller & reedy s charge to the field that more characterization of fp needs to be done in order to have consensus on their morphology and quantification . additionally , they indicated that this characterization might clarify some of the differences among subjects and explain some of the disparate results among investigators . by providing a uniform method of quantification , many of the discrepancies on the role of fp in taste and nutrition - related research may be rectified . the dichotomous key may be adjusted for the different image capture techniques . the known distance for the measurement scalecan easily be set to the diameter used in each lab and recession can be discounted if saran wrap or glass were placed over the tongue for image capture . in the got lab , it was found that the neutral tongue provided the best definition of papillae . this may be due to the amount of light in the lab which caused saran wrap or glass to reflect light back into the camera creating a glare that made assessment difficult . some labs have said they find the dye more challenging to count , but the got lab found a diluted blue food dye at a concentration of 1:36 provided the ideal contrast between fungiform and filiform papillae on the majority of tongues . the creation of a dichotomous key for fp characterization will allow for researchers in different labs , using a variety of image capture methods , to consistently analyze structures on the tongue and have confidence in the reporting of their results . finally , use of a dichotomous key may have purposes in other areas of scientific methodology where qualities of structures or objects are providing inconsistent numbers from study to study .\noutput:\n" }, { "from": "agent", "value": "the goal of the denver papillae protocol is to use a dichotomous key to define and prioritize the characteristics of fungiform papillae ( fp ) to ensure consistent scoring between scorers . this protocol builds off of a need that has arisen from the last two decades of taste research using fp as a proxy for taste pore density . fp density has historically been analyzed using miller & reedy s 1990 characterizations of their morphology : round , stained lighter , large , and elevated . in this work , the authors forewarned that stricter definitions of fp morphology needed to be outlined . despite this call to action , follow up literature has been scarce , with most studies continuing to cite miller & reedy s original work . consequently , fp density reports have been highly variable and , combined with small sample sizes , may contribute to the discrepant conclusions on the role of fp in taste sensitivity . the genetics of taste lab explored this apparent inconsistency in counting and found that scorers were individually prioritizing the importance of these characteristics differently and had no guidance for when a papilla had some , but not all , of the reported qualities of fp . the result of this subjectivity is highly variable fp counts of the same tongue image . the denver papillae protocol has been developed to remedy this consequence through use of a dichotomous key that further defines and prioritizes the importance of the characteristics put forth by miller & reedy . the proposed method could help create a standard way to quantify fp for researchers in the field of taste and nutritional studies ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: we report the unusual case of a 70 - year - old caucasian man who presented with a nonspecific symptom and was noted to have a giant retroperitoneal pseudocyst . a pseudocyst is defined as a fluid - filled cavity that is not lined by an epithelial surface . most pseudocysts arise from retroperitoneal structures like the pancreas and the adrenal glands . in this case reporta 70 - year - old patient was referred to the general surgical clinic complaining of bilateral reducible groin swellings . the right - sided swelling was slightly larger than the left and was also , at times , uncomfortable . he was fit and well otherwise aside from a slightly elevated bmi ( 28 kg / m ) . bilateral inguinal hernias were diagnosed and the patient was listed to undergo an elective laparoscopic bilateral inguinal hernia repair . electively the procedure was carried out through a totally extra - peritoneal approach . the procedure was uneventful aside from the incidental finding of a large right - sided cystic mass below the liver edge . the patient was later discharged as a day case and an urgent outpatient computed tomography ( ct ) of abdomen and pelvis was organized . the ct ( figs 13 ) was performed identifying a unilocular , cystic lesion arising from within the right side of the abdomen . this lesion was distinct and not found to be related to any of the intra - abdominal organs . the radiological dimensions of the lesion were 222019 cm . the findings were explained to the patient , and he was booked for laparotomy and excision of the cyst . figure 1 : axial slice from the ct imaging identifying the retroperitoneal pseudocysta large cyst was identified and found to be occupying most of the right retroperitoneal cavity . medially , the cyst was attached to the small bowel mesentery and extended from immediately below the liver to the pelvic brim . figures 4 and 5 show operative retrieval of the pseudocyst and the macroscopic appearances of the specimen . figure 5 : a large alexis wound retractor was utilized . in the image , centrally , the pseudocyst can be identified prior to retrieval . the intact excised pseudocyst . a large alexis wound retractor was utilized . in the image , centrally , the pseudocyst can be identified prior to retrieval . macroscopic histology showed an intact retroperitoneal cyst measuring 242113 cm containing turbid fluid and weighing 4035 g. microscopically the cyst wall was lined by foamy macrophages and fibrin , with some chronic inflammation noted in the wall as well . primary retroperitoneal pseudocysts are a rare entity and arise predominately from the mesentery and omentum without any significant communication with adjacent structures . they are characteristically unilocular or multilocular in appearance with abundant debris on abdominal ultrasound scan and an enhancing wall on ct imaging . cystic lesions in the retroperitoneum are rare with a reported incidence of between 0.0004 and 0.02 % per annum , with even a smaller percentage beingpseudocysts consist of serous fluid and due to their non - pancreatic etiology contain significantly low levels of amylase and lipases . histopathological assessment usually demonstrates a fluid - filled cavity devoid of epithelium that is not histologically similar to either pancreatic or adrenal tissue . in chronic cases , the surrounding fibrous capsule undergoes calcification and has been described as resembling an eggshell . non - pancreatic retroperitoneal pseudocysts generally grow at a slow , steady rate and only become symptomatic if they become large enough to compress adjacent anatomical structures . surgical excision is the mainstay of treatment and has the best outcome in the literature reviewed . an open approach is preferable if the patient is symptomatic , the mass is 6 cm or the possibility of malignancy is present . this case highlights the importance of a thorough clinical history / examination during a busy general surgical clinic . the patient initially presented with bilateral reducible groin swellings and was asymptomatic with regard to gastrointestinal / general symptoms . pseudocysts are a rare entity and can grow to large sizes without causing any specific symptoms . this combined with the minimal literature and scientific evidence available , we as clinicians are at risk of identifying and treating these patients at a later stage resulting in higher mortality and morbidity . the benefits of laparoscopic surgery have been highlighted in identifying incidental intra - abdominal pathologies when history and examination have failed . this report aims to add to the literature with regard to presentation , pathophysiology and management so that these patients are identified and treated at an earlier stage . written informed consent was obtained from the patient for publication of this case report and any accompanying images . a copy of the written consent is available for review by the editor of this journal . performed literature review , devised first and subsequent drafts ; m.s . conceived study , participated in design and coordination and helped to draft the manuscript .\noutput:\n" }, { "from": "agent", "value": "we present the case of a 70 - year - old man with a giant right - sided retroperitoneal pseudocyst , confirmed histologically after resection to be benign with appearances dissimilar to pancreatic and adrenal tissue . the cyst was noted incidentally on table at the time of laparoscopic surgery . retroperitoneal pseudocysts most commonly arise from the pancreas and adrenal glands occurring as a result of an inflammatory process . primary retroperitoneal pseudocysts are a rare entity . this case highlights the importance of examining the patient thoroughly and not focusing on the obvious . the mass was not palpated on initial review prior to listing for surgery , and the patient was asymptomatic from the mass ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: recent whole transcriptome studies have revealed that about three quarters of the human genome is capable of being transcribed , while protein - coding regions account for just 2 % of the genome ( 13 ) . therefore , the vast majority of transcribed sequences do not encode proteins , and are called non - coding rna ( ncrna ) . accumulating evidence shows that non - coding rnas play key roles in various biological processes , such as imprinting control , the circuitry controlling pluripotency and differentiation , immune responses , and chromosome dynamics ( 4 ) . ncrnas are as important as protein - coding genes to cellular functions ( 5,6 ) . notably , a growing number of long ncrnas ( lncrnas ) , which are considered to be 200 nt in length and are often multiexonic ( 7 ) , have been implicated in disease etiology ( 810 ) . it is therefore of great importance to collect lncrna information and store this information in a one - stop knowledge gateway for lncrnas , the noncode database . the development of high - throughput sequencing methodologies has reduced the cost of rna sequencing , and as a result there has been an explosive rise in the number of newly identified lncrnas . established a consensus set of 384066 predicted transcripts from 7256 rna - seq libraries , which were designated as the mitranscriptome assembly ( 11 ) . since then the revolutionary advancement of sequencing methods , such as single - molecule long - read techniques , leads us closer to the real lncrna transcriptome . given sufficient material , amplification - free sequencing of full - length cdna moleculesnoncode has collected data from literature published since the last update and includes the latest versions of several public databases ( ensembl ( 13 ) , refseq ( 14 ) , lncrnadb ( 15 ) and gencode ( 16 ) ) . after the removal of false and redundant lncrnas , noncode contains a total of 527,336 transcripts . in addition to the identification of new lncrnas , data on the genetics and biochemical properties of lncrnas has accumulated rapidly . of the papers retrieved from pubmed for lncrnas , we found that the vast majority studied lncrna function , especially the relationship between lncrnas and disease ( 810 ) . in large - scale searches for single - base differences between diseased and healthy individuals , about 40 % of the disease - related differences show up in genomic regions outside of protein - coding genes . this implicates non - coding regions as vital for genetic risk factors of disease ( 2 ) . in order to enable a systematic compilation and integration of this informationthe sources for these annotations were derived from literature mining , differential lncrna analysis utilizing public rna - seq data and microarray data and mutation analysis from public genome - wide association study ( gwas ) data . along with the ever increasing number of lncrnas and the amount and functional study data , genome - wide conservation information is required for biologists to study the mechanisms of lncrna actions . in order to explore the conservation information of lncrnas , noncode collected six new mammalian species ( chimpanzee , gorilla , orangutan , rhesus macaque , opossum and platypus ) ( 17 ) . users can browse the conserved counterparts of any human lncrna gene in other species through a phylogenetic tree layout . similar to the former iterations of noncode ( 1821 ) , the source of noncode 2016 includes the previous versions of noncode , the collated literature and other public databases . noncoding , non - coding , no code , non - code , lncrna and lincrna , and found 6532 new articles since 1 june 2013 ( the last collection date for noncode ) . we retrieved the newly identified lncrnas and their annotations from the supplementary material or web site of these articles . together with the newest data from ensembl , refseq , lncrnadb , gencode and the old versions of noncode data , literature data were processed through a standard pipeline for each species . all of the input data were processed into bed or gtf formats based on one assembly version , for example , hg38 for human and mm10 for mouse.combination . all of the normalized data files were combined together using the cuffcompare program in the cufinks suite ( 22 ) . after eliminating redundancy , every new transcript i d and the accompanying resources were extracted.filtering protein - coding rna . firstly , the rna was compared with the coding rna in refseq and ensembl , and the = and c transcripts were excluded . secondly , the rna was filtered through the coding - non - coding index ( cnci ) ( 23 ) program and only the rnas considered non - coding by cnci were kept.information retrieval . we assigned each transcript a name according to the criterion of noncode v4 and extracted basic information such as location ( 24 ) , exons , length , assembly sequence , source , etc.advanced annotation . advanced annotations included expression profiles , predicted functions , conservation , disease information , etc . human expression profiles were collected from 16 tissues of the human bodymap 2.0 data ( ena archive : erp000546 ) and eight cell lines ( geo accession no . gse30554 ) , while mouse data was collected from six different tissues ( ena archive : erp000591 ) . functions for the lncrna genes were predicted by lnc - gfp ( 25 ) , a coding non - coding co - expression network ( 26,27 ) based global function predictor.web presence . more annotation information has been added and a more user - friendly interface has been introduced . all of the input data were processed into bed or gtf formats based on one assembly version , for example , hg38 for human and mm10 for mouse . all of the normalized data files were combined together using the cuffcompare program in the cufinks suite ( 22 ) . after eliminating redundancy , firstly , the rna was compared with the coding rna in refseq and ensembl , and the = and c transcripts were excluded . secondly , the rna was filtered through the coding - non - coding index ( cnci ) ( 23 ) program and only the rnas considered non - coding by cnci were kept . we assigned each transcript a name according to the criterion of noncode v4 and extracted basic information such as location ( 24 ) , exons , length , assembly sequence , source , etc . advanced annotations included expression profiles , predicted functions , conservation , disease information , etc . human expression profiles were collected from 16 tissues of the human bodymap 2.0 data ( ena archive : erp000546 ) and eight cell lines ( geo accession no . gse30554 ) , while mouse data was collected from six different tissues ( ena archive : erp000591 ) . functions for the lncrna genes were predicted by lnc - gfp ( 25 ) , a coding non - coding co - expression network ( 26,27 ) based global function predictor . more annotation information has been added and a more user - friendly interface has been introduced . noncode contains 527,336 lncrna transcripts from 16 species ( human , mouse , cow , rat , chimpanzee , gorilla , orangutan , rhesus macaque , opossum , platypus , chicken , zebrafish , fruitfly , caenorhabditiselegans , yeast and arabidopsis , ) . according to the definition of lncrna genes ( 18 ) , a total of 101,700 and 86,935 genes were generated from 167,150 and 130,558 lncrnas from human and mouse ( shown in table 1 ) , respectively . following the nomenclature of noncode v4 ( 18 ) , both lncrna transcripts and genes were designated systematically : non + three characters ( representing a species ) + t ( transcript ) or g ( gene ) + six sequential numbers . noncode has annotated expression profiles from all the human and mouse transcripts and genes , and a large number of these genes were annotated with predicted functions . definitive evidence has proven that transcription of the non - coding genome has produced functional rnas ( 1 ) . in particular , lncrnas have been implicated in biological , developmental , and pathological processes , and acted through mechanisms such as chromatin reprogramming , cis regulation at enhancers , and post - transcriptional regulation of mrna processing ( 28 ) . lncrnas are therefore considered to be important regulators of tissue physiology and disease processes including cancer ( 11 ) . although we have collected functional interactions between ncrnas and biomolecules in npinter ( 2931 ) , we think it is also necessary to include disease information into noncode . recent published papers have been explored , and the proven associations between noncode transcripts and diseases has been integrated into the latest version . the noncode assembly also assessed the overlaps of transcripts with the unique disease - associated single - nucleotide polymorphisms ( snps ) from a catalog of gwass ( 32 ) and the snp database ( dbsnp ) ( 33 ) . there were also a lot of relational data between lncrnas and diseases which were analyzed from rna - seq and microarray data . after collecting the basic data , we compared it with the lncrnas in noncode and retained data that overlapped with noncode lncrnas . noncode 2016 contains 1110 lncrnas which were related to 284 diseases . among these associations , disease related data acquisition pipeline in the lncrna gene description pages , users can retrieve the related diseases of the entry , and also get the source of the information , such as the pmid ( s ) of the reference paper ( s ) . there is also mutational information retrieved from the literature , gwass and the dbsnp database . compared to protein - coding genes and small rnas ( e.g. mirnas and snornas ) , several reports have suggested that lncrnas are modestly conserved ( 11 ) . most lncrnas are less conserved in sequence ( 34 ) , but there are still many lncrnas that are conserved in their genomic loci , exonic sequences and promoter regions ( 35 ) . these are preserved across multiple species , attesting to their important functional potentials ( 36 ) . benefiting from next - generation sequencing technologies , ncrnas are now more easily identied via transcript sequencing . noncode has added six new species , mainly from multi - species rna - seq data ( 37,38 ) . an evolutionary tree from 12 commonly studied species ( human , mouse , cow , rat , chicken , zebrafish , chimpanzee , gorilla , orangutan , rhesus macaque , opossum and platypus ) was constructed using methods introduced in phylononcode ( 39 ) . each human lncrna gene counterpart from the other listed species can be retrieved through browsing the evolutionary tree ( shown in figure 2 ) . the counterpart of each lncrna was computed using the ucsc liftover tool ( 40 ) . in brief , liftover utilized blastz ( 41 ) , an independent implementation of the gapped blast algorithm specifically designed for aligning two long genomic sequences , as a core algorithm to detect homologous regions in other genomes . after mapping to the second species , however , a proper method of in silico transcript reconstruction is an ongoing challenge . according to an assessment by the paul bertone group , 40 % of known transcriptsthe complexity of higher eukaryotic genomes imposes severe limitations on transcript recall and splice product discrimination that are likely to remain limiting factors for the analysis of current - generation rna - seq data ( 42 ) . furthermore , multiple amplification steps during library preparation complicate the quantification of expression levels . to some extentgiven sufficient material , amplification - free and fragmentation - free sequencing of full - length cdna molecules provides a more direct view of rna molecules ( 12 ) . noncode contacted the authors of the third - generation single - molecule long - read survey of the human transcriptome paper ( 12 ) . after our analysis , the single - molecule lncrna transcripts were included into noncode . to meet the quality demands of researchersusers can choose the subset which is considered high quality . the quality controls include the source of the data , literature support , other database support and long - read sequencing method support . the controls also include selection of exon numbers , the lengths of the transcripts and prediction tools support . the web interface will return the subset according to the conditions users chose and allow users to download the data . noncode 2016 contains 527,336 lncrnas from 16 different species , this compares favorably with other lncrna databases . for example , lncipedia ( human only ) contains 111685 transcripts ( 43 ) , lncrnator ( human , mouse , fly , zebrafish , worm and yeast ) contains 34605 transcripts ( 44 ) , while the lncrnawiki ( human only ) contains 105255 transcripts ( 45 ) . as mentioned above , technical limitations imposed by short - read sequencing lead to a number of computational challenges in transcript reconstruction and quantification . for many transcripts , automated methods failed to identify all of the constituent exons , and in cases in which all exons were reported , the protocols tested often failed to assemble the exons into complete isoforms ( 42 ) . for example , although we have obtained all the data from mitranscriptome ( 11 ) , which contains 384066 human lncrnas from 7256 rna - seq libraries , the detection of precise refseq splicing patterns from mitranscriptome was only 31 % , and the fraction of annotated genes within the entire mitranscriptome was only 46 % . although it is reasonable to assume that unannotated transcription is unique to specific lineages , the low refseq detection rate was unusual . we therefore made a decision that noncode would not include mitranscriptome data in the current version . in the future , we will attempt to make clear the real reason ( s ) . perhaps a more comprehensive construction tool is required to answer this question . national high technology research and development program ( 863 program ) of china [ 2014aa021103 , 2014aa021502 ] ; training program of the major research plan of the national natural science foundation of china ; national natural science foundation of china ; chinese academy of science strategic project of leading science and technology [ xda01020402 ] . funding for open access charge : national high technology research and development program ( 863 program ) of china [ 2014aa021103 ] .\noutput:\n" }, { "from": "agent", "value": "noncode ( http://www.bioinfo.org/noncode/ ) is an interactive database that aims to present the most complete collection and annotation of non - coding rnas , especially long non - coding rnas ( lncrnas ) . the recently reduced cost of rna sequencing has produced an explosion of newly identified data . revolutionary third - generation sequencing methods have also contributed to more accurate annotations . accumulative experimental data also provides more comprehensive knowledge of lncrna functions . in this update , noncode has added six new species , bringing the total to 16 species altogether . the lncrnas in noncode have increased from 210 831 to 527,336 . for human and mouse , the lncrna numbers are 167,150 and 130,558 , respectively . noncode 2016 has also introduced three important new features : ( i ) conservation annotation ; ( ii ) the relationships between lncrnas and diseases ; and ( iii ) an interface to choose high - quality datasets through predicted scores , literature support and long - read sequencing method support . noncode is also accessible through http://www.noncode.org/ ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: spontaneous spinal epidural hematoma ( sseh ) is a rare condition of unknown origin typically produced by the rupture of an epidural vein . it usually presents when a healthy adult engaged in a normal activity suddenly develops back or neck pain .1 there have been many reports of sseh ,234 but few during pregnancy .5678910111213141516 in general , recurrent ssehs are uncommon .17181920 we report a case of sseh recurrence during pregnancy and its spontaneous resolution . a 27 - year - old primigravida at 37 weeks ' gestation suddenly felt a strong pain in her left shoulder and was admitted to the hospital emergency room . she denied any history of trauma and cited neither hypertensive disorders nor comorbidities during the term of her pregnancy . however , she had a history of fenestration surgery for sseh ( frankel a ) at 18 years old ( figs . 1 and 2 ) with complete recovery . her blood pressure was 177/97 mmhg , pulse rate was 83 beats per minute , and temperature was 36.4 c . he suspected a recurrence of the sseh from her past medical history and her recollection of a similarly intense pain experienced only once before during her first sseh . t1w1 - weighted ( left ) and t2w1 - weighted ( right ) magnetic resonance imaging showing the cervical epidural hematoma at the c4t1 level at 18 years old . t1w1 - weighted ( left ) and t2w1 - weighted ( right ) magnetic resonance imaging showing that the cervical epidural hematoma disappeared after operation at 18 years old . an emergency magnetic resonance imaging ( mri ) the orthopedic and obstetric doctors recommended a cesarean section for delivery and observation without steroids for the sseh . on the day following admission , a cesarean section was performed under general anesthesia and a healthy male infant weighing 3,256 g was delivered . during recovery , . t1w1 - weighted ( left ) and t2w1 - weighted ( right ) magnetic resonance imaging showing the epidural hematoma at the c4t1 level at 27 years old . sagittal view and axial view ( c6 level ) . at her 1 - month follow - upthree years later , she underwent a second cesarean section and gave birth to a male infant without recurrence of sseh . t1w1 - weighted ( left ) and t2w1 - weighted ( right ) magnetic resonance imaging showing that the epidural hematoma at the c4t1 level disappeared at 1 - month follow - up . the recommended treatment for this medical condition is commonly a surgical decompression to prevent neurologic deficit .21 previous reports suggest that the prognostic factors were strongly correlated with the timing of the surgical decompression ; therefore , an immediate decompression was recommended .21 the outcomes were better if the surgery was performed within 48 hours ( in cases with incomplete spinal cord dysfunction ) or 36 hours ( in cases with complete spinal cord dysfunction ) .3 several authors have reported cases of spontaneous resolution of sseh without an operative intervention .4222324 however , the conservative treatment has often resulted in a poor clinical outcome . we have no definitive tools to identify the patients who may recover spontaneously .22 if there is no motor function improvement , the treatment in most cases should be an immediate decompression .222324 the strategies must be determined for both the mother 's neurologic disorder and the fetus ' well - being . babies born before 37 weeks of pregnancy are defined as extremely preterm ( 28 weeks ) , very preterm ( 28 to 32 weeks ) , and moderate to late preterm ( 32 to 37 weeks ) .25 any child born at 36 weeks or earlier is considered a preemie . the organ function of the fetus is still immature , specifically the pulmonary capacity .26 there have been a small number of reports of pregnant women with an sseh .5678910111213141516 three cases before 31 weeks ' gestation were carried through term , but almost all infants born after 32 weeks were delivered by cesarean section . from 32 to 36 weeks , it is very difficult to decide if the best course of action is to deliver the baby or to continue the pregnancy . the prone position for the spine operation as well as the general anesthesia required have associated risks for the fetus ; however , if the pregnancy is sustained , the risk for respiratory distress syndrome and other respiratory morbidity can be reduced .26 in the studies reviewed , all of the women experienced neurologic deficits and were managed operatively5678910111213141516 ; therefore , this is the first case of spontaneous resolution . we chose nonoperative management with close observation for this patient because she had no neurologic deficit , only pain . sseh during pregnancy is an acute neurologic emergency , and a universally accepted idea is that this condition may be a consequence of venous bleeding . during pregnancy , women are in a hypercoagulable state , making it less likely for hematomas to develop . however , sudden changes in the central venous pressure can be transmitted directly from the visceral cavities to the epidural veins .15 according to steinmetz et al ,9 as the uterus and fetus enlarge during the late stages of pregnancy , the abdominal and pelvic venous dynamics are altered .15 this fluctuation in the venous pressures may lead to the rupture of a pre - existing pathologic venous wall .615 hypertension is a major cause of hematoma . hypertensive disorders associated with pregnancy are one of the most common obstetric problems . upon arrival in the emergency room , our patient 's blood pressure was elevated , although after admission it was monitored strictly and returned to normal . we can not definitively conclude if temporary high blood pressure caused the bleeding or if pain made her blood pressure higher . cases of relapse have rarely been reported , and at initial presentation , all cases were treated conservatively , achieving a spontaneous resolution .17181920 the recurrent intervals were a few minutes to 3 years .1819 this patient 's recurrence interval was about 10 years . the hospital that operated on her at age 18 for the initial sseh performed the fenestration and aspirated the hematoma . many patients undergo a cervical laminectomy or laminoplasty , and these operations might be needed to prevent recurrences . we report on a rare case of recurrent sseh during pregnancy with no neurologic deficits that was treated nonoperatively with close observation and resulted in spontaneous resolution . in such patients with no neurologic deficits , nonoperative management with close observation\noutput:\n" }, { "from": "agent", "value": "study design case report . objective to describe a patient with a recurrent spontaneous spinal epidural hematoma ( sseh ) during pregnancy that had spontaneous remission . methods a 27 - year - old primigravida at 37 weeks ' gestation suddenly felt a strong left shoulder pain without any trauma . she had a history of fenestration for a spontaneous cervical hematoma when she was 18 years old . an emergency magnetic resonance imaging revealed a recurrence of the cervical epidural hematoma at the c4t1 level , but she had no paralysis . results the patient subsequently underwent a cesarean section and delivered a healthy male infant . her spinal epidural hematoma disappeared . multislice computed tomography showed no evidence for a vascular malformation or tumor . three years after the initial cesarean section , she underwent a second one and delivered another male infant . conclusions we report on a rare case of recurrent sseh during pregnancy with no neurologic deficits that was treated nonoperatively with close observation and resulted in spontaneous resolution . in such patients with no neurologic deficits , nonoperative management with close observation may be a reasonable alternative ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: poly adp - ribose polymerase 1 ( parp - 1 ) is a critical enzyme in the repair of dna strand breaks . this 116 kda nuclear protein detects dna single strand breaks and utilizes nad as a substrate to poly ( adp - ribosyl ) ate nuclear proteins , resulting in relaxation of chromatin and recruitment of other repair proteins to the damaged site . parp - 1 is an attractive antitumor target because of this vital role in dna repair . the current clinical approaches to the development of parp - 1 inhibitors include either ( 1 ) the utilization as a single agent in brca1 or brca2 - deficient cancers where inhibition of parp results in synthetic lethality or ( 2 ) the utilization in combination with dna damaging therapeutics ( radiation or chemotherapy ) to increase maximum therapeutic benefit of these agents by blocking the repair process . there are multiple ongoing clinical trials evaluating the efficacy of parp - 1 inhibitors as chemopotentiators in several cancers , including non - small - cell lung cancer ( nsclc ) . however , early phase clinical studies of parp - 1 inhibitor , compound 1 , in combination with topotecan , dacarbazine , or cisplatin plus gemcitabine showed dose - limiting toxicity that was more pronounced than that seen with the chemotherapeutic agents alone . therefore , targeted delivery of parp inhibitors selectively to cancer cells could be a solution to overcome these systemic toxicity problems . diazeniumdiolate - based nitric oxide ( no ) releasing prodrugs developed in our laboratory have proven to be effective as anticancer agents in a number of in vitro and in vivo models . the lead compound , o - ( 2,4 - dinitrophenyl ) 1 - [ ( 4 - ethoxycarbonyl ) piperazin -1-yl ] diazen -1-ium-1,2-diolate ( js - k , 2 ) , exhibits a multifaceted mechanism of action initiated by depletion of intracellular gsh and induction of oxidative stress , followed by the activation of stress signaling , abrogated mitochondria function , dna damage , and apoptosis . dna single strand break damage ( measured by comet assay ) was observed in the h1703 nsclc cell line after a 1 h treatment with 2 , and massive dna damage was seen after 24 h. in multiple myeloma cells , 2 caused dna double strand break damage . we hypothesized that inhibition of parp may enhance the potency of 2 and other no - releasing prodrugs of the arylated diazeniumdiolate class . in this work , we have designed and synthesized no - releasing parp -1-inhibitor prodrugs that are activated by reaction with glutathione ( gsh ) , a reaction that is accelerated by glutathione s - transferase ( gst ) , a family of phase ii detoxification enzymes . we show that these hybrid prodrugs are effective against cancer cells in vitro and in vivo . activation of the compounds by gstp1 , an isoform of gst that is frequently overexpressed in cancers , should result in the preferential metabolism and thus release of cytotoxins in cancer cells , potentially diminishing systemic toxicity associated with parp inhibition . structural features to be merged in designing no - releasing parp inhibitors for the present study are color coded : green for the arylating fragment that is transferred to gsh in the activation step ; red for the parp inhibitor moiety ; and blue for the two molecules of cytolytic nitric oxide released on activation . our specific strategy here is to combine the structural features of the established parp - 1 inhibitor 1 and arylated diazeniumdiolate 2 , structures shown in scheme 1 . specifically , we wanted to produce molecules that link the parp - inhibitory skeleton of 1 ( the red portion of structure 1 in scheme 1 ; the black cyclopropane carboxamide group is not necessary for parp - 1 inhibition ) with the electrophilic aryl ring shown in green and the caged no molecules shown in blue in scheme 1 . accordingly , we reacted known compounds 3a and 3b ( 10 ) with 4 ( 7 ) to obtain the first two drug candidates , 5a and 5b , as shown in scheme 2 . our hypothesis was that attack by gsh on these molecules would lead to consumption of a reducing equivalent through irreversible arylation of the gsh , with simultaneous generation of two nos plus known parp inhibitors 6a and 6b , as illustrated in scheme 3 . the first step in the activation of these prodrugs is the arylation of gsh , liberating a diazeniumdiolate ion that spontaneously decomposes to no , freeing the parp - inhibitory part of the molecule . accordingly , 5a and 5b reacted smoothly with gsh to generate the expected products , shown in scheme 3 . the rates of reaction of 5a and 5b with 4 mm gsh in aqueous ph 7.4 phosphate buffer ( 0.1 m ) containing 50 m diethylenetriaminepentaacetic acid at 37 c were determined . the t1 / 2 for 5a was 11.2 min , and the t1 / 2 for 5b was 11.6 min . liquid chromatography / mass spectrometry ( lc / ms ) analysis of the reaction mixture after 2 half - lives confirmed that 25 % of the parent compound was still present while 75 % consisted of deacylated compound 1 ( 6b ) and the aryl - glutathione conjugate ( 7 ) ( scheme 3 , figure s1 ) . the ability of the new compounds to inhibit parp - 1 enzymatic activity was tested using an assay that measures incorporation of biotinylated poly adp - ribose onto histone proteins .5 a and 5b were compared to 1 and authentic compounds 6a and 6b that are products of 5a and 5b activation ( scheme 3 ) . parp - 1 enzyme ic50 values estimated for 6a , 6b , and 1 were 30.5 , 6.9 , and 15.5 nm , respectively ( figure 1 ) . both prodrugs 5a and 5b , without activation by gsh , were less potent , with ic50 of 123 nm for 5a and 58 nm for 5b . inhibition of parp - 1 enzyme activity by 5a , 5b , 6a , and 6b , compared with 1 . compounds 5a and 5b inhibited proliferation of an extensive panel of nsclc cell lines with ic50 concentrations ranging from 3 to 20 m ( table 1 ) . ic50 values for no - releasing parp - 1 inhibitor prodrugs were significantly lower than those of 1 for the most sensitive cell lines . the ic50 values correlated with endogenous ros levels and with levels of antioxidant enzyme peroxiredoxin 1 and dna repair enzyme 8 - oxoguanine dna glycosylase ( ogg1 , figure s2 ) . depleting the cell s gsh during prodrug activation combined with no release led to induction of oxidative / nitrosative stress ( figure s3 ) and cytotoxicity through cellular stress overload , especially in cells with high endogenous ros levels . since the proliferation screen and measurements of parp - 1 inhibitory activities of both prodrugs showed fluoro - substituted analogue 5b to be more potent than 5a , we decided to focus on 5b for further development . cellular levels of atp fall below a critical level , and cells with substantial dna damage can not enter apoptosis , rendering them resistant to this form of cell death or susceptible to necrosis . therefore , inhibition of parp - 1 in combination with substantial dna damage would conserve cellular energy and could allow tumor cells to undergo apoptosis in response to dna - damaging no , eliminating toxic effects or immune responses associated with necrosis . twenty - four - hour treatment with no - releasing parp - 1 inhibitor prodrug 5b resulted in significant dna strand break damage as observed by comet assay . treatment with 5b at 5 m resulted in a stronger comet signal , compared with 20 m 1 ( figure 2a ) . a strong apoptotic signal ( as evidenced by cleaved caspase 7 ) was seen in cells treated with 5b , while the same concentration of 1 did not trigger apoptosis ( figure 2b ) . treatment with no - releasing parp - 1 inhibitor prodrug 5b resulted in dna damage ( a ) , as shown by the comet assay in h1703 nsclc cells . the dna strand break damage caused by 5b was more extensive than that resulting from 1 treatment . actin served as a loading control . to validate the release of the parp - 1 inhibitor in cells , we evaluated cellular uptake and metabolism of 5b in a549 nsclc cells . cells were treated with 5b for varying time periods , and cell lysates were analyzed for the presence of the parent compound and its metabolites by lc / ms . the parent compound was not detected at any measured time point including a brief treatment of 5 min ( asterisk ( ) in figure 3 ) . at all timepoints measured up to 1 h , compound 6b and arylated gsh metabolite 7 were detected in equally abundant amounts , suggesting very rapid , presumably catalyzed , cellular metabolism ( figure 3 ) . in vitro metabolism of compound 5b . the human a549 ncslc cell line was treated with 10 m 5b . then the products were extracted at various time points and analyzed by lc / ms / ms . shown are extracted ion chromatograms ( eics ) , which were extracted at various m / z ratios including the [ m + h ] of 6b ( retention time ( tr ) of 11.9 min ) , arylated gsh ( 7 , tr = 13.8 min ) , and compound 5b ( tr = 18.2 min ) ( scheme 3 ) . the asterisk ( ) indicates where compound 5b should be , based on the elution profile of a lysate spiked with authentic compound 5b ( bottom panel ) . lung cancer cells frequently express high levels of gstp1 , the gst isoform that is often overexpressed in cancer cells . we have screened a panel of 20 nsclc cell lines for the level of expression of gstp1 protein using western blot . this experiment confirmed that the enzyme is highly expressed in a majority of nsclc cell lines , with little to none of the liver - specific a1 isoform ( gsta1 ) detected ( figure s4 ) . therefore , we studied the rate of reaction of 5b with gsh in the presence of recombinant gstp1 and found that the reaction was enhanced over 10-fold when the enzyme was present ( table 2 , row 3 ) . this strongly suggests that the prodrug , despite its reactivity with gsh alone , will be preferentially activated when gstp1 is present . importantly , the presence of gstp1 did not alter product distribution ( figure s5 ) . next , 5b was independently reacted with glutathione in the presence of gsta1 ; the a1 isoform was found to be a better catalyst for glutathione attack than gstp1 ( table 2 , row 3 ) . further synthetic approaches were taken to diminish gsta1 catalysis . only two measurements made in the first half - life for the gsta1 trials . in an effort to modify the structure of 5b to make it less susceptible to gsta1 - induced metabolism and to improve its suitability as a substrate for gstp1 , we employed a strategy developed previously to do so with compound 2 . in that case , molecular modeling suggested that adding and reducing steric bulk at different specific locations in the structure of 2 would accomplish this goal . as predicted , compound 8 ( paba / no , structure in scheme 4a ) was prepared and shown to be metabolized at similar rates by gstp1 and gsta1 , in contrast to 2 , which was an order of magnitude more efficiently metabolized by gsta1 ( table 2 , rows 1 and 2 ) . we chose a similar strategy in designing the bis - diazeniumdiolated parp - 1 inhibitor hybrid 13 shown in scheme 4b as a synthetic target . thus , boc - protected piperazine diazeniumdiolate 9 was reacted with aryl fluoride substituted diazeniumdiolate 10 to give adduct 11 , which upon removal of the protecting group gave 12 . this compound contains nucleophilic nitrogen in the piperazine ring that was reacted with 3b to produce the bis - diazeniumdiolated parp - 1 inhibitor 13 . compound 13 was subjected to a similar reactivity and metabolism analysis as 5b . not only was compound 13 more stable than 5b in reactions with gsh alone , but the rates of catalysis suggest that compound 13 is better accommodated in the active site of gstp1 than that of gsta1 ( table 2 , row 4 ) . molecular modeling experiments suggested that compound 13 fits nicely into the gstp1 active site while a steric clash may occur in the gsta1 active site ( figure 4 ) . compound 13 parp - 1 enzyme inhibitory activity in the presence or absence of gsh and gstp1 was also analyzed . top panels : transition state modeling of the 13glutathione adduct in the gsta1 and gstp1 active sites . bottom panel : inhibition of parp - 1 enzyme by compound 13 in the presence or absence of gsh / gstp1 . mass spectrometric analysis of the cellular metabolism of compound 13 in a549 lung adenocarcinoma cells and u937 human leukemia cells revealed that the compound is metabolized as designed to release no upon gsh / gst attack . the dearylation of the first diazeniumdiolate moiety results in spontaneous release of no and frees the parp -1-inhibitory component . the resulting glutathione conjugate reacts further with gsh , leading to attachment of two glutathionyl substituents to the dinitrophenyl ring ( scheme 4c ) . alternatively , the single glutathione conjugates could react with protein thiols instead of gsh , resulting in a protein adduct , in which gsh and the protein s thiol group are covalently cross - linked through the dinitrophenyl ring . this thiol modification ( cross - linking glutathionylation ) appears to be irreversible and likely plays an important role in mediating the cytotoxic activity of bis - diazeniumdiolates . it is also predictable that this irreversible modification will affect proper protein folding , which , if unresolved , leads to the unfolded protein response ( upr ) and endoplasmic reticulum ( er ) stress . we exploited this hypothesis and found that indeed treatment with 13 results in cellular protein glutathionylation and er stress ( figure 5a ) . treated cells were lysed and processed for immunoblotting under nonreducing conditions , and protein / gsh cross - links were detected with specific antibodies recognizing glutathione conjugated to proteins . as shown in figure 5a , glutathione attached to protein was detected within 1 h of treatment , and the signal became gradually stronger with time . the decrease in protein / gsh conjugate signal observed at 8 h was only seen upon the onset of apoptosis , as indicated by cleaved parp ( figure 5a ) . this essentially irreversible modification consumes gsh and results in a shift in the cellular redox balance toward a more oxidizing environment , generating oxidative / nitrosative stress . er stress induction was evidenced by phosphorylation of eif2 and up - regulation of chop , bip , and atf4 proteins ( figure 5b ) . activation of stress kinase p38 was seen within 15 min after treatment with 13 was initiated ( figure 5c ) and could be a result of ros / rns stress . we have observed rapid and persistent phosphorylation of p38 in u937 leukemia cells upon treatment with compound 2 . to determine whether the induction of ros / rns and stress signalingwere associated with cell death , cells were treated with compound 13 and then analyzed by western blot for markers of apoptosis . apoptosis was activated through the extrinsic pathway , as evidenced by caspase 8 activation within 6 h of treatment with 1 m 13 ( figure 5e ) . cleaved effector caspases 3 and 7 and cleaved parp signals were also observed ( figure 5e ) . ( a ) compound 13 causes cross - linking of gsh to protein thiols ( protein glutathionylation ) that is irreversible and induces endoplasmic reticulum ( er ) stress in a549 lung adenocarcinoma cells ( b ) . ( c ) activation of the p38 stress signaling pathway in a549 cells after treatment with 13 occurred rapidly , within 15 min after treatment was initiated , and phosphorylation persisted for 8 h. ( d ) tumor suppressor p53 and its effector , puma , are involved in cells bearing wild - type p53 ( a549 nsclc cell line ) . ( e ) treatment with 13 induced the extrinsic apoptosis pathway in a549 cells . cleavage of caspase 8 and the effector caspases 3 and 7 , as well as parp , was observed : f.l . , full length parp ; cl , cleaved . human lung adenocarcinoma cell line a549 , which expresses moderate levels of gstp1 , was chosen for assessment of activity of the prodrugs in vivo against xenografted cells in athymic mice . both compounds were administered at 92 mol / kg intravenously two times a week for a 4 - week period to assess anticancer activity . figure 6 shows significant reduction of the tumor growth in animals treated with compound 13 ( p 0.02 ) , compared to 1 or saline controls . importantly , treatment with either controls or diazeniumdiolate - based drugs did not affect body weights ( see caption to figure 6 ) . tumors from animals in each group were resected and extracted for analysis of metabolites . both the parent drugs and the liberated parp - 1 inhibitor were detected in some tumors from animals treated with compounds 5b and 13 , indicating unambiguous delivery of compound to tumors remote from the site of injection . compounds were administered intravenously at 92 mol / kg , 2 times a week for 4 weeks , and tumors were measured with a caliper . values are medians , and the relevant 95 % confidence interval bars are shown ( mann whitney test ) . stars indicate the significance of the differences between 13 - treated and 1 - treated and control mice at each time point . the average body weight for all mice was 22.90.31 g ( mean se ) at the beginning of the experiment . at the termination , the average weights of the control groups were 25.60.76 g ( n = 12 ) , 25.00.78 g ( n = 10 ) , and 25.00.77 g ( n = 11 ) for 1 , vehicle , and saline control , respectively . the weights of animals treated with 13 were 25.30.49 g ( n = 10 ) , and those treated with 5b were 27.70.82 g ( n = 11 ) . bortezomib ( ps - 341 , 14 ) is a boronic acid dipeptide derivative that selectively and potently inhibits the 26s proteasome . it has clinically validated activity against multiple myeloma and has undergone extensive evaluation in nsclc . preliminary in vitro studies established that 14 alone induces growth inhibition in several nsclc cell lines . it has been shown that , combined with cytotoxic agents in vitro , 14 enhanced the antitumor effect in nsclc and other solid tumors , and recently proteasome inhibition as a treatment for nsclc advanced to clinical trials . it has previously been shown that the proteasome inhibitor 14 has synergistic activity with compound 2 . ( 6 ) 14 induced ros generation in h460 nsclc cells . having shown that cytotoxicity of diazeniumdiolate - based no - releasing prodrugs correlated with intracellular ros levels , we hypothesized that co - treatment of lung adenocarcinoma cells with 14 and our prodrugs would result in enhanced cytotoxicity through ros / rns stress . also , proteasome inhibitors are known to induce the unfolded protein response and er stress . therefore , a combination of 14 with compound 13 , which causes irreversible , aryl - cross - linking glutathionylation of cellular proteins and induces er stress , might result in enhanced cytotoxicity . indeed , combination treatment of 14 and 13 exhibited enhanced toxicity as evaluated by colony forming assay ( figure 7 ) . this promising result suggests that further in vitro and in vivo trials of compound 13 combined with 14 are indicated . colony forming assay ( a549 cells ) indicated enhanced cytotoxicity of the combination of compound 13 with proteasome inhibitor 14 . we have designed prodrugs combining an arylated diazeniumdiolate with a parp - 1 inhibitor to achieve simultaneous delivery of a dna damaging agent and a dna repair inhibitor to the cell . previous work has shown that arylated diazeniumdiolates cause significant dna strand break damage . concurrent treatment with a dna strand break repair inhibitor dramatically exacerbates dna damage and cytotoxicity . second - generation molecules have been designed to be preferentially metabolized by cells containing high levels of gstp1 , e.g. , cancer cells . we conclude that compound 13 , a bis - diazeniumdiolate , is capable of irreversibly cross - linking gsh to protein thiols , causing the accumulation of misfolded proteins , leading to er stress ( figure 8 ) . this additional cytotoxic stress adds to the multifaceted proapoptotic mechanisms of arylated diazeniumdiolate action . starting materials were purchased from aldrich chemical co. ( milwaukee , wi ) unless otherwise indicated . chemical shifts ( ) are reported in parts per million ( ppm ) downfield from tetramethylsilane . ultraviolet ( uv ) spectra were recorded on an agilent model 8453 or a hewlett - packard model 8451a diode array spectrophotometer . prepacked silica gel flash chromatography columns were purchased from silicycle ( quebec city , canada ) or from yanazen science inc . in addition to nmr , uv , and hplc with hrms , chn combustion analysis was performed to determine purity of compounds .3 - [ ( 4 - oxo - 3h - phthalazin -1-yl ) methyl ] benzoic acid , 3a , was prepared as described by menear et al . to a slurry of 557 mg ( 1.6 mmol ) of the hydrochloride salt of 4 , 448 mg ( 1.6 mmol ) of 3a , and 608 mg ( 1.6 mmol ) of hatu in 5 ml of dimethylacetamidethe resulting solution was stirred at room temperature for 1 h , followed by addition of 40 ml of water . the resulting precipitate was collected by filtration and recrystallized from ethanol , giving 827 mg of an off - white solid : mp 114117 c ; uv ( acetonitrile ) max 294 nm ( = 18.9 mm cm ) ; h nmr ( dmso - d6 ) 3.633.68 ( m , 8h ) , 4.38 ( s , 2h ) , 7.287.30 ( m , 1h ) , 7.397.46 ( m , 3h ) , 7.817.98 ( m , 4h ) , 8.26 ( d , 1h ) j = 7.4 hz , 8.568.59 ( dd , 1h ) j = 2.7 , 7.4 hz , 8.88 ( d , 1h ) j = 2.7 hz , 12.06 ( s , 1h ) ; c nmr ( dmso - d6 ) 37.7 , 50.2 , 116.5 , 122.5 , 125/6 , 125.9 , 126.5 , 127.8 , 128.3 , 129.2 , 129.6 , 130.2 , 130.7 , 132.0 , 133.9 , 135.6 , 137.3 , 138.93 , 142.6 , 145.3 , 153.2 , 159.8 , 169.4 ; hrms ( esi ) m / z calculated for c26h23n8o8 [ m + h ] = 575.1639 , found 575.1548 , ppm = 1.5 calcd for c26h22n8o8h2o : c , 52.70 ; h , 4.08 ; n , 18.91 . found : c , 52.66 ; h , 3.73 , n , 18.50 . a solution of 685 mg ( 2.3 mmol ) of 3b ( 10 ) in 30 ml of n , n - dimethylformamide was cooled to 4 c . hatu ( 950 mg , 2.5 mmol ) was added , and the resulting slurry was stirred under nitrogen . a solution of 765 mg ( 2.19 mmol ) of 4 ( 5 ) and 753 l ( 5 mmol ) of diisopropylethylamine in 60 ml of dimethylformamide was added , and the resulting solution was stirred at room temperature overnight . the solution was cooled to 4 c and ice water ( 200 ml ) was added , giving a solid precipitate . the product was collected by filtration , washed with water , and allowed to dry to give 1.3 g of crude material . recrystallization from ethanol afforded 853 mg of pure 5b : mp 150153 c ; uv ( acetonitrile ) max 295 nm ( = 20.5 mm cm ) ; h nmr ( dmso - d6 ) 3.41 ( b , 1h ) , 3.58 ( b , 1h ) , 3.72 ( b , 1h ) , 3.84 ( b , 1h ) , 4.33 ( s , 2h ) , 7.25 ( t , 1h ) j = 9.0 hz , 7.377.46 ( m , 2h ) , 7.82 ( t , 2h ) j = 9.0 hz , 7.877.97 ( m , 3h ) , 8.24 ( d , 1h ) j = 7.8 hz , 8.548.57 ( dd , 1h ) j = 2.4 , 7.8 hz , 8.86 ( d , 1h ) j = 2.4 hz , 12.58 ( s , 1h ) ; c nmr ( dmso - d6 ) 36.9 , 45.2 , 50.5 , 116.9 , 118.52 , 119.5 , 122.6 , 124.0 , 125.8 , 126.5 , 127.9 , 129.3 , 130.2 , 131.9 , 132.6 , 133.9 , 135.2 , 137.3 , 142.6 , 145.2 , 154.1 ( d ) jc f = 246 hz , 159.8 , 164.4 ; hrms ( esi ) m / z calculated for c26h22fn8o8 [ m + h ] = 593.1545 , found 593.1538 , ppm = 1.1 calcd for c26h21fn8o8h2o : c , 51.15 ; h , 3.80 ; n , 18.35 ; f , 3.11 . found : c , 51.45 ; h , 3.70 , n , 18.41 ; f , 3.42 . a partial solution of 2.52 g ( 0.0087 mol ) of o - ( 2,4 - dinitro -5-fluorophenyl ) 1 - ( n , n - dimethylamino ) diazen -1-ium-1,2-diolate ( 10 ) ( 5 ) in 120 ml of tert - butanol was stirred at room temperature . a solution of 2.34 g ( 0.0087 mol ) of sodium 1 - [ 4 - ( tert - butoxycarbonyl ) piperazin -1-yl ] diazen -1-ium-1,2-diolate ( 9 ) in 120 ml of 5 % aqueous sodium bicarbonate was added gradually through a pressure equalizing addition funnel , and the resulting mixture was stirred at room temperature overnight . the reaction mixture was treated with 150 ml of water and the resulting yellow solid was collected by filtration , washed with water , and dried to give 1.33 g of product . the material was placed on a silica gel column and eluted with hexane / ethyl acetate to give 3.6 g ( 80 % ) of 11 as a yellow powder : mp 123125 c ; uv ( acetonitrile ) max 292 nm ( = 23 mm cm ) ; h nmr ( cdcl3 ) 1.49 ( s , 9h ) , 3.28 ( s , 6h ) , 3.603.61 ( m , 4h ) , 3.653.67 ( m , 4h ) , 7.57 ( s , 1h ) , 8.86 ( s , 1h ) ; c nmr ( cdcl3 ) 28.3 , 41.8 , 50.5 , 81.0 , 105.3 , 125.5 , 154.2 , 154.3 .24.46 . found : c , 39.44 ; h , 4.79 ; n , 24.09 . to a solution of 3.6 g ( 0.007 mol ) of 11 in 300 ml of ethyl acetate was added 70 ml of 2 m hcl in ether . the product was collected by filtration , washed with ethyl acetate , and allowed to dry , giving 3.1 g ( 98 % ) of 12 : mp 135137 c ; uv ( ethanol ) max 288 nm ( = 28 mm cm ) ; h nmr ( dmso - d6 ) 3.26 ( s , 6h ) , 3.333.35 ( b , 9h ; 4h for piperazine , 5h for water ) , 3.893.91 ( m , 4h ) , 7.82 ( s , 1h ) , 8.90 ( s , 1h ) , 8.41 ( b , 2h ) ; c nmr ( dmso - d6 ) 41.6 , 47.2 , 105.6 , 125.7 , 131.5 , 131.9 , 153.6 , 154.1 . this salt was used for the next step without further purification . to a solution of 2.05 g ( 0.00687 mol ) of 3b ( 10 ) and 2.85 g ( 0.0075 mol ) of hatu in 150 ml of n , n - dimethylformamide was added 2.6 ml ( 0.015 mol ) of dipea . to the solutionwas gradually added 3.1 g ( 0.00687 mol ) of 12 in 150 ml of n , n - dimethylformamide , and the resulting solution was stirred at room temperature overnight . the solution was treated with 250 ml of cold aqueous ammonium chloride solution , and the resulting precipitate was collected by filtration and washed with water . the solid containing water and dimethylformamidewas taken up in dichloromethane , dried over sodium sulfate , filtered through a layer of anhydrous magnesium sulfate , and evaporated in vacuo . the yellow moist solid was triturated with ether to give , after filtration , 2.16 g of 13 . purification was carried out with preparative hplc : mp 122125 c ; uv ( 0.2 % dmso / ethanol ) max 287 nm ( = 32 mm cm ) ; h nmr ( acetone - d6 ) 3.30 ( s , 6h ) , 3.583.97 ( m , 8h ) , 7.147.22 ( m , 1h ) , 7.447.54 ( m , 2h ) , 7.79 ( s , 1h ) , 7.807.88 ( m , 1h ) , 7.947.96 ( m , 2h ) , 8.328.34 ( m , 1h ) , 8.86 ( s , 1h ) , 11.75 ( s , 1h ) ; c nmr ( acetone - d6 ) 37.9 , 41.7 , 51.0 , 51.2 , 105.5 , 110.75 , 116.5 , 116.9 , 124.8 , 125.9 , 126.4 , 127.2 , 129.5 , 132.1 , 134.1 , 136.0 , 145.6 , 153.4 , 155.1 , 155.6 ( d ) jc f = 201.0 hz , 160.3 , 165.1 . for further decomposition and biological screening , a portion of the compound was purified on a phenomenex luna c18 column , 3 m , 150 mm 2.0 mm , with a gradient consisting of water and acetonitrile containing 0.1 % formic acid . hrms ( esi ) m / z calculated for c28h27fn11o10 [ m + h ] = 696.1921 , found 696.1928 , ppm = 0.96 . calcd for c28h26n11fo10h2o : c , 47.13 ; h , 3.95 ; f , 2.66 ; n , 21.59 . found : c , 47.14 ; h , 4.08 ; f , 2.73 ; n , 21.45 . intracellular levels of reactive oxygen / nitrogen species were quantified by oxidation of the ros / rns - sensitive fluorophore 5 - ( and -6 ) - chloromethyl -2,7-dichlorodihydrofluorescein diacetate ( dcf - da , invitrogen , carlsbad , ca ) . cells growing on six - well plates ( 610 / well ) were loaded with 5 m dcf - da in hanks balanced salt solution ( hbss ) at 37 c and 5 % co2 . after 30 min of incubation , hbss containing the probe was removed , cells were rinsed with hbss , and 3 ml of fresh hbss was added to each well followed by addition of compounds ( 10 m ) or dmso as a control . after 60 minthe cells were collected by scraping in hbss , and dcf fluorescence was measured by using a perkinelmer life and analytical sciences ( waltham , ma ) ls50b luminescence spectrometer with the excitation source at 488 nm and emission at 530 nm . the intracellular level of nitric oxide and its oxidation products after treatment with compounds was estimated by using the fluorophore 4 - amino -5-methylamino-2,7-difluorofluorescein ( daf - fm ) diacetate ( invitrogen ) . cells growing in six - well plates were loaded with 2.5 m daf - fm diacetate in hbss at 37 c and 5 % co2 . after 30 min of incubation the cells were rinsed with hbss to remove excess probe . test compounds in fresh hbss were added to the cells at 10 m final concentration . after 30 min of incubation , the fluorescence of the benzotriazole derivative formed on daf - fm s reaction with aerobic no was analyzed by using a perkinelmer life and analytical sciences ls50b luminescence spectrometer with the excitation source at 495 nm and emission at 515 nm . all experiments were performed at least three times , each time at least in triplicate . parp enzyme inhibition was measured using an ht universal colorimetric 96 - well parp assay kit ( trevigen , gaithersburg , md ) , according to the manufacturer s protocol with the following small modifications : when inhibitory activities of activated prodrugs were studied , gsh ( 4 mm ) was added in the presence and absence of gstp1 in pbs , ph 7.4 . reactions were initiated by the addition of prodrug after a 10 min incubation at 37 c and carried out for another 10 min . cell lines were obtained from the american type culture collection ( manassas , va ) and cultured according to the supplier s protocol . for proliferation assays , cells were seeded at 110 per well ( h1693 , h322 m , h1703 , h1944 , h1355 , h2122 , h441 , h1568 ) or 510 per well ( h460 , h1792 , a549 , h2023 , h2030 , h23 ) in 96 - well plates and allowed to adhere for 24 h. compounds were prepared as 10 mm stock solutions in dmso . increasing drug concentrations in 10 l of pbs were added to 100 l of the culture medium and incubated for 72 h. the mtt assay ( promega , madison , wi ) was performed according to the manufacturer s protocol . each concentration was represented in six repeats , and the screening was performed as at least two independent experiments . ic50 values were calculated by using sigma plot software ( systat software , inc . gsh ( 4 mm ) was added in the presence and absence of gstp1 or gsta1 in 0.1 m phosphate buffer solution , ph 7.4 , containing 50 m diethylenetriaminepentaacetic acid ( dtpa ) . reactions were initiated by the addition of substrate after the gsh - containing buffer and enzyme reached thermal equilibrium . typical substrate concentrations were 10 m with a gst concentration of 40 nm . in each experimentthe data were analyzed at 302 nm and the rate was derived by fitting the data to an exponential curve typical for first order processes . the metabolism of each compound was studied in the human a549 nsclc cell line and the human u937 leukemia cell line . in each case cellsthe a549 cell line was treated with 10 m of each compound and incubated for varying time points . at each timepoint the cells were lysed via scraping in 400 l of 10 mm hcl and 400 l of hplc grade acetonitrile . the u937 cell line was treated with 5 m of each compound and by two cycles of freeze ( 80 c ) and thaw ( 37 c ) in 400 l of 10 mm hcl and 400 l of hplc grade acetonitrile . to each lysatethe precipitate was removed by centrifugation at 12000 g for 15 min , followed by syringe filtration of the supernatant and analysis by lc / ms . the system used for analysis is an agilent 1200 hplc instrument coupled with an agilent 6520 accurate - mass quadrupole time - of - flight ( q - tof ) lc / ms / ms instrument . separations were performed on a phenomenex luna column , c185 m , 2.1 mm 150 mm , at a flow rate of 0.2 ml / min under h2o / acetonitrile / 0.1 % formic acid gradient conditions . the alkaline comet assay was performed as described . transition state modeling of the 13glutathione adduct in the gsta1 and gstp1 active sites was carried out as described . briefly , the initial models of the meisenheimer complex of compound 13 ( gs13 ) bound to gstp1 or gsta1 was built on the basis of the gstcd in the gstp1gstcd structure ( pdb entry 1aqx ) or in the gsta1gstcd model complex . the initial gsta1gstcd model complex was built on the basis of the crystal structures of the gstcd found in the active sites of gstm1 ( pdb entry 4gst ) and gstp1 ( pdb entry 1aqx ) , and then it was docked into the active site of gsta1 in complex with the gsh adduct of ethacrynic acid ( pdb entry 1gse ) . the gstp1gs13 and gsta1gs13 complexes built in dimeric forms because gsh interacts with the side chains from both subunits of gst . the dimeric model complexes were subject to geometry optimization using the macromodel module of schrdinger , llc ( macromodel , version 9.6 ) . most of the primary antibodies were from cell signaling technology ( danvers , ma ) , with the exception of atf3 which was from santa cruz biotechnology ( santa cruz , ca ) . to analyze for glutathionylation of cellular proteins , lysates were separated by gel electrophoresis ( 412 % nupage gel ) under nonreducing conditions , transferred to pvdf membranes , and probed with anti - glutathione conjugated to protein monoclonal antibody ( virogen ) . human lung adenocarcinoma cell line a549 was obtained from the american type culture collection and cultured in rpmi 1640 medium with 10 % fetal bovine serum , according to the cell supplier s protocol , for a maximum of four passages before use . cells were harvested at 7080 % confluence , washed with phosphate buffered saline , suspended in phosphate buffered saline , and implanted subcutaneously at 510 cells / 0.2 ml into ncr nu / nu athymic mice , obtained from charles river . frederick national laboratory for cancer research is accredited by aaalac international and follows the public health service policy for the care and use of laboratory animals . animal care was provided in accordance with the procedures outlined in the guide for care and use of laboratory animals ( national research council , 1996 ; national academy press , washington , dc ) . when the tumors reached approximately 3 mm 3 mm , the mice were distributed randomly into groups of 12 for treatment . compounds were injected into the tail veins of the mice , at 92 mol / kg body weight ( in 20 l of dmso solution ) , 2 times per week for 4 weeks . control groups were treated with saline or dmso . tumor volumes in mm were estimated by the formula ( / 2 length width ) . blood was collected under isoflurane anesthesia into eppendorf tubes containing 50 % acetonitrile / 10 mm hcl for drug metabolite analysis . all experiments ( with the exception of the proliferation assay and in vivo study ) were performed at least three times , each time at least in triplicate . statistical tests were carried out by using instat , version 3.00 ( graphpad software inc . pairwise comparisons included the t test , with the welch correction or application of the mannsignificance of correlations was assessed by the pearson linear correlation or the spearman test as appropriate .\noutput:\n" }, { "from": "agent", "value": "we report the antitumor effects of nitric oxide ( no ) releasing derivatives of the parp - 1 inhibitor olaparib ( 1 ) . compound 5b was prepared by coupling the carboxyl group of 3b and the free amino group of arylated diazeniumdiolated piperazine 4 . analogue 5a has the same structure except that the f is replaced by h. compound 13 is the same as 5b except that a me2n n ( o ) = no group was added para and ortho to the nitro groups of the dinitrophenyl ring . the resulting prodrugs are activated by glutathione in a reaction accelerated by glutathione s - transferase p1 ( gstp1 ) , an enzyme frequently overexpressed in cancers . this metabolism generates no plus a parp - 1 inhibitor simultaneously , consuming reducing equivalents , leading to dna damage concomitant with inhibition of dna repair , and in the case of 13 inducing cross - linking glutathionylation of proteins . compounds 5b and 13 reduced the growth rates of a549 human lung adenocarcinoma xenografts with no evidence of systemic toxicity ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: genetics informs us about human disease in at least two major ways , one through mendelian diseases and the other through complex traits . mutations that lead to mendelian inheritance of disease usually alter the function of single genes ( 1 ) , reducing or modifying the function of the protein product by changing the encoded amino acid sequence ( 2 , 3 ) . in addition , some mendelian diseases are caused by debilitating mutations in promoters or enhancers of a gene , resulting in a deficiency of the protein product and the consequent pathological phenotype ( 4 , 5 ) . genetic variants causing mendelian disease are rare in the human population ( 6 ) because selective pressure against their deleterious effects keeps their allele frequency low . because the genetic variants causing monogenic diseases are rare , mapping studies are confined to detailed analyses of affected families and kindreds ( 6 ) . the online mendelian inheritance in man ( omim ) database ( 1 , 7 ) currently lists almost 3400 phenotypes for which the molecular basis is known . susceptibilities to many common diseases such as coronary artery disease and many forms of cancer and type 2 diabetes have substantial genetic components , but in contrast to the mendelian diseases , these phenotypes are affected by variants at multiple loci ( 6 , 8 , 9 ) . mapping the multiple loci that contribute to these important traits usually follows a case - control design ( fig . the mapping experiments examine snps to ascertain the genotypes that are significantly more prevalent in the affected group than in the non - affected group ; these genotypes are associated with the trait of interest . when genotypes are determined at snps throughout the genome of each individual , the studyepigenetic data link gwas results to hypotheses about how specific snps affect a phenotype . a , in a gwas , individuals are grouped into cases or controls , denoted by different colors for stick figures . dna samples from each person are genotyped at a large number of polymorphic sites , illustrated as panels of gray or colored circles . snps for which the frequency of one allele is significantly different between the groups ( e.g. the yellow allele at one snp is more frequent in cases , whereas red is more frequent in controls ) are identified , and those passing stringent filters and replication are analyzed further as lead snps . b , epigenetic features in chromosomal regions containing the lead snp and linked snps are examined for evidence of crms . in this illustration , a snp in ld with the lead snp is in chromatin that is hypersensitive to dnase , monomethylated at histone h3 lysine 4 , and bound by a transcription factor ( tf ) . c , combining the genetic and epigenetic information leads to testable hypotheses such as allele - specific binding by a transcription factor causes differential expression of a target gene . conducting a gwas for complex traits has been a formidable challenge because the contribution of any one locus to the phenotype is expected to be small compared with the sizable effects of variants causing monogenic disorders . furthermore , the mapping experiments need to cover the entire human genome at a sufficiently high resolution for discovery . of course , the fact that the diseases are common means that large cohorts of individuals can be recruited for case - control studies , with thousands of affected and non - affected persons enrolled in a study , thus providing substantial power . recent advances such as the hapmap project ( 10 ) have enabled effective mapping of multiple loci for complex traits in humans . a driving assumption for gwass is that common diseases are likely caused by common variants ( 9 , 11 ) . because the phenotypic effect of any one variant is expected to be small , these alleles may reach sufficiently high frequencies to be considered common ( at least 5 % ) . the hapmap project determined combinations of allelic configurations of loci ( haplotypes ) that are common in several human populations . this allowed the development of high - throughput approaches to ascertain the genotype for individuals at 1 million snps across the genome , giving a good resolution for gwass ( fig . high - throughput high - resolution genotyping coupled with the large cohorts available for many complex traits enabled the completion of the first gwas in 2005 ( 12 ) , and the number of completed gwass has increased each subsequent year . the national human genome research institute maintains a catalog of published gwas results ( 13 ) , and as of mid-2011 , it contained the results of 1449 gwass for 237 traits . a critical step in interpreting the results of the gwas is moving from maps of loci associated with a trait to identifying the genetic variants that actually contribute to the trait ( 14 , 15 ) . in the case of mendelian disorders , once a locus was strongly implicated in the disease , attention was rightly focused on the protein - coding genes in the region because many of the causative variants impact the structure of the encoded protein . however , it is likely that a substantial fraction of genetic variants contributing to complex traits in humans are involved in gene regulation , just as has been observed in model organisms ( 8 , 16 ) . most phenotype - associated variants discovered in gwass are far from protein - coding regions , even appearing in gene deserts ( 13 ) , which is similar to the genomic distribution of most cis - regulatory modules ( crms ) such as promoters and enhancers . strikingly , trait - associated variants from gwass are more likely to be associated with quantitative variation in gene expression than are other variants on the genotyping arrays ( 17 , 18 ) , further supporting the expectation that many variants associated with complex traits affect gene expression . thus , what is needed is to match the high - resolution maps of phenotype - associated variants to reliable information about the locations of crms ( fig .1 , b and c ) . enhancers can be located very far from their target genes ( 19 ) , and virtually any noncoding sequence in the human genome could potentially be a crm . although both interspecies conservation and direct assays for biochemical features of chromatin associated with crms can be used to predict the locations of regulatory regions ( 15 , 20 , 21 ) , interpretation of the results from gwassthis minireview will cover recent advances in building a more comprehensive catalog of crms in humans and the use of that catalog to predict functions that are altered by phenotype - associated snps discovered through gwass . the expression levels of genes in humans ( and eukaryotes in general ) are determined by both chromatin structure and the transcription factors that are bound to the crms ( 2224 ) . the molecular mechanisms regulating gene expression are a complex interplay among enzymes and factors that catalyze hundreds of reactions , including covalent modification of histones ; alteration of nucleosomal structure and stability ; binding of transcription factors to specific dna sequences ; recruitment of coactivators , repressors , and polymerases ; and initiation , pausing , and elongation of transcription . the details of how these reactions lead to appropriate levels of expression at the right time and place are specific for each gene , and a full understanding of regulation requires intensive study of each locus . however , some features of the biochemical machinery employed in regulated expression are common to most genes and their crms ( 25 ) . the most obvious feature is the presence of transcripts in the steady - state rna . measurement of rna levels using any of a variety of methods provides a good monitor of the expression of a gene ( 2630 ) . most are in regions of the chromatin that are accessible to macromolecules , reflecting the need for the crm to interact with proteins such as transcription factors . these accessible regions can be mapped by treating nuclei with a dnase and determining the sites of cleavage . such dnase - hypersensitive sites ( dhss ) are a general feature of almost all active crms ( 31 ) . particular histone modifications can distinguish categories of crms and expression states of genes ( 24 , 32 ) . antibodies specific to individual histone modifications are used to immunoprecipitate chromatin ( histones and dna ) bearing that modification . dna isolated by chip is then assayed for the presence of segments of interest ( 33 ) . the chromatin around active promoters has high levels of trimethylation at lysine 4 of histone h3 ( h3k4me3 ) , whereas the chromatin around enhancers has high levels of monomethylation at the same position ( h3k4me1 ) ( 25 , 34 , 35 ) . acetylation of histone h3 at lysine 27 is associated with active promoters and enhancers ( 32 ) . the chromatin of transcribed regions is marked by di - and trimethylation at lysine 79 of h3 ( h3k79me2 / me3 ) in the initial portion of the transcription unit , followed by methylation at lysine 36 ( h3k36me3 ) in the distal portion ( 36 ) . other histone h3 methylations mark distinct portions of the repressed chromatin , with trimethylation at lysine 27 ( h3k27me3 ) or lysine 9 ( h3k9me3 ) covering different sets of repressed genes ( 37 , 38 ) . crms such as enhancers and promoters are clusters of binding sites for transcription factors ( 39 ) , and thus , occupancy by transcription factors is a good indicator of potential regulatory regions . using a chip approach but with antibodies against individual transcription factors , one can obtain reliable maps of transcription factor occupancy ( 4042 ) . however , because a distinct battery of factors is bound at each crm and because many transcription factors are present in a limited number of cell types , maps of binding by many transcription factors are needed to find a broad range of crms . conversely , once a region has been identified as a crm , the set of bound proteins can be used to better understand regulation and the impact of genetic variation on that regulation ( fig . transcripts , dhss , histone modifications , and transcription factor occupancy can all be considered epigenetic features ( 43 ) . they are biochemical attributes that lie on top of ( epi , on or above ) the genetic material ( dna ) , and they reflect or influence the expression of genes . the epigenetic features are dynamic : rna is made and degraded , histone modifications are added and removed , and transcription factors bind to and dissociate from dna . however , the steady - state levels of these epigenetic features are characteristic of the chromatin containing a given segment of dna in a given cell type , and that steady - state level can be inherited at least in somatic cells . this is thought to be a cellular memory for expression status ( 44 ) , and the epigenetic features can be used as a monitor of gene activity and crm location . detailed studies of the molecules and biochemical events that regulate expression of individual genes in chromatin led to the discovery of the connections between epigenetic features and regulation . dna that is highly enriched for the feature of interest can be mapped comprehensively , most commonly using second - generation sequencing methods ( 42 , 45 , 46 ) . transcriptomes can be determined by sequencing rna after fragmentation and conversion to complementary dna ; this is called rna - seq ( 30 ) . dna in chromatin with a certain modification or bound by a particular transcription factor can be determined by sequencing the dna enriched by chip ; this is called chip - seq ( 47 , 48 ) . dna in exposed regions of chromatin , i.e. dhss , can be identified by enriching for dna cut by nucleases in chromatin and sequencing from the cleaved ends ; this is called dnase - seq ( 49 , 50 ) . a few community projects are assaying a broad collection of epigenetic features across a wide spectrum of cell types in humans and model organisms . in these consortia , complementary work in multiple laboratories is coordinated to cover a substantial portion of the matrix of features and cell types . consistent data standards are established , and the data are released as soon as it is replicated . one of the major community projects is the encode project , which aims to establish an encyclopedia of dna elements ( 51 ) . the various branches of this consortium are determining transcriptomes , mapping histone modifications and transcription factor occupancy , and identifying accessible chromatin , in addition to manually curating the annotation of genes ( 42 , 46 ) . in the production phase culminating this year , all assays are being run on a set of human cell lines that represent some important human tissues , and some assays such as dnase - seq are being conducted on a wide range of cell types , including primary cells . parallel work is being done in caenorhabditis elegans ( 52 ) and drosophila melanogaster ( 53 ) as the modencode project . another community project is the nih roadmap epigenomics mapping consortium ( 54 ) , which is part of the international human epigenome consortium . the nih roadmap epigenomics mapping consortium is mapping histone modifications by chip - seq and accessible chromatin by dnase - seq in many human tissues and cell types , with an emphasis on primary cells from healthy individuals . over 250 data sets have been released to date . several studies have shown that epigenetic data such as those being generated in these community projects can be highly effective at predicting crms . dna segments in chromatin with the h3k4me1 modification are validated as enhancers in cell transfection assays at a high rate ( 55 ) , and dna segments bound by the coactivator p300 are frequently validated as enhancers in transgenic mice ( 56 ) . hence , it is reasonable to expect the epigenetic data from these consortia to be good predictors of gene regulatory function ( 46 ) . the extensive epigenetic data , although not comprehensive , are already proving to be useful for finding potential regulatory regions that could be affected by genetic variants ( fig . several recent studies have shown that snps associated with complex traits are enriched in regions implicated in gene regulation based on epigenetic features . one study used statistical modeling to integrate information about several histone modifications in multiple cell lines , generating a segmentation , or partitioning , of the human genome into classes associated with different functions ( 37 ) . the segmentation classes with properties of enhancers were significantly enriched for phenotype - associated snps . the integrative analysis of encode data ( 46 ) showed that the phenotype - associated snps in the gwas catalog are enriched in dnase - sensitive regions and in dna segments bound by transcription factors . these studies initially examined the lead snps from the gwas , i.e. the snps on the genotyping arrays that are most highly associated with the trait of interest . although these need not be the functional snps , a notable fraction of them ( 34 % ) are in dhss ( 46 ) . of course , in many cases , the functional snp is not the lead snp , but rather another variant in linkage disequilibrium ( ld ) with the lead snp is the functional one ( fig . when all snps in ld with the lead snps are included as phenotype - associated , then for a large fraction of the phenotype associations , at least one snp is found in a dna segment associated with regulatory function via the epigenetic data . for example , the lead or linked snp is found in a dhs for 7080 % of the phenotype associations reported in the gwas catalog ( 46 , 57 ) . this strong correspondence between phenotype - associated variants and function - associated dna indicates that current epigenetic data are already useful for interpretation of gwas snps . biochemical indicators of gene regulatory regions have long been used to interpret heritable phenotypes in humans , starting with mendelian traits . early examples are the use of dhss to understand the impact of large deletions in the complex of genes encoding - globins ( 5 , 58 , 59 ) and - globins ( 60 ) . dhss distal to the genes were shown to be enhancers that when deleted led to thalassemias , which are inherited anemias resulting from inadequate production of one or more globin polypeptides . a gene desert located upstream of the myc gene contains genetic variants that are associated with breast and prostate cancers ( 61 , 62 ) . the myc gene is an intriguing candidate for the target of the snps , given its role in cell cycle control , but all of the phenotype - associated variants are distal to the myc gene , and from position alone , it is not clear how they may work . however , high - resolution mapping of several epigenetic features shows that some of the phenotype - associated variants are in transcription factor - binding sites in enhancers . the binding affinity is allele - specific , and the different alleles affect chromatin looping to the presumptive target myc ( 6365 ) . thus , the genetic variants do affect regulated expression of a target gene that could help explain cancer predisposition . importantly , alignment of the encode data in this region with the significant variants from the gwas also reveals that key variants are found in the transcription factor - occupied dna segments mapped by this consortium ( 42 ) . this is true even though neither prostate nor breast tissue was used in the analysis at that time . even without complete coverage of all tissues and factors , informative insights are gleaned from examining the gwas results in the context of epigenetic features . recently , investigators employed encode epigenetic data as an initial guide to discover regulatory regions in which genetic variation is affecting a complex trait . ( 66 ) used encode data to help find likely causative variants in an enhancer in the hbs1l - myb locus , one of three loci associated with quantitative levels of fetal hemoglobin in adult red blood cells . their fine - mapping showed that the most strongly associated variants are clustered in the intergenic region ( fig .2 a ) , and a scan of encode data showed that the variants are in dna segments with epigenetic features expected for enhancers ( fig .2 , b and c ) . guided by the initial encode data , the authors focused further analysis in patients and controls and showed that the variants affect a transcriptional enhancer ( 66 ) . other recent examples of the use of encode or other epigenetic data as guides for functional studies of trait - associated variants are studies of the tcf7l2 intronic enhancer strongly associated with type 2 diabetes ( 67 ) , the gene desert at chromosome 9p21 associated with coronary artery disease ( 68 ) , and a locus associated with susceptibility to colorectal cancer ( 69 ) . gwas variants associated with high levels of fetal hemoglobin in adults found in an enhancer marked by epigenetic features . a , fine mapping of genetic variants between the genes hbs1l and myb on human chromosome 6 ( chr6 ) , with the position of snps along the x axis ( assembly grch37 / hg19 ) and the logarithm ( base 10 ) of the 1 / p value for the association with the trait on the y axis . b , current view of genomic data for the same 148 - kb interval as in a , showing from top to bottom the position of the 3 - bp deletion implicated in the trait ( hmipdel ) ; genetic variants from the gwas catalog ( vertical green lines ) ; gene annotation ; and signal tracks for dhss in k562 cells , gata1 occupancy in peripheral blood - derived erythroblasts , tal1 occupancy in k562 cells , and gata2 occupancy in k562 cells . the signal tracks are from the encode consortium ( 42 , 46 , 78 ) . c , view focused on a 3 - kb region containing the 3 - bp deletion implicated in the trait and an enhancer bound by gata factors and tal1 . some links between specific epigenetic features and trait - associated variants are found at multiple loci affecting a complex trait , suggesting that common regulatory mechanisms could be operating at multiple loci . each phenotype in the gwas catalog can be associated with multiple loci , and in several cases , the loci affecting a given trait are associated more frequently than expected with a particular feature such as occupancy by a particular transcription factor or appearance of a dhs in a given cell line ( 46 , 57 ) . for example , variants associated with crohn disease are over - represented in dna segments bound by gata2 ( in human umbilical vein endothelial cells ( huvecs ) ) and are sensitive to dnase in t - helper cells .3 ) . high - resolution mapping reveals a cluster of variants in ld that are strongly associated with crohn disease ( fig . are variants that affect the level of expression of ptger4 , a gene located 300 kb away that encodes the ep4 prostaglandin receptor ( 70 ) . examination of selected encode tracks within this region shows that the trait - associated variants are in or close to dhss that are binding sites for a gata transcription factor ( fig . the data from the t - helper cells are likely to be more relevant to autoimmunity than those from huvecs , and one could hypothesize that the genetic variation could be affecting affinity for gata3 , a related protein that regulates gene expression in t - cells ( 71 ) . this is an example of a readily testable hypothesis grounded in the examination of the gwas and encode data ( fig . gwas variants associated with crohn disease and other autoimmune diseases found in potential regulatory regions marked by epigenetic features . a , fine mapping of genetic variants in a 2 - mb interval on human chromosome 5 ( chr5 ) . b , current view of genomic data for the same interval as in a , showing from top to bottom genetic variants from the gwas catalog , followed by signal tracks for gata2 occupancy in huvecs and dhss in huvecs and t - helper 1 ( th1 ) and t - helper 2 ( ths ) cells , with gene annotation at the bottom . c , view focused on a 50 - kb region containing a cluster of variants associated with autoimmune diseases . the different disease associations are marked by the color of the circle at the top of the vertical green lines . the data from community projects such as encode and nih roadmap epigenomics mapping consortium may not cover the tissues , developmental stages , or transcription factors of greatest relevance to a particular phenotype . however , in many cases , they provide initial insights that help guide more definitive experiments . these may be cases in which a regulatory region is active in multiple cell types or is bound by several different transcription factors . application of genomic technologies continues to stimulate discovery in biochemistry and molecular biology as the networks of regulatory interactions begin to be understood not only in model organisms ( 72 ) but also in humans . the results from gwass reveal genomic locations in which genetic variation impacts susceptibility to the most common diseases of humans . it is now clear that many of these loci are involved in gene regulation , and the deep knowledge of the biochemistry of gene regulation can be coupled with high - throughput genomic assays to help identify candidate regulatory regions in the loci identified by gwass . no longer will finding a key genetic variant in a gene desert mean the end of a search for a molecular connection between genotype and phenotype . this minireview has emphasized the use of epigenetic features mapped by encode and other projects for interpreting gwas results . this approach has considerable power now , and plans are in place to increase substantially the coverage of cell types , transcription factors , and other epigenetic features ( described at www.genome.gov/10005107 ) . the large scale of these community projects and their commitment to rapid data release will ensure that data sets of closer relevance to a wider range of phenotypes will become available . assays with higher resolution for mapping regulatory elements will also be used more widely ( 7375 ) . of course , the genome - wide mapping of epigenetic features originated in individual laboratories , and they will continue to provide important data sets and insights for regulation . indeed , it is likely that individual or small groups of laboratories will explore epigenetic features in the cell types most closely related to the phenotypes of interest . the capacity of second - generation sequencing machines is increasing , which means that many more laboratories will be generating and analyzing genome - wide epigenetic data . this diversity of investigator - initiated projects should complement the community projects and likely fill gaps in coverage that are most relevant to the phenotypes of interest . several challenges must be met to effectively harvest the insights from the plethora of genome - scale genetic and epigenetic results . initial efforts using statistical modeling ( 76 , 77 ) are being applied to some of the data from the community projects . opportunities abound for novel approaches that have the capacity for even larger numbers of data sets and that provide more accurate predictions . strong collaborations among teams of these investigators should lead to insights into connections between multiple genotypes and complex phenotypes of even greater importance to medicine .\noutput:\n" }, { "from": "agent", "value": "complex traits such as susceptibility to diseases are determined in part by variants at multiple genetic loci . genome - wide association studies can identify these loci , but most phenotype - associated variants lie distal to protein - coding regions and are likely involved in regulating gene expression . understanding how these genetic variants affect complex traits depends on the ability to predict and test the function of the genomic elements harboring them . community efforts such as the encode project provide a wealth of data about epigenetic features associated with gene regulation . these data enable the prediction of testable functions for many phenotype - associated variants ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the international cancer genome consortium ( icgc ) is a multidisciplinary , multi - institutional collaborative effort aiming to systematically and comprehensively characterize somatic mutations in 50 different cancer types and subtypes ( 1 ) . five hundred tumor genomes , as well as matched normal control genomes for each cancer type , will be analyzed using high - throughput next - generation sequencing technologies to detect a wide range of somatic mutations , including single nucleotide mutations , small insertions / deletions , copy number alterations , translocations and other chromosomal structural rearrangements . genome - wide methylation state analysis and whole - transcriptome sequencing have also been planned to provide additional molecular - level characterizations . to make the effort more scalable each member institution specializes in generating data for a particular tumor type . at the time of writing , figure 1 . international cancer genome consortium ( icgc ) projects ( march 2011 ) . international cancer genome consortium ( icgc ) projects ( march 2011 ) . one of the major goals of icgc is to rapidly bring these data to the cancer research community in order to accelerate studies on the discovery of cancer causes , to enhance the accuracy of diagnoses and to improve treatments . in order to achieve this task , the data generated by the consortium members have to be managed efficiently . amongst the most important data management challenges faced by the consortium is the high complexity and heterogeneity of the data types involved , the necessity to link different data types , and the need to protect controlled data . furthermore , the high volume of data and the distributed nature of the sources make traditional centralized approaches to data management impractical . consequently , the icgc has adopted federated data architecture to address their data management needs . the scalability of the system is improved by having each member institution store and process data locally ; the data federation software then presents these separate sources as a single access point for remote data access . biomart , an open source data federation system ( 2 ) , has been chosen as the icgc data management platform . biomart s flexible data model makes it generally applicable to a wide range of biological data types and built - in query optimizations make it suitable for large data sets . in addition , biomart supports an industry - standard security framework that is needed to provide secure access to the controlled data . finally , a large number of existing expert - maintained public annotation databases can be readily federated , adding value to the interpretation of the icgc experimental data . the architecture of the icgc data management system has been modeled on the biomart central portal ( 3 , 4 ) . for a number of years , the portal has been successfully providing a single point of access to a large number of biological databases distributed across the world . each biomart database federated in this portal is maintained independently , released and updated on its own schedule . similarly , each icgc member maintains their local biomart database where clinical annotations and the data produced from genomic analyses are deposited . however , in order to make these data comparable across different cancer projects and create a unified icgc data set , a mechanism for enforcing uniformity is required . thus , the same set of data models , controlled vocabularies , ontologies and reference data sets are used in all of the icgc member databases . furthermore , a gene - centric data model adopted from ensembl mart ( 5 ) is used to reference experimental data to the same set of annotated genes . in order to link individual biomart databases into a unified system , these servers can each access data in three ways : they can access their own local databases directly ; they can communicate with the other icgc biomart servers , in order to retrieve data from remote databases ; and they can communicate with non - icgc biomart servers , such as cosmic ( 6 ) and reactome ( 7 ) , to retrieve publicly - available annotation data . in this manner , the biomart server maintained by each icgc member acts as a fully featured icgc data portal , providing unified access to all the consortium data . the users select a combination of different data sets and specify query criteria using a variety of graphical user interfaces and analysis tools that are available from the portal . application programming interfaces ( apis ) for java , rest , soap and sparql are also available for programmatic access . behind the scenes , biomart software breaks down this query into smaller parts that are distributed to the remote data sources . the results are collected and compiled into a single unified results set that is presented to the user . some of the data in the portal has access restrictions in order to preserve patient privacy . to protect this sensitive data , communication between biomart serverswhen a user logs into an icgc data portal server using his / her openid , the server will consult the central registry to ensure that the user is authorized to access the data ( figure 2 ) . at present the portal contains data from 24 cancer projects , consisting of 3478 genomes and 13 cancer types and subtypes . this includes the data generated from seven studies performed by five icgc participating institutions located in four countries . the data portal also hosts data from other large - scale cancer genome projects including the cancer genome atlas ( tcga ) ( 8 , 9 ) , tumor sequencing project ( tsp ) ( 10 ) and johns hopkins university ( 1114 ) . open access data sets include ( i ) simple somatic mutations , ( ii ) copy number alterations , ( iii ) structural rearrangements , ( iv ) gene expression , ( v ) mirna , ( vi ) dna methylation and ( vii ) exon junctions . secure access to controlled data sets , such as germline variations , is available to authorized users . a summary of data currently available on the data portal is shown in table 1 . in addition to cancer genomic data , the data portal also federates several public databases ( table 2 ) . currently this includes ensembl genome database ( 5 ) , kyoto encyclopedia of genes and genomes ( kegg ) ( 1517 ) , reactome ( 7 ) , cosmic ( 6 ) , pancreatic expression database ( 18 ) and the breast cancer campaign tissue bank ( 19 ) , and the number of resources is continuously growing . table 1 . the summary of data available on the icgc data portal divided by cancer projectsourcecancer projectdata setsimple mutationscopy number alterationsstructural rearrangementsgene expressionmirna expressionexon junctionsdna methylationgermline variationsicgcbreast carcinoma ( wtsi , uk ) liver cancer ( ncc , jp ) liver cancer ( riken , jp ) malignant melanoma ( wtsi , uk ) pancreatic cancer ( oicr , ca ) pancreatic cancer ( qcmg , au ) small cell lung carcinoma ( wtsi , uk ) tcgaacute myeloid leukemiabreast invasive carcinomacolon adenocarcinomaglioblastomamultiformekidney renal clear cell carcinomakidney renal papillary cell carcinomalung adenocarcinomalung squamous cell carcinomaovarian serous cystadenocarcinomarectum adenocarcinomastomach adenocarcinomauterine corpus endometrioid carcinomaotherbreast cancer ( jhu , us ) colorectal cancer ( jhu , us ) glioblastomamultiforme ( jhu , us ) lung adenocarcinoma ( tsp , us ) pancreatic cancer ( jhu , us ) table 2 . public databases federated with the icgc data portalsourceurldescription of contentsensemblwww.ensembl.orggenome annotationreactomewww.reactome.orgpathway annotationkeggwww.genome.jp / keggpathway annotationcosmicwww.sanger.ac.uk / genetics / cgp / cosmic / somatic mutations in cancerpancreatic expression databasewww.pancreasexpression.orgpancreatic cancer expression databreast cancer campaign tissue bankwww.breastcancertissuebank.org/bio-informatics.phpbreast cancer expression data the summary of data available on the icgc data portal divided by cancer project public databases federated with the icgc data portalthe data portal provides three major interactive entry points : identifier search , analysis and database search ( figure 3 ) . identifier search ( figure 3a ) lets users input identifiers that are commonly used in public annotation databases ( e.g. hgnc gene symbol , ensembl i d , refseq i d , uniprot i d and other accessions ) and returns links to the corresponding gene report page , which displays basic gene description , pathway annotation , mutations found in the cosmic database , as well as pancreas and breast cancer expression data ( figure 4 ) . in addition , the gene report displays a summary of mutation frequencies in the selected gene across all cancer projects ( figure 4d ) . records in the gene report ( i.e. genomic coordinates , pathway name , publication ) are linked to appropriate resources when available , allowing users to easily retrieve additional information on their data of interest . three main entry points are available : ( a ) identifier search , ( b ) analysis and ( c ) database search . figure 4 . gene report for kras includes : ( a ) gene annotation data from ensembl , pathway annotation from ( b ) kegg and ( c ) reactome , ( d ) summary of mutation frequencies in each cancer project , ( e ) mutation data from cosmic , expression data from ( f ) pancreatic expression database and ( g ) breast cancer campaign tissue bank ( bcctb ) . different sections of this page come from federated biomart sources . three main entry points are available : ( a ) identifier search , ( b ) analysis and ( c ) database search . gene report for kras includes : ( a ) gene annotation data from ensembl , pathway annotation from ( b ) kegg and ( c ) reactome , ( d ) summary of mutation frequencies in each cancer project , ( e ) mutation data from cosmic , expression data from ( f ) pancreatic expression database and ( g ) breast cancer campaign tissue bank ( bcctb ) . different sections of this page come from federated biomart sources . to help with the interpretation of cancer data , gene and pathway analysis tools are available in the analysis section of the data portal ( figure 3b ) . these tools enable users to view the most commonly affected genes or pathways in one or more cancer projects . results are presented in an easy - to - follow chart that can be exported as an image file , and the numerical data can also be downloaded for further processing ( figure 5 ) . ( a ) affected pathways are shown in a chart , with bars representing the number of affected genes in each pathway . ( b ) by clicking on the bar , users are able to view and download the genes that were mutated in each pathway . ( a ) affected pathways are shown in a chart , with bars representing the number of affected genes in each pathway . ( b ) by clicking on the bar , users are able to view and download the genes that were mutated in each pathway . using the database search entry point ( figure 3c ) users can interactively query the database by several data types : genes , samples , simple mutations , copy number alterations , structural rearrangements , gene expression , mirna , dna methylation and exon junctions . the quick interface contains a pre - selected set of the most commonly used filters such as gene type , mutation type and chromosome , and outputs a fixed set of attributes . the flexible interface contains additional filters and a selection of attributes , allowing the user to choose which data are displayed in the output . the advanced interface contains the complete set of filters and attributes , including technological platforms used for sequencing , and clinical parameters such as patient gender and tumor histopathology . to demonstrate the utility of the icgc data portal we present several queries that can be performed using different query interfaces . search for genes affected by copy number loss and also detected as deletion from structural rearrangement analysis . ( figure 6 ) data setscancer projectsfiltersattributesgenespancreatic cancer ( qcmg , au ) rearrangement type : deletionensembl gene idcopy number alteration type : lossgene symbolgene description figure 6 . a screenshot of the quickquery interface . query # 2 ( flexible search ) : retrieve clinical staging data for colorectal cancer patients with non - synonymous simple mutations in genes that are involved in wnt signaling pathway . ( figure 7 ) data setscancer projectsfiltersattributesgenescolorectal cancer ( jhu , us ) pathway : signaling by wnttumor sample idconsequence type : non_synonymous _ codingmutation idmutation typedonor iddiagnosis idclinical staging ( who ) ensembl gene idgene symbol figure 7 . a screenshot of the flexiblequery interface . a screenshot of the flexiblequery interface . query # 3 ( advanced search ) : in pancreatic cancer data set , retrieve all rna - seq expression data for genes that are affected by copy number gains . ( figure 8 ) data setscancer projectsfiltersattributesgenespancreatic cancer ( qcmg , au ) copy number alteration type : gainensembl gene idplatform : solid sequencinggene expression : sample idnormalized read countraw read count figure 8 . a screenshot of the advancedquery interface . the icgc data portal is the first project to successfully federate large amounts of cancer genomics data and rich annotation data in a single access point . it presents a scalable approach , not only in the traditional sense of parallelizing data processing and storage , but also in a more general sense of outsourcing the external annotation expertise , by federating annotations from independently maintained databases . this approach has proved to be successful in addressing icgc data management needs and can be useful for similar , large - scale collaborative projects . the icgc data portal will continue to expand by adding more data , both from within the project in the form of new cancer genomics data from icgc members , and by integrating other public annotation databases to further the depth of analysis possible through the data portal . additionally , new tools will be developed to increase the flexibility and utility of the system . this includes tools for icgc deployers , to further streamline the data processing , transformation and loading processes , and tools for users , to add new methods of data visualization and analysis to the portal .\noutput:\n" }, { "from": "agent", "value": "the international cancer genome consortium ( icgc ) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types . to make this data available , the icgc has created the icgc data portal . powered by the biomart software , the data portal allows each icgc member institution to manage and maintain its own databases locally , while seamlessly presenting all the data in a single access point for users . the data portal currently contains data from 24 cancer projects , including icgc , the cancer genome atlas ( tcga ) , johns hopkins university , and the tumor sequencing project . it consists of 3478 genomes and 13 cancer types and subtypes . available open access data types include simple somatic mutations , copy number alterations , structural rearrangements , gene expression , micrornas , dna methylation and exon junctions . additionally , simple germline variations are available as controlled access data . the data portal uses a web - based graphical user interface ( gui ) to offer researchers multiple ways to quickly and easily search and analyze the available data . the web interface can assist in constructing complicated queries across multiple data sets . several application programming interfaces are also available for programmatic access . here we describe the organization , functionality , and capabilities of the icgc data portal.database url : http://dcc.icgc.org" } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the national library of medicine 's ( nlm ) medline / pubmed biomedical literature database ( ) is rapidly expanding and as of the 2006 edition , the baseline database contains more than 15 million citations . a number of papers have introduced tools to perform searches more advanced than those available with the current entrez - pubmed user interface to mine the abstracts ( 14 ) . to have more control in conducting searches , investigators have also started to reorganize the medline data into structured relational systems ( 5 ) or to exploit different data formats and create new databases ( ) . these nlm citations are available in several formats ( e.g. medline , asn .1 , and so on ) . importing these citation data into a traditional , relational database limits the query capability to sql ( structured query language ) techniques . the extensible markup language ( xml ) format , however , is emerging as a de facto standard for the hierarchical organization of data in a highly granular structure , and provides a much richer query capability beyond what is available through traditional sql . oracle xml db , available in oracle 9i and 10 g , recognizes this new format . it supports both the necessary massive storage requirements and the extensions to traditional sql that enable a different kind of query which is hierarchical and highly granular . an early study using oracle xml db involved the evaluation of data - form standards and database technologies for medical informatics systems ( 6 ) ( ) . as described by wang et al . ( 6 ) , the set of utilities associated with xml db permits data to be represented both as xml elements from xml documents and as cells within relational tables . a recently developed website that includes a specialized , oracle - based resource for the clostridial neurotoxins , botdb ( 7 ) ( ) , has been extended to conduct literature searches of medline / pubmed using botxminer . the application of xml db for botxminer was based , in large measure , on the documentation and thorough analysis of an original implementation using xml - formatted medline citations ( ) . an advantage offered by botxminer over pubmed is that it can make certain queries possible that can not be performed using the entrez - pubmed interface . the practical example herein illustrates how citations , containing user - supplied search terms , selected medline search fields and terms , are grouped and displayed as hyperlinked tabulated or graphic results . a more detailed technical description of the architecture associated with botxminer andof the more than 15 million medline xml records created through the 2005 production year that were loaded into oracle xml db , a limited reference subset was generated for botxminer using the search wordstetanus . this subset has 26563 citations , a value that represents 1 % of the total number that are available . the search option ( data not shown ) allows the user to query the standard fields of a medline output [ author , terms in the title or abstract , pubmed identification number ( pmid ) and so on ] by entering desired words or terms in the appropriate boxes and by selecting an optional range of publication years . initially , the user - provided search words or terms are searched for within each medline xml file . these results are then grouped by botxminer with terms contained in a select list of medline fields : the medical subject headings ( mesh ) qualifier or descriptor names , author , chemical , keyword and gene symbol . advanced search feature is also available that allows the user to search the common medline fields of journal title , mesh and chemical in addition to the title and abstract . the option to specify a range of publication years is also applicable to the group articles and theadvanced search . queries may contain common logical operators for literature searches that are supported by oracle text : and ( & ) , not ( ) , or ( ) and accum ( , ) ( meaning either term is acceptable but both are preferred ) . other operators use context grammar : near ( ;) for proximity searches , and minus ( ) for a lower preference . output graphics can presently be viewed in png , html or svg formats and have so far been tested using microsoft internet explorer ( ie ) v. 6 , netscape v. 8 and the mozilla firefox v. 1 browsers . the html format offers the advantage of being able to hyperlink the graphic points ( rectangles and circles ) to the citation summary information . label information is presented as a pop - up label when moving the mouse over the rectangles and circles . for the svg option , an interactive graphic view of the results is dynamically produced using the aisee graphics package ( ) . the svg format also has interactive hyperlinks while its associated plug - in ( available for ie and netscape ) provides the user with a drop - down feature menu to zoom in and zoom out , pan across the image , save the image , and other graph features . in the svg format under ie , positioning the mouse over the rectangles and circles produces the label information within the window status bar . at present , the firefox browser does support the svg format by using the aisee software but does not support the drop - down feature menu . for these reasons , it is recommended that , at this time , the botxminer graphics be viewed in the svg format using either the ie or the netscape browsers . as a practical example , a search was conducted to find potential interactions between the snare proteins ( three of which are substrates for the proteolytic botulinum neurotoxins ) and other proteins . the substrates of interest [ syntaxin - 1a , synaptobrevin ( vamp ) and snap - 25 ] are intimately involved in the evoked release of neurotransmitter from synaptic vesicles . protein interactions may , thus , help to predict what other cellular functions might be affected in addition to the toxin - induced blockade of neurotransmission . group articles advanced search was used with the query : near ( ( snare , interact % ) , 5 ) ( figure 1 , back panel ) . snare and interact % ( or interacts , interacting , etc . ) that are separated by no more than five words . this query resulted in a tabulated listing of 83 group ( chemical ) terms that appeared in 18 medline xml files ( figure 1 , middle panel ) .18 produces a list of all the retrieved citations ( figure 1 , front panel ) . values for the number of articles for a given term are hyperlinked to a second table that lists citations associated with the selected term ( data not shown ) . the pmid numbers are hyperlinked to their corresponding medline pages , which are presented in a modified format , while article titles in this table are hyperlinked to their pubmed abstracts ( data not shown ) . another way to visualize these data is in a network graph format ( figure 2 , upper panel ) with a method analogous to that used in chilibot ( 2 ) and pubnet ( 3 ) . before a graph , there are 83 group terms ( chemical names ) and 859 connections ( circles ) between these terms . all pairs of chemical terms are connected by color - coded lines and circles that show the relative number of articles for two co - occurring chemical terms . each rectangle is hyperlinked to a list of citations containing the group ( chemical ) term , whereas each circle is hyperlinked to a list of citations that contain the pair of terms associated with that connection ( data not shown ) . these graphical views also allow the user to quickly focus on and recognize patterns for the most frequent co - occurring terms . in this example , the cluster of terms near the top of the graph is examined more closely with thezoom in option ( accessed through the drop - down menu with the right - hand mouse button ) that is used with svg ( figure 2 , lower panel ) . in this panel , the pairs are only associated with a single paper ( gray lines and circles ) . protein interactions between the snares and other proteins including calmodulin , neurotransporters and other synaptic proteins were readily identified using this approach . one goal in the development of botxminer was to mine the maximum amount of information from the medline xml files without doing any natural language processing . this development began with l. c. wang 's original documentation ( ) that described how the whole collection of medline data can be stored inside oracle xml db in object - relational tables . since entire medline xml files are stored in this database , the structure of these files is maintained , in contrast to writing new code to parse the data and to subsequently store them into relational tables . the schema - based , structured type data storage strategy is made more efficient in botxminer with oracle 's text indexing capability which makes proximity searches with operators such as near , a context grammar operator , and wildcard searches feasible . the group articles feature of botxminer allows the user to look at a single , tabulated list of relevant grouped terms and to quickly retrieve citations of interest . finally , botxminer has the first user interface for medline xml files that are stored in oracle xml db . in comparison to other publicly available pubmed search applications , the differences exhibited by botxminer provide an opportunity for its descendants to enhance searches of the continually growing biomedical literature . in the tools described by oliver et al . ( 5 ) , medline xml files that have been downloaded are subsequently parsed and stored in schema - defined relational tables . devising appropriate schema to optimallyin contrast , pubfinder ( 4 ) stores abstracts in its database and creates a reference dictionary of commonly used words . the user needs to provide pmids of abstracts of interest which are processed for word frequencies and compared to the reference dictionary . applications , such as chilibot ( 1 ) , pubgene ( 8 ) and medminer ( 9 ) , require , as a minimal user - supplied input , a recognized gene name to conduct its pubmed search . textpresso ( 10 ) , as part of its knowledge retrieval strategy , uses a text - to - xml converter to systematically mark up sentences by its specialized ontology ( that is presently based on caenorhabditis elegans ) from full - length , searchable articles . the example query provided here illustrates the power of botxminer to help the user to efficiently and selectively search for co - occurrences of grouped terms from medline xml files and to focus on the general problem of protein protein interactions . since we have created a database from the entire set of medline xml files , it is anticipated that a variety of other , specialized citation subsets ( e.g. cytoskeletal proteins , signal transduction pathways and diseases such as cancer ) will be developed that are similar in design to botxminer . it is further anticipated that botxminer will serve as a template for future applications that will mine the entire medline and other very large sources of biomedical information . literature search conducted in botdb using botxminer and the group articles ( advanced search option ) . the end - user types in a desired word or term ( words separated by logical or other operators ) and selects one or more of the medline search fields and one of the six presently available terms . middle panel : tabulated results are shown for the query near ( ( snare , interact % ) , 5 ) , thethe resulting list of chemical terms are tallied in the form of an alphabetically sorted table that can be expanded by clicking on a number .18 associated with the total number of articles ( middle panel ) is hyperlinked to these citations . graphical view link ( figure 1 , middle panel ) produces a dynamic network graph ( upper panel ) that shows the interconnectedness of the chemical terms which , in turn , are linked to references ( color - coded lines ) with the number of co - occurrences labeled in the small circles . this graph displays all the terms from the table ( figure 1 , middle panel ) that are connected by the number of articles in which they co - occur . the lines and circles are color coded depending on the number of articles : gray , the terms co - occur in 1 article ; yellow , co - occurrence in 25 articles ; pink , co - occurrence in 610 articles ; green , co - occurrence in 10 articles .\noutput:\n" }, { "from": "agent", "value": "this paper outlines botxminer , a publicly available application to search xml - formatted medline data in a complete , object - relational schema implemented in oracle xml db . an advantage offered by botxminer is that it can generate quantitative results with certain queries that are not feasible through the entrez - pubmed interface . after retrieving citations associated with user - supplied search terms , medline fields ( title , abstract , journal , mesh and chemical ) and terms ( mesh qualifiers and descriptors , keywords , author , gene symbol and chemical ) , these citations are grouped and displayed as tabulated or graphic results . this work represents an extension of previous research for integrating these citations with relational systems . botxminer has a user - friendly , intuitive interface that can be freely accessed at ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: epidural hematomas ( edh ) comprise 2 % of total traumatic brain injury ( tbi ) but its mortality rate is as high as 33 % .18 ) this particular neurosurgical emergency has been known for a long time . its heterogeneous responses to the treatment in the different subgroups of populations require further international attention and investigation .1115 ) korea has recently attempted to collect a large cohort of data relating to multiple aspects of tbi for the past few years . fatality of edh has also partly urged the actions to emphasize the importance of epidemiological monitoring for prevention , revisiting the safety laws , and the upgrading trauma centers to ultimately improve the facilities and systems for better functional outcomes . the evolving nature of edh is especially observed dynamically at the acute settings of different types of trauma ; hence , the authors thought that this specific disease deserves a spot light for national investigation . to our knowledge , though it is preliminary , this is the first report to attempt in evaluating the multi - center data registered in the korean trauma data bank system ( ktdbs ) to unravel the patterns of clinical course of edh in korea and to identify the significant parameters in determining the outcomes of edh . the aim of this project was to conduct an epidemiologic research on the epidemiology of tbi in korea . the data sheet of the ktdbs was composed of 392 items , containing information regarding the characteristics and etiology of the injury , diagnosis , treatment , and complications with respect to the outcome of patients . two thousand six hundred ninety - eight patients were added to the database over its duration of the project . of 2,698 cases of tbi patients , 377 case of edh were retrieved from the database . thus , the final cases of 285 patients with edh were evaluated for this study . the following clinical parameters were compared with respect to the final outcome : age , gender , presence of skull fracture , treatment plan , degree of brain injury , time interval from trauma to hospital , types of injury mechanisms , time interval from trauma to initial computed tomography ( ct ) , treatment plan after the initial ct , time interval from initial ct to follow - up ct , the reasons for follow - up ct , use of mannitol , prophylactic use of prophylactic anticonvulsant , time taken to decide a surgical treatment , and types of surgery . the difference of glasgow coma scale ( gcs ) between the gcs upon arrival of the hospital and the lowest gcs during the hospital stay were also analyzed . outcome of 6 months following injury by the glasgow outcome scale ( gos ) in which ' good outcome ' was defined as a good recovery or a moderate disability , and ' poor outcome ' was severe disability , vegetative state , or death .7 ) data are expressed according to the properties of the variable . , we performed the two - sample t - test or chi - square test ( fisher 's exact test ) as appropriate . logistic regression analysis was used to identify the factors to predict the poor outcome and the result were expressed as odds ratio ( or ) with 95 % confidence interval ( ci ) . a p - value less than 0.05 was considered statistically significant and all statistical analyses were conducted using sas 9.4 version ( sas inc . , cary , nc , usa ) . the aim of this project was to conduct an epidemiologic research on the epidemiology of tbi in korea . the data sheet of the ktdbs was composed of 392 items , containing information regarding the characteristics and etiology of the injury , diagnosis , treatment , and complications with respect to the outcome of patients . two thousand six hundred ninety - eight patients were added to the database over its duration of the project . of 2,698 cases of tbi patients , 377 case of edh were retrieved from the database . thus , the final cases of 285 patients with edh were evaluated for this study . the following clinical parameters were compared with respect to the final outcome : age , gender , presence of skull fracture , treatment plan , degree of brain injury , time interval from trauma to hospital , types of injury mechanisms , time interval from trauma to initial computed tomography ( ct ) , treatment plan after the initial ct , time interval from initial ct to follow - up ct , the reasons for follow - up ct , use of mannitol , prophylactic use of prophylactic anticonvulsant , time taken to decide a surgical treatment , and types of surgery . the difference of glasgow coma scale ( gcs ) between the gcs upon arrival of the hospital and the lowest gcs during the hospital stay were also analyzed . outcome of 6 months following injury by the glasgow outcome scale ( gos ) in which ' good outcome ' was defined as a good recovery or a moderate disability , and ' poor outcome ' was severe disability , vegetative state , or death .7 ) , we performed the two - sample t - test or chi - square test ( fisher 's exact test ) as appropriate . logistic regression analysis was used to identify the factors to predict the poor outcome and the result were expressed as odds ratio ( or ) with 95 % confidence interval ( ci ) . a p - value less than 0.05 was considered statistically significant and all statistical analyses were conducted using sas 9.4 version ( sas inc . , cary , nc , usa ) . in order to identify the clinical factors associated with poor outcome , the study population was divided into two subgroups of good and poor outcome . the parameters of clinical characteristics were compared between these two groups . according to the demographic statistics of the patients , older age ( p = 0.0003 ) , more severe the degree of brain injury ( p 0.0001 ) , cases of surgical edh with craniectomy ( p 0.0001 ) , shorter time interval from trauma to hospital before 6 hours , shorter time interval from trauma to initial ct ( p = 0.0078 ) and the decreasing pattern of gcs between and initial and final gcs ( p = 0.0374 ) were strong predicting factors of poor outcome ( table 1 ) . the injury mechanism of falls was more common in the patients with good outcome ( 121/232 , 52.16 % ) , however , it was not statistically significant ( p = 0.0537 ) . use of mannitol for controlling increased intracranial pressure ( icp ) upon the arrival at emergency department was higher in the patients with poor outcome ( 10/14 , 71.43 % ) . on the other hand , those with good outcome received no treatment of mannitol for edh ( 29/60 , 48.33 % ) . again , the use mannitol was neither statistically significant ( p = 0.0504 ) . according to the 1:1 univariate analysis , cases of surgical edh showed the odd of poor outcome 9.51 times higher than those of non - surgical edh . compared to the patients with mild brain injury , those with moderate brain injury showed the odds of poor outcome 7.04 times higher than those with mild brain injury while those with severe brain injury showed the odds 39.6 times higher than those with mild brain injury . shorter time interval from trauma to hospital before 6 hours showed the odds of poor outcome 8.41 times higher compared to that after 6 hours . finally , the odds of poor outcome are shown 1.46 times higher when the patients ' final gcs is lower than the initial gcs . clinical parameters associated with the poor outcome on the univariate analysis were entered into the multivariate model for further evaluation . the degree of brain injury ( or of 9.36 in moderate injury ; 95 % ci , 1.68 - 52.23 ; and or of 55.56 in severe injury ; 95 % ci , 7.49 - 412.35 , respectively ; p = 0.0004 ) and the gcs differences between the initial and final gcs ( or of 1.39 ; 95 % ci , 1.06 - 1.81 ; p = 0.0180 ) showed a statistically significant result as strong determining factors related to poor outcome ( table 2 ) . of note , prophylactic use of anticonvulsant did not affect the functional outcome ( table 3 ) . there was an interesting difference in the use of mannitol in treating edh between the urban and rural regions [ 22/27 ( 81.48 % ) and 15/47 ( 31.91 % ) , respectively ; p 0.0001 ] ( table 4 ) . there was 63.83 % ( 30/47 ) of patients who received no mannitol treatment in the rural hospitals . edh is a complex entity of trauma in which the neurologic damage evolves after the impact .21828 ) different mechanisms of injury with edh are usually involved to create a diverse traumatic environment . in addition , different types of brain injuries result in multiple subdivisions of inconstant consequences .5 ) as the population ages with longer life expectancy , trends of injury have also been changing with more injuries in the geriatric population .61524 ) as well as we have already witnessed in the analysis of our database , age is a major determinant of functional outcome .1524 ) for example , an injury mechanism of falls from heights is one of the leading causes of tbi in the elderly older than 65 years with a high risk of death .22 ) even ground - level falls are risks to the elderly when it is generally and easily known to be a low risk in the younger population .19 ) our data on edh from ktdbs showed that falls are associated with good outcome of edh ( though it was not statistically significant ) . nevertheless , this alarms us to collect more systematized data to confirm the difference , if there is any , in the domestic and international epidemiology of edh . the results may even different in the types of brain injury other than edh as well . it is imperative to be aware of the new injury types in the geriatric population . as far as the degree of brain injury is concerned , one will immediately think of the pathological mechanism of early events of tbi , which is still much less understood though there is a great effort of basic research undertaken internationally to uncurtain the injury mechanisms at the cellular levels .827 ) however , macroscopically , the severity , duration of impact , duration without treatment , and nature of injuries determine the degree of brain injury . degree of brain injury is often characterized by severe brain swelling , combination with traumatic subarachnoid hemorrhage , cerebral vasospasm , and delayed cerebral infarction after trauma .1826 ) edh with additional intracranial injuries would act together in a simultaneous manner implicating to worsen the patients ' condition . the accumulative damage will add on to escalate the extent of brain injury , which will eventually affect the functional outcome as we have already demonstrated in the analysis of our data . in the end , patients with severe gcs and the management of icp determines the final outcome in patients with edh as the response of recovery is dependent on the treatment effects during the clinical course and possibly on the patients ' predisposing co - morbidity .5 ) one must also bear in mind that there are also extrinsic factors which can potentially threaten the patients outside the hospital . namely , the secondary injury by such as hypoxia or hypotension occurred , before the patient entered the emergency department due to lack of professional pre - hospital management , will be as critical as the impact of irreversible primary damage of neuronal pathways of consciousness at the first place .10 ) a clinical deterioration of a patient with edh is related with the size of edh and its time - dependent enlargement . there was an analytical study reported that a ct scan performed less than 6 hours after the onset of trauma had an increased risk of hematoma enlargement .25 ) our analysis of edh data from ktdbs also confirms that the time interval from trauma to the initial ct scan before 6 hours is associated with a poor functional outcome . it is also reported that a series of ct scans in non - operative edh patients should be obtained within 6 to 8 hours after the initial injury for better outcomes with prompt decision of treatment .20 ) moreover , ding et al. 3 ) reported that the non - surgical patients with routine repeat ct scans have a better outcome than those with non - routine repeat ct . however , the same authors also mentioned that routine follow - up ct scans 48 hours after trauma may not also be required .316 ) according to the guidelines of the brain trauma foundation ( btf ) , the volume of edh and the initial gcs are determinants of surgical indication of edh . not all patients benefit from the operation of edh .21218 ) our data showed that the poor outcomes are more associated with the cases of surgical edh . furthermore , the cases of decompressive craniectomy with hematoma evacuation of edh are also associated with a poor outcome ( p 0.0001 ) . it is rather ironic that the act of surgery is not guaranteeing the functional outcome of the patients while the neurosurgeons have put so much effort and time to open the skull to relieve the increased icp . oppositely speaking , the patients undergoing the operation to decompress the icp would have been already in a life - threatening condition due to severe brain injury that the surgery is the last resource for their survival . the surgery within 24 hours is indicative of a fast progression of the disease . whereas the surgery 24 hours after trauma somewhat suggests a slow nature in the development of hematoma enlargement , henceforthpark et al. 14 ) also reported that the ultra - early decompressive craniectomy for tbi did not improve the patient outcome after all . surgery should not be the only solution of treating edh .21218 ) at the same time , surgery should not be mandatory robotically even if the guidelines of btf say so . there are number of clinical articles on the management of non - surgical edh in the selected patients , such as elderly patients .21218 ) these data should be heavily considered in establishing more systematic and tailored protocols for treating edh .121418 ) gcs is a static measurement of consciousness of neurological patients . it may fluctuate from time to time and it may change dramatically early after injury . the proper assessment of initial gcs should be carried out ideally after hemodynamic and respiratory resuscitation of tbi patients . nevertheless , under the same name of edh , some patients would exhibit neurological deterioration meanwhile others would improve as time passes by . however , because of the unreliability of initial gcs in a certain group of patients , we retrieved the data from the ktdbs and attempted to calculate the difference between the initial and the final gcs in order to assess the functional outcome . as a result , we found that the larger the difference of gcs from the initial to the final gcs in a decreasing manner , the poorer the functional outcome of the patients . sufficient cerebral perfusion and prevention of increased icp is a crucial tactic in managing tbi .23 ) protocols of icp management vary inevitably due to different experiences , and they vary even among neurosurgeons within the same institution . according to our data , mannitol seems to be sitting in the middle of controversy in the context of icp management of edh patients . although mannitol was not directly associated with final outcome ( table 1 ) , the individual institutional protocols in treating edh and the time of mannitol given during the course of disease progression have not yet met a consensus in korea ( table 4 ) . if this is true , the effect of mannitol on the outcome of the patients with edh must be scrutinized carefully in the near future . implementation of evidence - based recommendations by btf is related with the improvements in mortality in tbi .9 ) adoption and integration of the basic guideline to individual institutional protocols is a step forward to treating a diverse pool of patients with edh .421 ) in hoping to be of some contribution for building a korean prognostic model of edh , we attempted to classify the clinical parameters in association with the functional outcomes by the analysis of data based on the ktdbs . by sharing the trauma data nation - wide and adopting the prognostic models , this national study will soon activate the improvement in the quality of neurosurgical care of edh .25 ) this study is a retrospective review of collected data from only 23 trauma centers in korea , thus , these results may not yet reflect the whole edh population in korea . non - operative groups of patients may be biased if the patient 's family disagreed on the surgical treatment . a new prospective database needs to be more specified with more information and details regarding the decision making of treatments in the clinical practice . this data set did not include the predisposing co - morbidities and medical conditions of patients , thus , this will underestimate the differences in the course of coagulopathy of the individuals with edh to a certain extent .17 ) this study has defined the clinical outcome as a functional outcome , not mortality , and this was assessed with the gos . we may have to differentiate the severe edh from mild edh as the survival factors will be more relevant for severe edh . the quality of health care systems have to be taken account in the analysis as it possibly determines the long - term outcome of the patients .25 ) in order to elucidate the variability of responses to edh , a basic research on biomarkers and genetic components of the individual patients will be required in the analysis as well . for example , the recovery is poorer in patients with stroke or tbi who have the apolipoprotein e - 4 ( apoe - 4 ) allele than in those who do not have this allele .13 ) this is one of many examples of genomics partially playing a role in the complex course of disease . as the population ages with longer life expectancy , trends of injury have also been changing with more injuries in the geriatric population .61524 ) as well as we have already witnessed in the analysis of our database , age is a major determinant of functional outcome .1524 ) for example , an injury mechanism of falls from heights is one of the leading causes of tbi in the elderly older than 65 years with a high risk of death .22 ) even ground - level falls are risks to the elderly when it is generally and easily known to be a low risk in the younger population .19 ) our data on edh from ktdbs showed that falls are associated with good outcome of edh ( though it was not statistically significant ) . nevertheless , this alarms us to collect more systematized data to confirm the difference , if there is any , in the domestic and international epidemiology of edh . the results may even different in the types of brain injury other than edh as well . it is imperative to be aware of the new injury types in the geriatric population . as far as the degree of brain injury is concerned , one will immediately think of the pathological mechanism of early events of tbi , which is still much less understood though there is a great effort of basic research undertaken internationally to uncurtain the injury mechanisms at the cellular levels .827 ) however , macroscopically , the severity , duration of impact , duration without treatment , and nature of injuries determine the degree of brain injury . degree of brain injury is often characterized by severe brain swelling , combination with traumatic subarachnoid hemorrhage , cerebral vasospasm , and delayed cerebral infarction after trauma .1826 ) edh with additional intracranial injuries would act together in a simultaneous manner implicating to worsen the patients ' condition . the accumulative damage will add on to escalate the extent of brain injury , which will eventually affect the functional outcome as we have already demonstrated in the analysis of our data . in the end , patients with severe gcs and the management of icp determines the final outcome in patients with edh as the response of recovery is dependent on the treatment effects during the clinical course and possibly on the patients ' predisposing co - morbidity .5 ) one must also bear in mind that there are also extrinsic factors which can potentially threaten the patients outside the hospital . namely , the secondary injury by such as hypoxia or hypotension occurred , before the patient entered the emergency department due to lack of professional pre - hospital management , will be as critical as the impact of irreversible primary damage of neuronal pathways of consciousness at the first place .10 ) a clinical deterioration of a patient with edh is related with the size of edh and its time - dependent enlargement . there was an analytical study reported that a ct scan performed less than 6 hours after the onset of trauma had an increased risk of hematoma enlargement .25 ) our analysis of edh data from ktdbs also confirms that the time interval from trauma to the initial ct scan before 6 hours is associated with a poor functional outcome . it is also reported that a series of ct scans in non - operative edh patients should be obtained within 6 to 8 hours after the initial injury for better outcomes with prompt decision of treatment .20 ) moreover , ding et al. 3 ) reported that the non - surgical patients with routine repeat ct scans have a better outcome than those with non - routine repeat ct . however , the same authors also mentioned that routine follow - up ct scans 48 hours after trauma may not also be required .316 ) according to the guidelines of the brain trauma foundation ( btf ) , the volume of edh and the initial gcs are determinants of surgical indication of edh . not all patients benefit from the operation of edh .21218 ) our data showed that the poor outcomes are more associated with the cases of surgical edh . furthermore , the cases of decompressive craniectomy with hematoma evacuation of edh are also associated with a poor outcome ( p 0.0001 ) . it is rather ironic that the act of surgery is not guaranteeing the functional outcome of the patients while the neurosurgeons have put so much effort and time to open the skull to relieve the increased icp . oppositely speaking , the patients undergoing the operation to decompress the icp would have been already in a life - threatening condition due to severe brain injury that the surgery is the last resource for their survival . the surgery within 24 hours is indicative of a fast progression of the disease . whereas the surgery 24 hours after trauma somewhat suggests a slow nature in the development of hematoma enlargement , henceforth , this is clinically associated with good outcome in our data analysis . park et al. 14 ) also reported that the ultra - early decompressive craniectomy for tbi did not improve the patient outcome after all . surgery should not be the only solution of treating edh .21218 ) at the same time , surgery should not be mandatory robotically even if the guidelines of btf say so . there are number of clinical articles on the management of non - surgical edh in the selected patients , such as elderly patients .21218 ) these data should be heavily considered in establishing more systematic and tailored protocols for treating edh .121418 ) it may fluctuate from time to time and it may change dramatically early after injury . the proper assessment of initial gcs should be carried out ideally after hemodynamic and respiratory resuscitation of tbi patients . nevertheless , under the same name of edh , some patients would exhibit neurological deterioration meanwhile others would improve as time passes by . however , because of the unreliability of initial gcs in a certain group of patients , we retrieved the data from the ktdbs and attempted to calculate the difference between the initial and the final gcs in order to assess the functional outcome . as a result , we found that the larger the difference of gcs from the initial to the final gcs in a decreasing manner , the poorer the functional outcome of the patients . sufficient cerebral perfusion and prevention of increased icp is a crucial tactic in managing tbi .23 ) protocols of icp management vary inevitably due to different experiences , and they vary even among neurosurgeons within the same institution . according to our data , mannitol seems to be sitting in the middle of controversy in the context of icp management of edh patients . although mannitol was not directly associated with final outcome ( table 1 ) , the individual institutional protocols in treating edh and the time of mannitol given during the course of disease progression have not yet met a consensus in korea ( table 4 ) . if this is true , the effect of mannitol on the outcome of the patients with edh must be scrutinized carefully in the near future . implementation of evidence - based recommendations by btf is related with the improvements in mortality in tbi .9 ) adoption and integration of the basic guideline to individual institutional protocols is a step forward to treating a diverse pool of patients with edh .421 ) in hoping to be of some contribution for building a korean prognostic model of edh , we attempted to classify the clinical parameters in association with the functional outcomes by the analysis of data based on the ktdbs . by sharing the trauma data nation - wide and adopting the prognostic models , this national study will soon activate the improvement in the quality of neurosurgical care of edh .25 ) this study is a retrospective review of collected data from only 23 trauma centers in korea , thus , these results may not yet reflect the whole edh population in korea . non - operative groups of patients may be biased if the patient 's family disagreed on the surgical treatment . a new prospective database needsto be more specified with more information and details regarding the decision making of treatments in the clinical practice . this data set did not include the predisposing co - morbidities and medical conditions of patients , thus , this will underestimate the differences in the course of coagulopathy of the individuals with edh to a certain extent .17 ) this study has defined the clinical outcome as a functional outcome , not mortality , and this was assessed with the gos . we may have to differentiate the severe edh from mild edh as the survival factors will be more relevant for severe edh . the quality of health care systems have to be taken account in the analysis as it possibly determines the long - term outcome of the patients .25 ) in order to elucidate the variability of responses to edh , a basic research on biomarkers and genetic components of the individual patients will be required in the analysis as well . for example , the recovery is poorer in patients with stroke or tbi who have the apolipoprotein e - 4 ( apoe - 4 ) allele than in those who do not have this allele .13 ) this is one of many examples of genomics partially playing a role in the complex course of disease . the primary aim of the present study was to investigate how clinical parameters from the onset of trauma and during the treatment influence the patient outcome . this is the first report identifying the factors associated with poor and good outcomes of patients with edh . a new strategy may be required to prevent patients being severely disabled for a long - term as it is eventually linked with the socio - economic problems in this country . the epidemiology of edh is changing , therefore , the pre - hospital care , diagnostic instruments , critical care monitoring , and treatment have to be changed and validated continuously for better outcome . the degree of brain injury and the gcs difference were notable factors that were significant in determining the functional outcome of edh . however , some issues have to be raised for further investigation as our current data is based mainly on the admission characteristics . the data from ktdbs will eventually serve as the basis for designing the optimal standards in the acute care of edh and other tbi . in the end , the implementation of the revised guidelines fit for korean trauma systems will be important in effectively preventing poor prognostic aspects of edh .\noutput:\n" }, { "from": "agent", "value": "objectivethe aim of this preliminary collaborative study was to assess the clinical characteristics , management , and outcome of epidural hematoma ( edh ) based on the data collected and registered in the korean trauma data bank system ( ktdbs ) . methodsof 2,698 patients registered in the ktdbs between september 2010 and march 2014 , 285 patients with edh were analyzed . twenty - three trauma centers participated in the study voluntarily to collect data . we subcategorized the patients into two groups with good and poor outcomes . various clinical characteristics and the time intervals with regard to treatment course were investigated to determine the relationship between these parameters and the functional outcome.resultsof multiple parameters for this analysis , older age ( p = 0.0003 ) , higher degree of brain injury ( p < 0.0001 ) , cases of surgical edh ( p < 0.0001 ) , time interval from trauma to hospital before 6 hours , and the decreasing pattern of glasgow coma scale ( gcs ) between and initial and final gcs were strongly associated with poor outcome . use of prophylactic anticonvulsant did not affect the functional outcome . there was an interesting difference in the use of mannitol in treating edh between the urban and rural regions ( p < 0.0001 ) . conclusionthis is the first multi - center analysis of etiology of injury , pre - hospital care , treatment , and functional outcome of edh in korea . the degree of brain injury and the gcs difference were notable factors that were significant in determining the functional outcome of edh ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the number of people with diabetes is increasing due to population growth , aging , urbanization , and increasing prevalence of obesity and physical inactivity . predictions show that the number of people with diabetes worldwide will double in the next generation . in the quality of diabetes management in five countries with advanced economies ( australia , canada , new zealand , usa , and uk ) has been analysed . yearly costs ( e.g. , 132 billions usd in the usa ) and deaths due to diabetes ( e.g. , 143308 people in the usa ) are reported in that paper . in face of such a disastrous situationimproving accessibility of the african population to diabetes care seems to be a big challenge in most of african countries such as the democratic republic of congo ( drc ) , a country which is four times bigger than france and where the number of care centers is reduced . drc has 71 million inhabitants . around 7 % of the population in the capital city kinshasamost of diabetic patients in the drc do not control regularly their glucose values , occasional checks are the only executed options . what are the factors which are responsible for deficiency in the successful management of diabetes in africa ? a number of obstacles make the detection , prevention , monitoring , and treatment of diabetes difficult in most african countries . the first group of difficulties is related to the health facilities which are not sufficient to cope with the scale of the problem . prevention and education are not sufficiently promoted , although they should be given high priority . there are not enough medical specialists and the few existing focus their work in big cities without addressing the needs of rural populations . therefore , patients from rural areas are forced to spend money and time travelling long and expensive journeys to access diabetes care . another point , the priority of health politics in several african countries is oriented on the management of transmissible diseases such as hiv and not to chronic diseases like diabetes and high blood pressure . it is impossible for the majority of the population to afford the cost of the diabetes medication in particular insulin . due to life condition , patients are unable to control a proper diet , especially when the family eats by hand in the same dish . limited resources push the population to focus on high calorie foods rich in fat , sugar , and salt . the third group of difficulties is related to the sociocultural context which has a considerable weight in africa . africans have difficulty accepting the concept of chronic illnesses requiring lifelong treatment , so when diabetes is well balanced , patients often stop the treatment thinking the disease is cured . moreover , patients do not find it useful to carry out regular glucose checks although this is necessary for the adaptation of the insulin therapy . the next point deals with the fact that the struggle against obesity faces the belief that being fat is a sign of wealth , good health , and beauty . according to the african tradition , womenweight loss , even if it is wanted , raises suspicion of possible hiv infection in the continent . the last obstacle is caused by traditional medicine which plays a key role in many african countries . this practice is often dangerous when it advices diabetes patients to stop effective treatments and use empirical drugs which have the advantage of being cheap . information and communication technologies have great potential to address some of the challenges faced by the public health care . a number of literature have been oriented on the exploitation of mobile devices for completing traditional therapy ; other works have been focused on the architectural issues of a telemedicine intervention . a significant number of telemedical products in the area of diabetes management have been developed in the last decade . this is justified by the fact that recent studies have depicted a very critical situation ; over 10 % of the united states population over the age of 20 has diabetes . as a result , diabetes is now ranked amongst the ten first leading causes of death . a web - based system for monitoring patients with type 2 diabetes is presented in . in that system weight , blood sugar , and blood pressureare recorded using an application implemented on the mobile phone . in bayer 's gluckofact deluxe softwarethe software recognizes the bayer glucose meter connected to the personal computer and stores automatically the data in a database . the visualization of the recorded data is well organized . however , that software is not extended for online applications . this obliges the patient to regularly visit his doctor or to use another system in order to send the recorded data . the software helps in tracking daily diabetic data ; it has a simple interface for data entry and uses different devices for entering data ( windows - pc , android phones , windows mobile phones , iphones , and java phones ) . it has been proved in that telemedicine is a suited instrument to support health care providers in the effective management and prevention of diabetes complications . solution to the four listed main difficulties in properly addressing diabetes in africa can be solved by providing a cost - effective telemedical system and a suitable educational program in order to increase the population awareness . this is the focus of this paper , in which we propose and validate an innovative mobile health application . the system manages a secure collection , processing , storage , and sharing of diabetes - related data and thus reduces the frequency of physical consultations to the treating physician . the system enables the organization of health information through a structured gathering of all relevant diabetes data in one central place enabling only access of authorized medical staff . the system helps improve the quality of service in the care process of diabetes by benefiting from rapid advances in mobile , web , and communication technologies . we strongly believe that the outcome of this work will contribute toward the establishment of a model for diabetes management in countries where access to diabetes care is limited and number of medical care personnel is reduced due to high personnel costs . the diabetes management system mobil diab , presented in this paper , can serve as a complete hospital management system which supports several hospitals , each hospital having its own medical staff and patients and every clinician coaching a group of patients assigned to him . moreover , since e - health systems store sensitive data and should have a proper security and privacy framework and mechanisms , this paper extends the state - of - the art by presenting a system which enables a secure data access , communication , and storage . investigation of the impact of using this system mobil diab in assisting the therapy and treatment of diabetes is the major focus of this paper . mobil diab system is an innovative solution for the assistance and care of diabetes patients . it enables diabetes patients to manage their self - control data around the clock using their mobile devices ( android , iphone , and ipads ) and / or web - based applications . medical care personnel access patients ' data through a protected web portal . the platform is responsible for the following tasks : connection of web and mobile applications , user - hierarchical model ( administration , hospital , doctor , and patient ) , access control of different user categories , and secure interface to hospital information systems . the concept of the system aims at empowering patients to better manage their disease by allowing them to monitor their blood sugar trends over an extended period of time and draw some actionable conclusions . acquired data are then sent using http / https protocol to the central platform which ensures a secure storage and further processing of the information , figure 1 . mobil diab guarantees a series of benefits for patients , health care staff , and public health system . benefits for the patients include , among others , unimpeded patient mobility , data input via smart phones and / or via web , regular self - control of diabetes - related data enables the right care to be administrated at the right time , potential to improve care process and quality of service , improvement in patient 's motivation through their involvement in the therapy process , reduced check - up frequency to doctors , and use of mobile health technologies encourages diabetes patients to change their behavior / lifestyle and improve their health . benefits for the health care staff involve , among others , the following : complete and regular data input which is helpful for individual therapy plan , minimization of errors caused by lack of information about the disease history , improvement of the care process quality , getting specialist opinions , access to patients ' data worldwide independent from time and location , and automatic alarm message in case of critical data from a patient . benefits for the health system include , among others , the following : delaying and reducing diabetes complications , minimizing hospitalization rates due to diabetes complications , reducing death rates from diabetes , speeding up the transition of patients from hospitals to their own homes which leads to a reduction in costs , and enabling the organization of health information through a structured gathering of all relevant data in one central place . the system helps to easy track patterns and trends in diabetes management process , helps in taking right treatment decisions and lead to a better glucose control , is suitable for self - care , home care , family physicians , clinics , and hospitals , presents statistics that cover everything doctors and patients need , allows risk monitoring with automated alarm message to care provider and trusted person , preserves mobility through the use of apps and web technologies , and acquires a highly secured database platform with end - to end encryption and data are worldwide available in all major languages . the mobile application mobil diab has an intuitive user interface which is self - explained . you can choose the action you wish to perform as shown on the screenshot of figure 2 . data are automatically synchronized in background with the online system so that medical care providers receive these data in real time . to record diabetes - related data , these data may include , amongst others , the blood glucose measurement , insulin intake , sport done with duration , blood pressure measurements , and body weight and size . data acquisition can also take place automatically from glucose meters supporting the ieee 11073 personal health data standards . therapy plans , instructions , and recommendations sent by the doctor from the doctor portal are received directly in the mobile application . for patients without smartphones ( mobil diab app ) , they can still get these doctors ' feedbacks in the protected patients ' portal , through their email address or as sms if this service was activated . the web structure of the system is conceived in order to serve as a complete hospital management system . four web - based portals are integrated to the system and hosted from the central platform . they are designed for four different types of users : patients , doctors , hospital administrators , and system administrator . the graphic shows the glucose measurements of one day , amount of carbohydrate taken ( blue color facing up ) , and units of insulin injected ( purple color facing down ) . clear graphical representation of trends and statistics enables clinicians to make appropriate decisions on therapy adjustment . the tool helps medical staff save their times while providing high quality service to diabetes patients . for emergency cases , an sms is automatically generated and sent to the treating physician , to alert him to check the critical situation in the portal and be able to give direct instructions to the patient . the patent - protected platform illustrated by figure 5 has been developed to help bridge the gap between health and mobility . diverse healthcare modules have been implemented and other are planned in order to meet a complete health care service package from diabetes , dermatology , stress , fitness , and long - term health conditions up to the assisted - living for senior . the platform helps consumers track health , wellness , and vital information using a highly secure infrastructure . moreover , interfaces to hospital information systems and practice management software are supported . in this work , the four - layer architecture of the platform enables users to securely share sensitive information . using different devices , such as smartphones and computers , users can access functionalities of applications supported by the core of the platform through the communication layer . security is a general requirement in modern computing environments , but in e - health systems security is an imperative requirement because those systems handle very sensitive data like medical and personal data . the platform acquires features enabling the following.authentication : methods and mechanisms which allow an entity to prove its identity to a remote end.authorization : access control mechanisms and the ability of an entity to access shared resources.data integrity : mechanisms which ensure that when there is an interchange of data between two peer entities , the received data and the original ones are the same , and that no intermediate alteration has occurred.data confidentiality : it assures that stored or transmitted data are well protected from possible disclosure . a mean used to achieve data confidentiality is through cryptographic mechanisms.privacy : it can be defined as an entity 's ability to control how , when , and to what extent personal information about the entity will be communicated to third parties.secure data communication and storage.data availability : data can be accessed by authorized users independently from time and location . authentication : methods and mechanisms which allow an entity to prove its identity to a remote end . authorization : access control mechanisms and the ability of an entity to access shared resources . data integrity : mechanisms which ensure that when there is an interchange of data between two peer entities , the received data and the original ones are the same , and that no intermediate alteration has occurred . data confidentiality : it assures that stored or transmitted data are well protected from possible disclosure . privacy : it can be defined as an entity 's ability to control how , when , and to what extent personal information about the entity will be communicated to third parties . data availability : data can be accessed by authorized users independently from time and location . our proposed architecture addresses authentication and authorization issues , since each user is classified to a category that defines what he / she has access to . all data are encrypted using the symmetric encryption method aes ( advanced encryption standard ) . for the protection of user 's privacy , an implemented mechanism allows different groups of users to have access to different types of medical data . the platform is composed of several modules , each one supporting its group of tasks . this platform was also presented in . in order to test the effectiveness of the diabetes management system mobil diab in the context of african health care system , a trial was conducted in two cities in the eastern part of the democratic republic of congo ( goma and butembo ) . patients diagnosed with type 2 diabetes and aged between 35 and 75 years were recruited randomly . a total of 40 patients were included in the trial phase . for classification and evaluation purpose , the cohort was divided into a control group ( conventional therapy without the use of telemedicine system ) and an intervention group ( treatment with the use of telemedicine system mobil diab ) . to verify the comparability of the two groups , table 3 shows that the control and intervention groups in terms of anthropometric data and metabolic control parameter are almost the same at the beginning of the trial : the mean age for the intervention group is 53.3 years with a standard deviation of 10.7 years and for the control group is 53.35 years with a standard deviation of 9.59 years . the mean hba1c value for the whole intervention group before the trial was 8.67 % and for the control group was 8.59 % . the trial was conducted for a period of two months . during this trial period , medical staff of four local hospitals belonging to the health department of the baptist community in central africa ( cbca ) accessed the system and coached the patients based on the analysis of the sent data . at the end of the trialeach participant had to fill a questionnaire evaluating the system mobil diab based on the three following metrics : usability and design , efficiency and therapy satisfaction , and acceptance and appreciations . questions for patients were as follows.q1 : how often could you successfully use the system?q2 : how easy was it for you to cope with the application?q3 : how do you evaluate the input options and design of the application?q4 : how do you evaluate the output options and visualization possibilities?q5 : how do you evaluate the design of the application?q6 : do you find mobil diab as a tool which motivates you in the control of your blood glucose levels?q7 : did feedbacks ( messages and therapy ) from doctors help in the diabetes management process?q11 : would you wish to continue using mobil diab for managing your diabetes?q12 : would you recommend the system to other users ? q4 : how do you evaluate the output options and visualization possibilities ? q5 : how do you evaluate the design of the application ? q6 : do you find mobil diab as a tool which motivates you in the control of your blood glucose levels ? q7 : did feedbacks ( messages and therapy ) from doctors help in the diabetes management process ? each medical care personnel had to evaluate the system by answering the following questions.q1 : how difficult was it for you to use the doctor web application to interact with your patients?q2 : how do you evaluate the design of the doctor portal?q3 : how often could you successfully use the system?q4 : how do you evaluate the representation of diabetes data in the portal?q5 : how do you evaluate the monthly representation of patient 's data on graph?q6 : how do you evaluate the feature for report generation?q7 : how do you appreciate the page summarizing all important patient 's data at glance?q8 : is the provided information in portal enough for improving the therapy adaptation?q12 : would you wish to continue using mobil diab for coaching your diabetes patients?q13 : would you recommend the system to other medical care personnel ? q1 : how difficult was it for you to use the doctor web application to interact with your patients ? q5 : how do you evaluate the monthly representation of patient 's data on graph ? q7 : how do you appreciate the page summarizing all important patient 's data at glance ? q12 : would you wish to continue using mobil diab for coaching your diabetes patients ? a 10 - point scale from 1 to 10 was used for questionnaire , with higher scores representing a better evaluation of the system based on the given question . patients and medical care staff provided their evaluations as presented in tables 1 and 2 . moreover , based on the analysis of patients ' data collected during the trial period , the improvements in clinical outcome could be evaluated . two metrics were used for this purpose : the mean amplitude of glycemic excursions ( characterized by the mean blood glucose and its standard deviation ) and the glycated hemoglobin ( hba1c ) , as table 3 presents the results . before the trial could startall the involved partners ( patients , medical care providers , support teams , administrators , internet and telephone providers , developers , and policy makers ) worked closely together during the development and adaptation process of the system . user requirements , functionalities and design , relevant standards and rules , and methodology and market analysis were discussed with all the involved players . analysis of feedbacks from each stage constituted important input for the following stage . at the end , final modifications were made to obtain the final pilot ready for use in a larger scale . through collaboration with the local university , the ruwenzori state university in butembo , democratic republic of congo , both its faculty of medicine and faculty of applied sciences will keep on conducting research in order to contribute to the adaptation of the system to meet other local specific needs . each question was evaluated based on a 10 - point - scale from 1 to 10 point with high scores reflecting positive feedback from the user . three metrics were considered for evaluation : usability and design , efficiency and therapy satisfaction , and acceptance and appreciations . score regarding usability and design was the average score for questions 1 , 2 , 3 , 4 , and 5 and resulted in a mean value of 7 points out of ten . score for efficiency and therapy satisfaction was the average score for questions 6 and 7 and resulted in a mean value of 7.43 points out of ten . at last , score related to acceptance and appreciationswas averaged from questions 11 and 12 and resulted in a mean value of 8.65 points out of ten . score regarding usability and design was the average score for questions 1 and 2 and resulted in a mean value of 7.56 points out of ten . score for efficiency and therapy satisfaction was the average score for questions 3 , 4 , 5 , 6 , 7 , and 8 and resulted in a mean value of 7 points out of ten . acceptance and appreciations score was averaged from questions 12 and 13 and resulted in a mean value of 8.75 points out of ten . two metrics were used to assess the improvement in the quality of metabolic control : the mean amplitude of glycemic excursions ( characterized from the mean bg and its standard deviation ) and the mean hba1c of each group . we should notice that the mean amplitude of glycemic excursions is the measure of diabetic instability , or a characteristic of blood glucose behavior and the hba1c is the standard measure of average glycemic control predicting diabetes complications in type 1 and type2 . the approximate mapping between hba1c values given in percentage ( % ) and mean bg ( estimated average glucose ) measurements was calculated using the following equation : ( 1 ) hba1c [ % ] = ( mean bg [ mg / dl ] +86 ) 33.3 . positive results have been noticed at the end of the trial , this is particularly evident in a significant improvement in the mean hba1c values for the intervention group . the mean hba1c for that group was 8.67 % before the start of the trial and could be reduced to 6.89 % at the end . this value of 1.78 % in the improvement of hba1c indicates that the risk of diabetes complications has been reduced or postponed , thus leading to cost savings . moreover , an important improvement could be noticed in the mean amplitude of glycemic excursions . this is shown in table 3 by an important reduction of the glucose variability ( characterized by the standard deviation of the mean bg ) . the mean bg standard deviation was 48.6 mg / ml for the control group whereas ; this could be reduced to 33 mg / dl for the intervention group at the end of the trial . patients found the system as a helpful tool , since it helped them increase their motivation for regular glycemic control , motivated them to fix some goals or targets values for blood glucose control for the future , and helped them to control their meal since they could access easily the database containing the amount of carbohydrate for each meal and portion they were taking . medical care personnel listed such benefits as follows : the system allowed them to coach several patients at the same time and at a distance , and modernization of health care system allowed them to get rich and useful data through a secure system . the amelioration in the clinical results is due to these above listed benefits provided by the system . however , some disadvantages such as costs for internet connection and time needed for getting used to the application were the preoccupation of both categories of the users . wishes from both categories of the subjects included to the trial ( medical staff and patients ) for the amelioration of the system were collected and included the following : extend the drug list and meal database in the application to include all local foods , and applied drugs , since some of them were missingmore sensitizing activities and training sessions about the system to patients and medical staffinclude the support of the glucose measuring device kit in the modelcreate a framework for sport activities for patients extend the drug list and meal database in the application to include all local foods , and applied drugs , since some of them were missing more sensitizing activities and training sessions about the system to patients and medical staff include the support of the glucose measuring device kit in the model create a framework for sport activities for patientsan it - enabled diabetes management with fully integrated provider - patient system has been presented in this paper . results from the trial conducted in two eastern cities of the democratic republic of congo have proved how the system mobil diab is suited not only for developed countries but also for communities traditionally underserved , those in remote or rural areas with few health services and staff . this population can access diabetes care using mobil diab , because the system overcomes distance and time barriers between health - care providers and patients . the use of mobil diab showed improvement of clinical outcomes of the patients from the intervention group involved in the conducted trial . this has been demonstrated from the amelioration of both the hba1c ( from 8.67 % to 6.89 % ) and the mean amplitude of glycemic excursions which is characterized from both the mean blood glucose and its standard deviation . the decrease of the blood glucose fluctuations is demonstrated from results of the mean blood glucose standard deviation from the intervention group compared to the control group at the end of the study ( 33.0 mg / ml instead of 48.6 mg / ml ) . this proves how the use of the system could help patients stabilize better their glucose values . positive evaluations of the system from patients and medical staff have been presented based on three metrics : usability and design , efficiency and therapy satisfaction , and acceptance and appreciations . the model developed from the conducted pilot in the democratic republic of congo can be extended and applied for other countries in order to enhance awareness on the diabetes management in the continent and to improve the quality of service in the care process .\noutput:\n" }, { "from": "agent", "value": "the demand for new healthcare services is growing rapidly . improving accessibility of the african population to diabetes care seems to be a big challenge in most countries where the number of care centers and medical staff is reduced . information and communication technologies ( ict ) have great potential to address some of these challenges faced by several countries in providing accessible , cost - effective , and high - quality health care services . this paper presents the mobil diab system which is a telemedical approach proposed for the management of long - term diseases . the system applies modern mobile and web technologies which overcome geographical barriers , and increase access to health care services . the idea of the system is to involve patients in the therapy process and motivate them for an active participation . for validation of the system in african context , a trial was conducted in the democratic republic of congo . 40 subjects with diabetes divided randomly into control and intervention groups were included in the test . results show that mobil diab is suitable for african countries and presents a number of benefits for the population and public health care system . it improves clinical management and delivery of diabetes care services by enhancing access , quality , motivation , reassurance , efficiency , and cost - effectiveness ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: our research is approved by the ethics committee of medical college hospitals , kolkata , west bengal , india . each of the authors for preparing this case report , dr . kallol dasbaksi ( corresponding author ) , dr . plaban mukherjee have contributed to the study concept or design , data collection , data analysis or interpretation , for writing the paper .\noutput:\n" }, { "from": "agent", "value": "highlightsthis case presentation , emphasizes the typical manifestations of hepatic but associated asymptomatic pericardial hcs.hepatic hydatid cyst presenting as a painless abdominal lump preceded painful presentation for a few months.asymptomatic pericardial hydatid cyst could have presented with pericardial tamponade due to rupture , if ignored further.the origin of the pericardial hydatid cyst could have been due to trans diaphragmatic passage of scolices from the hepatic location , as the usual pulmonary involvement was absent ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: economic evaluation of health technologies ( drugs , devices , etc ) has become widespread across the world , with government agencies ( eg , national institute of clinical excellence ( nice ) in england and wales ) employing these techniques on a routine basis to make decisions about which healthcare to fund .14 but there has been very little progress in economic evaluation for public health and in particular within public policy .58 in 2005 , the remit for nice was expanded to include public health , reflecting a growing desire to broaden the scope of such evaluations and address issues of resource allocation across all sectors impacting on health .910 provision of acceptable housing conditions may be regarded as a cornerstone of healthy public policy , representing a major public investment with the potential to improve health and contribute wider public health strategies to improve population health and reduce health inequalities .1113 in 2009 , a systematic review of the health impact of housing interventions , including studies from around the world , concluded that housing improvements can lead to health improvements .14 this was especially the case for warmth improvements targeted at those with poor health , living in poor housing . some of the studies in the 2009 systematic review included reports on the costs associated with the interventions and a small number reported having undertaken economic evaluations .14 given the growing desire of policy makers to demonstrate value for money from interventions , we undertook a further review of these studies to identify and extract data which could be used to inform estimates of the relative costs and benefits of housing improvement , and illustrate the challenges of economic evaluation in this field . this paper presents the results of this review , providing details of the cost and economic analyses reported alongside housing intervention studies and accompanying health impacts . the paper uses these data to examine the economics of housing investment and also to reflect on the current state of health economic analysis in housing . as an example of health economic evaluation of a substantial public investment and policy area , the lessons may have a wider methodological relevance to topics of interest to healthy public policy , such as welfare reforms or transport initiatives . prior to detailing the process undertaken for this systematic review of economic data and analysis , we detail the definitions used to distinguish between differing types of cost studies and economic evaluations ( table 1 ) . these definitions are routinely applied in the field of health economics and have been proposed for the economic appraisal of public health interventions .45715 types of economic studies ( an assessment of cost is common to all study types detailed ) 5715 qaly , quality adjusted life year . table 1 details three forms of cost study which are common within the literature , namely cost - offset , cost - minimisation and cost - consequence . cost - offset studies simply detail the costs of the intervention alongside the cost savings achievable ( eg , days in hospital averted ) . cost - minimisation studies compare the costs ( including any cost savings ) for an intervention with the costs of the status quo under the assumption that the outcomes are equivalent between the two . cost - consequence studies present the costs ( including any cost savings ) associated with an intervention and the status quo alongside a list of the various possible outcomes achieved . there is no attempt to identify or value the collective outcomes within a single metric . as such , while cost consequence studies provide a useful descriptive summary , and first step towards a full economic evaluation , they can not be used to determine value for money or identify priority interventions . these approaches are not formally economic evaluation techniques because they do not allow for a formal comparative analysis in terms of costs and outcomes . in a situation where policy involves the provision of a specific amenity ( eg , a new heating / insulation system ) then a comparison of costs is all that is required to establish the least costly way to provide the desired amenity . however , this assumes that provision of the specific amenity is , by some definition , a good thing ( eg , it improves health outcomes ) . where budgets are constrained there is an unavoidable opportunity cost of undertaking any policy , as funds spent on one intervention will limit the funds available for other interventions . the aim of economic evaluation is to assist policy makers to identify interventions / policies which represent good value for money . the value for money associated with a new intervention is determined by comparing the additional costs required and additional outcomes achieved , with the status quo or current intervention . where an intervention / policy provides greater outcomes at lower costs , it is said todominate the current intervention / policy and a decision about adopting the new intervention / policy is straightforward . however , where an intervention / policy provides greater outcomes at greater cost , a decision must be made about whether to spend these additional resources to achieve these additional outcomes . where outcomes of different interventions / policies are valued using common metrics ( see table 1 ) , the value for money associated with them can be directly compared to indicate where these outcomes can be achieved at the lowest price . these interventions represent the best value for money compared with the alternatives available and , where resources are scarce , could be consideredeconomically worthwhile . there are three main forms of economic evaluation : cost - effectiveness analysis , cost - utility analysis and cost - benefit analysis ( table 1 ) . each method involves a comparative analysis of alternative courses of action in terms of both their costs and consequences .4 with each method costs are measured in monetary units , while the measurement and valuation of outcomes differs . as such , the methods are traditionally classified by outcome .15 cost - effectiveness analysis typically involves measuring a specific , one - dimensional , health or clinical outcome , for example asthma attacks averted . cost - utility analysis is a special type of cost - effectiveness where multidimensional health outcomes are reduced to a single dimension reflecting individuals preferences for the diverse health outcomes . the most commonly used outcome in cost - utility analysis is the quality adjusted life year ( qaly ) . for both cost - effectiveness and cost - utility studies , value for money is identified using a measure of the additional cost per additional outcome ratio ( eg , an incremental cost / qaly ratio ) and comparing that to an external threshold or to the ratio achieved by alternative policies . in contrast , cost - benefit analysis involves the measurement and valuation of all outcomes of interest in monetary terms . here the value for money is identified by positive net economic benefit associated with the interventions ( ie , the monetary value of the outcomes exceeds the net costs of the intervention less any costs savings achieved elsewhere ) . this paretian definition of cost - benefit analysis is the established , standard definition used within health economics . it allows a broad spectrum of outcomes ( all those of importance to the individual ) to be included within the metric , but requires the , often complex , valuation of outcomes in monetary terms . all housing intervention studies and their associated papers included in the 2009 systematic review of the health impacts of housing improvement14 were examined for reports of costs and economic analyses . details of the scope of the review ( inclusion and exclusion criteria ) , and evidence appraisal are available in the 2009 publication along with the findings of the review .14 forty - five medical and social science databases , as well as websites and grey literature were searched to identify studies of housing improvement which assessed change in any health outcome . a separate search for economic studies was not undertaken but economic studies which included health outcomes following housing improvement would have been identified in the broad search . all available data on costs and , where available , details of any economic analysis were extracted by one reviewer ( cm ) and checked by a second reviewer ( ef or ht ) . the cost data were tabulated alongside a summary of reported heath impacts and an indication of overall study quality as used in the original review ( a = minimal bias , b = some bias , c = considerable bias ) .14 where a study reported plans to undertake economic analysis , the authors were contacted for an update on progress and available data , or reasons for not completing the economic analysis . studies which only presented cost data ( table 2 ) were further examined for the potential to have conducted an economic evaluation , that is , presence of a suitable health outcome which could be linked to cost and compared to an alternative ( table 1 ) . studies which reported having undertaken an economic evaluation ( table 3 ) were examined to determine the precise form of that analysis ( table 1 ) . summary of housing improvement studies reporting cost data without economic evaluation ( ordered by intervention type , study quality and date ) * study design : rct , randomised controlled trial ; contr 'd b & a , controlled before & after ; uba , uncontrolled before & after ; xcba , controlled before & after using area level cross sectional data at both time points ; xuba , uncontrolled before & after using area level cross sectional data at both time points ; rc , retrospective controlled study ; housing improvement studies reporting an economic evaluation ( ordered by intervention type , study quality and date ) * study design : rct , randomised controlled trial ; cba , controlled before & after ; uba , uncontrolled before & after ; rc , retrospective controlled study . * * effect direction : upward arrow , positive health impact ; downward arrow , negative health impact ; sideways arrow , no change / mixed effects / conflicting findings . sample size : final sample size ( individuals ) in intervention group : large arrow , 300 ; medium arrow , 50300 ; small arrow , 50 . statistical significance : black arrow , p 0.05 ; grey arrow , p 0.05 ; empty arrow , no statistics / data reported . table 1 details three forms of cost study which are common within the literature , namely cost - offset , cost - minimisation and cost - consequence . cost - offset studies simply detail the costs of the intervention alongside the cost savings achievable ( eg , days in hospital averted ) . cost - minimisation studies compare the costs ( including any cost savings ) for an intervention with the costs of the status quo under the assumption that the outcomes are equivalent between the two . cost - consequence studies present the costs ( including any cost savings ) associated with an intervention and the status quo alongside a list of the various possible outcomes achieved . there is no attempt to identify or value the collective outcomes within a single metric . as such , while cost consequence studies provide a useful descriptive summary , and first step towards a full economic evaluation , they can not be used to determine value for money or identify priority interventions . these approaches are not formally economic evaluation techniques because they do not allow for a formal comparative analysis in terms of costs and outcomes . in a situation where policy involves the provision of a specific amenity ( eg , a new heating / insulation system ) then a comparison of costs is all that is required to establish the least costly way to provide the desired amenity . however , this assumes that provision of the specific amenity is , by some definition , a good thing ( eg , it improves health outcomes ) . where budgets are constrained there is an unavoidable opportunity cost of undertaking any policy , as funds spent on one intervention will limit the funds available for other interventions . the aim of economic evaluation is to assist policy makers to identify interventions / policies which represent good value for money . the value for money associated with a new intervention is determined by comparing the additional costs required and additional outcomes achieved , with the status quo or current intervention . where an intervention / policy provides greater outcomes at lower costs , it is said to dominate the current intervention / policy and a decision about adopting the new intervention / policy is straightforward . however , where an intervention / policy provides greater outcomes at greater cost , a decision must be made about whether to spend these additional resources to achieve these additional outcomes . where outcomes of different interventions / policies are valued using common metrics ( see table 1 ) , the value for money associated with them can be directly compared to indicate where these outcomes can be achieved at the lowest price . these interventions represent the best value for money compared with the alternatives available and , where resources are scarce , could be consideredeconomically worthwhile . there are three main forms of economic evaluation : cost - effectiveness analysis , cost - utility analysis and cost - benefit analysis ( table 1 ) . each method involves a comparative analysis of alternative courses of action in terms of both their costs and consequences .4 with each method costs are measured in monetary units , while the measurement and valuation of outcomes differs . as such , the methods are traditionally classified by outcome .15 cost - effectiveness analysis typically involves measuring a specific , one - dimensional , health or clinical outcome , for example asthma attacks averted . cost - utility analysis is a special type of cost - effectiveness where multidimensional health outcomes are reduced to a single dimension reflecting individuals preferences for the diverse health outcomes . the most commonly used outcome in cost - utility analysis is the quality adjusted life year ( qaly ) . for both cost - effectiveness and cost - utility studies , value for money is identified using a measure of the additional cost per additional outcome ratio ( eg , an incremental cost / qaly ratio ) and comparing that to an external threshold or to the ratio achieved by alternative policies . in contrast , cost - benefit analysis involves the measurement and valuation of all outcomes of interest in monetary terms . here the value for money is identified by positive net economic benefit associated with the interventions ( ie , the monetary value of the outcomes exceeds the net costs of the intervention less any costs savings achieved elsewhere ) . this paretian definition of cost - benefit analysis is the established , standard definition used within health economics . it allows a broad spectrum of outcomes ( all those of importance to the individual ) to be included within the metric , but requires the , often complex , valuation of outcomes in monetary terms . all housing intervention studies and their associated papers included in the 2009 systematic review of the health impacts of housing improvement14 were examined for reports of costs and economic analyses . details of the scope of the review ( inclusion and exclusion criteria ) , and evidence appraisal are available in the 2009 publication along with the findings of the review .14 forty - five medical and social science databases , as well as websites and grey literature were searched to identify studies of housing improvement which assessed change in any health outcome . a separate search for economic studies was not undertaken but economic studies which included health outcomes following housing improvement would have been identified in the broad search . all available data on costs and , where available , details of any economic analysis were extracted by one reviewer ( cm ) and checked by a second reviewer ( ef or ht ) . the cost data were tabulated alongside a summary of reported heath impacts and an indication of overall study quality as used in the original review ( a = minimal bias , b = some bias , c = considerable bias ) .14 where a study reported plans to undertake economic analysis , the authors were contacted for an update on progress and available data , or reasons for not completing the economic analysis . studies which only presented cost data ( table 2 ) were further examined for the potential to have conducted an economic evaluation , that is , presence of a suitable health outcome which could be linked to cost and compared to an alternative ( table 1 ) . studies which reported having undertaken an economic evaluation ( table 3 ) were examined to determine the precise form of that analysis ( table 1 ) . summary of housing improvement studies reporting cost data without economic evaluation ( ordered by intervention type , study quality and date ) * study design : rct , randomised controlled trial ; contr 'd b & a , controlled before & after ; uba , uncontrolled before & after ; xcba , controlled before & after using area level cross sectional data at both time points ; xuba , uncontrolled before & after using area level cross sectional data at both time points ; rc , retrospective controlled study ; r , retrospective uncontrolled . housing improvement studies reporting an economic evaluation ( ordered by intervention type , study quality and date ) * study design : rct , randomised controlled trial ; cba , controlled before & after ; uba , uncontrolled before & after ; rc , retrospective controlled study . * * effect direction : upward arrow , positive health impact ; downward arrow , negative health impact ; sideways arrow , no change / mixed effects / conflicting findings . sample size : final sample size ( individuals ) in intervention group : large arrow , 300 ; medium arrow , 50300 ; small arrow , 50 . statistical significance : black arrow , p 0.05 ; grey arrow , p 0.05 ; empty arrow , no statistics / data reported . the study designs varied and included five randomised controlled trials ( rcts ) , and 23 non - randomised controlled studies . the better quality rcts and controlled studies were used to draw conclusions about effectiveness . the health outcomes reported included validated measures , for example sf - 36 , and self - reported measures , and covered four main domains : general health ; mental health ; respiratory health ; and other / illness and symptoms . twenty - nine studies reported costs or an economic analysis ; 25 of these studies1641 presented only basic cost data ( table 2 ) while four studies reported having undertaken an economic analysis ( table 3 ) .4246 details of the 25 studies reporting cost data without economic analysis are presented in table 2 ( see supplementary table 1 for full details of interventions , economic data and health impacts ) . eleven of the studies examined warmth and energy efficiency interventions ,1626 eight examined rehousing or retrofitting ,2735 two focused on pre-1965 rehousing from slums4041 and four focused on provision of basic housing needs .3639 over 75 % of the studies ( n = 19 ) were from the uk ,173541 with one study each from new zealand ,16 the usa ,40 mexico ,36 philippines ,37 pakistan38 and malawi .39 the study design and methodological quality of the studies varied , as assessed by the original systematic review criteria . these studies reported a diverse range of health outcomes , and the reported impacts suggest either improvement or no change in health status following housing improvement during the study period ( see supplementary table 1 ) . one study reported a deteriorated health status following housing improvement .22 six studies242633404748 presented data on both the cost of providing the intervention and other costs , including those incurred by the recipient , nine1623283034363949 presented only costs relating to the provision of the intervention and ten studies181925272931373841 presented only other costs , primarily to the recipient . the cost measures used varied and require different interpretations . for example , some studies reported intervention costs of a major housing led regeneration programme for an area beyond the included study population , while other studies reported average costs of the specific housing intervention per household . measures used for recipient costs did not always report direct data and some studies used residents assessments of these changes , for example changes in fuel consumption or bills , making it difficult to interpret . the measures of other costs to recipients were reported , nine studies reported changes in fuel use or costs ,1719252731384748 six changes in rent ,172627314041 three changes in healthcare spending ,243338 two changes in household costs1729 and one changes in income .37 one study compared the ability to manage financially between the intervention and control group .18 drawing on the most commonly reported recipient costs , all six studies which reported numerical data for changes in fuel costs reported a reduction following energy efficiency improvements .171925263147 each of the five studies which reported numerical data for changes in rent reported increased rent following housing improvement .2627314041 of the 25 studies which presented only cost data , 11 ( 8 from the uk ) were assessed to have sufficient data for an economic evaluation . analysis linking cost data to health outcomes could have been conducted to present a cost - effectiveness , cost - utility or cost - benefit analysis ( table 2 ) .162023262830353639 two studies , both from the uk , reported plans to conduct an economic evaluation but this was either not conducted or not publicly available at the time of this review . neither of these studies was among the 11 reporting data amenable to economic evaluation ; eick et al24 did not have data for a comparator group and caldwell et al25 did not have data on intervention costs . eick et al24 presented data on medical costs before and after the intervention and reported plans for a cost - benefit analysis . caldwell et al ( 2001 ) originally planned to examine issues of cost - effectiveness but this was not undertaken due to poor quality data . two studies were from the uk4446 and two from new zealand .424350 the methodological study quality , with respect to assessment of health impacts in the original systematic review , varied ; two studies were assessed to have a minimal risk of bias ( grade a ) ,424550 one study was assessed to have some risk of bias ( grade b ) 4446 and one study was assessed to have considerable potential for bias ( grade c ) .43 three of these studies reported undertaking a cost - benefit analysis . these studies fall short of full cost - benefit analysis , as defined above , as they did not include a monetary valuation of all important outcomes . this hybrid approach involves identifying and listing the costs and benefits associated with an intervention or policy change , in much the same way as in a cost - consequence study .75152 the costs and some of the benefits are then measured in monetary units where appropriate values are either available or can be postulated , otherwise they are simply listed in their natural units ( eg , time ) . for example , a uk study44 presented cost data for medical treatments , prescriptions and fuel use and imputed a monetary benefit of reduced school absences . a study from newzealand4250 presented a benefit - cost ratio based on the cost of the intervention , changes in the costs of medical service use , and the economic value imputed for reduced co2 emissions and the reduction in lost days of school and work . another study from new zealand43 presented a feasibility study for a cost - benefit analysis with a direct benefit to cost ratio , however the authors provided no details of the methods used or the outcomes measured . the findings from all three studies suggested net economic benefits associated with the interventions based on the outcomes measured in monetary terms ( ie , the monetary value imputed for these outcomes exceeds the net costs of the intervention less any costs savings achieved elsewhere ) . in addition , both new zealand studies indicate small , but positive , benefits to cost ratios associated with the intervention .424350 one study reported undertaking a cost - effectiveness analysis which met the criteria employed by this review .45 this uk study used health indicator data ( sf - 36 ) to conduct a cost - effectiveness analysis . although data were not presented numerically ( it was narratively reported that the results were not statistically significant ) , this means that the intervention ( improved housing ) was more costly and less effective than the status quo . two further economic studies of housing interventions were identified when contacting study authors about completion of ongoing housing studies which might contribute to an update of the original housing review . these studies were published recently and were not included in the original systematic review .5354 edwards et al53 report an economic evaluation , as defined here , presenting an estimate of the additional cost per point improvement on the pedsql asthma specific scale . in addition , we are aware of the economic evaluation undertaken alongside the scottish housing and regeneration project ( submitted to jech lawson , kearns , petticrew , fenwick , investing in health : is social housing value for money ? a cost - utility analysis . ) ; however at the point at which our review was undertaken , results for this analysis were not available . details of the 25 studies reporting cost data without economic analysis are presented in table 2 ( see supplementary table 1 for full details of interventions , economic data and health impacts ) . eleven of the studies examined warmth and energy efficiency interventions ,1626 eight examined rehousing or retrofitting ,2735 two focused on pre-1965 rehousing from slums4041 and four focused on provision of basic housing needs .3639 over 75 % of the studies ( n = 19 ) were from the uk ,173541 with one study each from new zealand ,16 the usa ,40 mexico ,36 philippines ,37 pakistan38 and malawi .39 the study design and methodological quality of the studies varied , as assessed by the original systematic review criteria . these studies reported a diverse range of health outcomes , and the reported impacts suggest either improvement or no change in health status following housing improvement during the study period ( see supplementary table 1 ) . one study reported a deteriorated health status following housing improvement .22 six studies242633404748 presented data on both the cost of providing the intervention and other costs , including those incurred by the recipient , nine1623283034363949 presented only costs relating to the provision of the intervention and ten studies181925272931373841 presented only other costs , primarily to the recipient . the cost measures used varied and require different interpretations . for example , some studies reported intervention costs of a major housing led regeneration programme for an area beyond the included study population , while other studies reported average costs of the specific housing intervention per household . measures used for recipient costs did not always report direct data and some studies used residents assessments of these changes , for example changes in fuel consumption or bills , making it difficult to interpret . the measures of other costs to recipients were reported , nine studies reported changes in fuel use or costs ,1719252731384748 six changes in rent ,172627314041 three changes in healthcare spending ,243338 two changes in household costs1729 and one changes in income .37 one study compared the ability to manage financially between the intervention and control group .18 drawing on the most commonly reported recipient costs , all six studies which reported numerical data for changes in fuel costs reported a reduction following energy efficiency improvements .171925263147 each of the five studies which reported numerical data for changes in rent reported increased rent following housing improvement .2627314041 of the 25 studies which presented only cost data , 11 ( 8 from the uk ) were assessed to have sufficient data for an economic evaluation . analysis linking cost data to health outcomes could have been conducted to present a cost - effectiveness , cost - utility or cost - benefit analysis ( table 2 ) .162023262830353639 two studies , both from the uk , reported plans to conduct an economic evaluation but this was either not conducted or not publicly available at the time of this review . neither of these studies was among the 11 reporting data amenable to economic evaluation ; eick et al24 did not have data for a comparator group and caldwell et al25 did not have data on intervention costs . eick et al24 presented data on medical costs before and after the intervention and reported plans for a cost - benefit analysis . caldwell et al ( 2001 ) originally planned to examine issues of cost - effectiveness but this was not undertaken due to poor quality data . two studies were from the uk4446 and two from new zealand .424350 the methodological study quality , with respect to assessment of health impacts in the original systematic review , varied ; two studies were assessed to have a minimal risk of bias ( grade a ) ,424550 one study was assessed to have some risk of bias ( grade b ) 4446 and one study was assessed to have considerable potential for bias ( grade c ) .43 three of these studies reported undertaking a cost - benefit analysis . these studies fall short of full cost - benefit analysis , as defined above , as they did not include a monetary valuation of all important outcomes . this hybrid approach involves identifying and listing the costs and benefits associated with an intervention or policy change , in much the same way as in a cost - consequence study .75152 the costs and some of the benefits are then measured in monetary units where appropriate values are either available or can be postulated , otherwise they are simply listed in their natural units ( eg , time ) . for example , a uk study44 presented cost data for medical treatments , prescriptions and fuel use and imputed a monetary benefit of reduced school absences . a study from new zealand4250 presented a benefit - cost ratio based on the cost of the intervention , changes in the costs of medical service use , and the economic value imputed for reduced co2 emissions and the reduction in lost days of school and work . another study from new zealand43 presented a feasibility study for a cost - benefit analysis with a direct benefit to cost ratio , however the authors provided no details of the methods used or the outcomes measured . the findings from all three studies suggested net economic benefits associated with the interventions based on the outcomes measured in monetary terms ( ie , the monetary value imputed for these outcomes exceeds the net costs of the intervention less any costs savings achieved elsewhere ) . in addition , both new zealand studies indicate small , but positive , benefits to cost ratios associated with the intervention .424350 one study reported undertaking a cost - effectiveness analysis which met the criteria employed by this review .45 this uk study used health indicator data ( sf - 36 ) to conduct a cost - effectiveness analysis . although data were not presented numerically ( it was narratively reported that the results were not statistically significant ) , a bootstrapped cost - effectiveness estimate presented graphically suggested that the intervention was dominated . this means that the intervention ( improved housing ) was more costly and less effective than the status quo . two further economic studies of housing interventions were identified when contacting study authors about completion of ongoing housing studies which might contribute to an update of the original housing review . these studies were published recently and were not included in the original systematic review .5354 edwards et al53 report an economic evaluation , as defined here , presenting an estimate of the additional cost per point improvement on the pedsql asthma specific scale . in addition , we are aware of the economic evaluation undertaken alongside the scottish housing and regeneration project ( submitted to jech lawson , kearns , petticrew , fenwick , investing in health : is social housing value for money ? a cost - utility analysis . ) ; however at the point at which our review was undertaken , results for this analysis were not available . studies investigating the health impacts of housing improvement have frequently provided some details on costs or economic analysis ( n = 29/45 ) .14 however , the majority of these ( n = 25/29 ) present data on intervention and / or recipient costs only and , despite sufficient data , opportunities to conduct economic analysis have been missed . where studies report conducting economic evaluations , the majority of the reported analyses would be more accurately described as a balance sheet approach . findings from the studies which report costs only , suggest that fuel costs may reduce following provision of warmth and energy efficiency improvements , and that rents may increase following housing improvement . changes in fuel costs are largely dictated by the unit cost of fuel and may not be directly linked to changes in fuel use or levels of warmth . in addition , changes in housing costs to recipients , including rent and fuel , may be mediated by welfare provision and changes in the individual 's eligibility for welfare benefits such as housing benefit . as such , neither of these changes can necessarily be taken to indicate an improvement , or not , for the recipient of the intervention . the three studies which presented a balance - sheet approach reported a positive net economic benefit following the intervention , based on the outcomes valued in monetary terms .424450 one cost - effectiveness study45 reported that the intervention was more costly and less effective , in terms of sf - 36 score , than the status quo ,45 indicating that the intervention was not cost - effective . this may reflect the fact that mental and physical health ( measured by sf - 36 ) deteriorated following housing improvement ; or , and perhaps more likely , that the disruption during housing upgrading led to deterioration in health outcomes and the relatively short period of follow - up ( maximum of two years ) failed to capture the longer term impacts of the intervention . the longest follow - up in this group of studies was 3.5 years after the intervention ( range 1 month to 3.5 years ) . expectations that health impacts will be observed in this short timescale may be naive and it may be more realistic to hypothesise that the potential for health benefits could be many years after the intervention , perhaps only in the next generation of residents . a full economic evaluation should ideally consider the impacts over the lifetime of the intervention . however , attributing longer term impacts to a historical intervention , even in large scale datasets with minimal attrition , introduces an additional level of confounding . immeasurable confounding is an important issue even for short term studies . as such , data on longer term health impacts may be useful but requires careful interpretation .55 the near absence of economic evaluation of housing improvementscan not solely be explained by difficulties in collecting suitable data . over 40 % of the studies which presented cost data alone , had sufficient data to conduct an economic evaluation , but had not done so . this comparative data on costs and health outcome for the intervention and status quo could have been presented to provide a measure of value for money of the intervention , for example in terms of the additional cost per unit of effectiveness achieved . the specific form of the evaluation would depend on the measure of health outcome collected with data such as sf - 36 , eq - 5d , etc used to determine qalys for a cost - utility analysis , monetary values of health outcome used within a cost - benefit analysis and other measures of health / clinical outcome used within a cost - effectiveness analysis ( see table 1 ) . where economic analysis was conducted , most ( n = 3/4 ) of the studies claimed to have undertaken a cost - benefit analysis but had in fact presented a balance sheet approach . this hybrid approach can be helpful for policy - makers by identifying the costs and outcomes associated with a policy / intervention and who bears / receives these impacts .751 in each of these three studies , the authors calculated the net economic benefits associated with the interventions of interest , as required to establish value for money in a full cost - benefit analysis . however , none of these studies included changes to health outcomes within the benefits assessment in their calculation , despite all three collecting data on health outcomes . as such , none of these studies provides a full monetary assessment of the benefits associated with the interventions of interest . instead the economic benefits calculation was restricted to a monetary valuation for increased school and / or work attendance and reductions in co2 emissions . all three included changes in health service utilisation within the calculation , although these cost changes were frequently misreported as benefits . first , the importance of and need for collecting data over a reasonable period of follow - up to allow detection of long term health improvements . second , the importance of employing wider perspectives through inclusion of costs and savings in other sectors ( eg , education or the environment ) to give greater potential to show cost offsets and / or cost - effectiveness of housing interventions . third , and perhaps most importantly , a lack of familiarity with the techniques of economic evaluation such that studies with relevant data often fail to make best use of it , while other studies fail to collect relevant data or misrepresent analyses that are undertaken . rigorous economic evaluation of public health interventions , including those in housing , is seen as a priority . future studies planning an economic evaluation need to make best use of all available data as well as ensuring that all relevant data are collected . to facilitate this , economic evaluations should be planned alongside the intervention with health economists included from the outset . when undertaken appropriately , economic evaluation provides the potential to make a significant contribution to healthy housing policy . economic evaluation assessing the costs and health benefits of healthy public policy interventions has been advocated but has rarely been undertaken . housing investment represents a substantial policy investment area which is considered to have potential to contribute to a wider public health strategy to improve population health and reduce health inequalities . some studies assessing the health impact of housing improvement have reported some data on costs and economic analysis . examination of the nature of cost data and economic analysis reported in these studies may help to explain why economic evaluation has rarely been conducted and provide tangible examples of the potential to develop economic evaluation of healthy public policy investment . despite availability of cost data , opportunities to conduct economic evaluations of housing interventionsa small number of studies have reported economic evaluation but the term has often been misappropriated . future studies planning an economic evaluation should ensure that it is planned alongside the intervention to ensure that all relevant data are collected and available data are fully utilised . increasingly policy - makers , seeking to spend money from limited budgets , want evidence of value for money associated with changes in public policy . appropriately conducted economic evaluations have the potential to identify public policies which represent good value for money . existing economic analyses of the health impacts of housing improvement have often fallen short of undertaking economic evaluations . improved planning and better use of available datashould ensure that economic evaluations are undertaken which can provide policy - makers with the evidence they require .\noutput:\n" }, { "from": "agent", "value": "backgroundeconomic evaluation of public policies has been advocated but rarely performed . studies from a systematic review of the health impacts of housing improvement included data on costs and some economic analysis . examination of these data provides an opportunity to explore the difficulties and the potential for economic evaluation of housing.methodsdata were extracted from all studies included in the systematic review of housing improvement which had reported costs and economic analysis ( n = 29/45 ) . the reported data were assessed for their suitability to economic evaluation . where an economic analysis was reported the analysis was described according to pre - set definitions of various types of economic analysis used in the field of health economics.results25 studies reported cost data on the intervention and / or benefits to the recipients . of these , 11 studies reported data which was considered amenable to economic evaluation . a further four studies reported conducting an economic evaluation . three of these studies presented a hybrid balance sheet approach and indicated a net economic benefit associated with the intervention . one cost - effectiveness evaluation was identified but the data were unclearly reported ; the cost - effectiveness plane suggested that the intervention was more costly and less effective than the status quo.conclusionsfuture studies planning an economic evaluation need to ( i ) make best use of available data and ( ii ) ensure that all relevant data are collected . to facilitate this , economic evaluations should be planned alongside the intervention with input from health economists from the outset of the study . when undertaken appropriately , economic evaluation provides the potential to make significant contributions to housing policy ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: we have reported a 78 year old man with complaint of abdominal pain and vomiting . in patientspreoperative evaluation for surgical management of an intra - abdominal mass , a large intracardiac mass has found incidentally during the echocardiography . pathologic biopsy of right atrial mass that has removed by open heart surgery shown : non hodgkin - b cell lymphoma . the patient has treated by chop chemotherapy regiment successfully and after completion of treatment , there was complete response . gross tumor formation in any of the cardiac chambers has been rare , particularly at the time of presentation and diagnosis of lymphoma ( 2 ) . symptoms were usually very subtle and non - specific , particularly in the setting of co - existing comorbidities ( 3 ) . as imaging modalities and treatment options for lymphoma have improved , more unusual disease presentation might be observed more frequently . in this articlewe have reported a 78 - year - old man with an incidental large cardiac mass whose symptoms was abdominal pain and vomiting in the setting of pre - operative evaluation for surgical management of intra - abdominal mass . a 78 - year - old man has affected by abdominal pain , vomiting and weakness and has evaluated at june 2013 . studying his medical history , he had hip joint replacement surgery , then in initial physical examination has shown no significant finding , except a few tenderness on the middle abdominal quadrant . in laboratory assessment , complete blood count , renal function tests - alkaline phosphatase and lactate dehydrogenase were normal , but hemoglobin and transaminases were abnormal as follows : hb = 9.1 mg / dl , ast = 71 u / lit , alt = 656 u / lit . in abdominal ct scan , there was a 7161 mm mass at the aortic bifurcation in favor of tumoral lesion or adenopathy . ecg had no significant and specific changes and in echocardiography , a large mass with diameter of 7460 mm has seen in right atrium ( figure 1 ) and lv ejection fraction was 65 % . also , in thoracic sections of ct scan , an intra - cardiac mass has seen ( figure 2 ) . bases on these new findings management of the patient has changed to cardiac surgery and open heart surgery has recommended and performed at august 2013 . pathologic examination of removed cardiac mass has reported as below after immunohistochemistry study : hmb 45 and ck : negative ; cd20 : positive . compatible with non - hodgkin lymphoma in favor of b - cell origin ( figures 3 and 4 ) . he has referred to oncologist after recovery of heart surgery ( september 2013 ) . in evaluation of medical history and further physical examination , he had no history of fever and sweating , but weight loss of 2 - 3 kg during recent weeks . karnowsky performance status was 80 % . at physical examination , he had an adenopathy of 21 cm at left jugulodigastric chain , and the another of 31 cm at left supraclavicular area and physical exam was normal otherwise . in bone marrow biopsy , the patient has planned to treat by r - chop chemotherapy regimen ( rituximab - cyclophosphamide - doxorubicin - vincristine - prednisolone ) . he could not provide rituximab due to economic problems , therefor he has received only chop regimen . after first cycle of treatment , cervical adenopathies have disappeared and at the end of seventh cycle , imaging of the neck , chest and abdominopelvic cavity by ct scan had no positive finding of disease but the patient has not satisfied to undergo bm biopsy for second time . patient treatment has completed after eight cycles of chop chemotherapy regimen at february 2014 , but he was in good condition , without any evidences of disease after six months of follow up . cardiac masses have been arising from the heart or pericardium , were potentially lethal whether defined as benign or malignant . metastatic deposits have represented the vast majority of cardiac malignancies ; the common primary malignancies sources have included cancers of lung , esophagus and breast as well as lymphoma , leukemia and melanoma ( 5 ) . cardiac involvement as an initial presentation of malignant lymphoma was a rare occurrence ( 2 ) . secondary involvement of the heart has seen in 8.7 - 27.2 % of documented clinical case of lymphoma ( 2 , 6 , 7 ) . despite its life - threatening nature ( 8 ) , the cardiac manifestations of lymphomatous involvement of the heartthese symptoms and signs might include arrhythmias , pericardial effusion or tamponade , tumor embolization and obstruction of blood flow and valvular dysfunction . these symptoms have related on tumor location , size , growth rate , degree of invasion and friability . in the present case and many other reports the majority of intracavital tumors have occurred on the right site of the heart , the reason for which has yet been to be found ( 1 , 11 ) . plain chest radiographs lack sensitivity and specificity as an initial diagnostic tool but could demonstrate cardiomegaly or specific chamber enlargement . echocardiography was the first non - invasive study for examining the chambers of the heart and pericardium ( 12 ) but trans esophageal echocardiography ( tee ) was a more sensitive technique for assessing patients ( 13 ) . ct scan and mri with gadolinium contrast injection were useful tools for demonstrating morphology , location , extension of disease , blood flow and cardiac function ( 14 , 15 ) . fdg - pet imaging has recently reported to reveal previously unsuspected cardiac involvement ( 16 , 17 ) . although traditionally this has required a thoracostomy , less invasive procedures has recently been available such as tee - guided biopsy , endomyocardial biopsy , or percutaneous intracardiac biopsy with combined fluoroscopy and tee or pericardial fluid sampling ( 18 , 19 ) . the available literature suggested systemic chemotherapy was the only effective therapy ( 18 ) and the majority of cases have treated with combination chemotherapy with varying results ( 20 , 21 ) . there was an improvement in response and survival rates by adding of monoclonal therapies to chemotherapy ( 22 ) . radiation therapy has indicated in cardiac mass that progresses despite chemotherapy and its adverse side effects have been pericarditis , cardiomyopathy , diastolic dysfunction , conduction defects and coronary artery disease . cardiac involvement was rare as an initial presentation of malignant lymphoma and has often been subclinical . these tumors have seen more common in the right site of the heart and tee , ct scan and mri with gd were effective tools in assessment of patients . pathologic diagnosis would be essential to management of cardiac masses and the only effective treatment has been chemotherapy .\noutput:\n" }, { "from": "agent", "value": "introduction : cardiac involvement as an initial presentation of malignant lymphoma has been a rare occurrence.case presentation : we have reported a 78 year old man with complaint of abdominal pain and vomiting . in patients preoperative evaluation for surgical management of an intra - abdominal mass , a large intracardiac mass has found incidentally during the echocardiography . pathologic biopsy of right atrial mass that has removed by open heart surgery shown : non hodgkin - b cell lymphoma . bone marrow biopsy was taken and was positive for lymphomatous involvement.conclusions : the patient has treated by chop chemotherapy regiment successfully and after completion of treatment , there was complete response ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: marchiafava - bignami disease ( mbd ) is a rare neurological complication of chronic alcoholism , pathologically characterized by callosal lesions consisting of demyelination and necrosis . recently , mri findings of the callosal and cortical lesions in the acute and chronic stages have been investigated ; however , the evolution of these lesions is still unknown . we present serial changes of callosal and cortical lesions on mri in an acute state in a case with severe mbd . a 55 - year - old man with a long history of alcohol abuse ( japanese liquor , shochu distilled from barley ) was found by his neighbor lying on the floor , losing consciousness after groaning loudly . physical examination on admission revealed a body temperature of 36.7 c , a blood pressure of 198/117 mm hg and a heart rate of 134 beats / min . neurological examination revealed a stuporous state , coarse horizontal nystagmus and positive plantar reflexes on both sides . laboratory tests showed increased total bilirubin ( 2.0 mg / dl ; normal 1.2 mg / dl ) and gamma - glutamyl transpeptidase ( 143were normal , and the level of vitamin b1 was 20 ng / ml ( normal 19 ng / ml ) . mri taken on admission revealed a high intensity area on fluid - attenuated inversion recovery ( flair ) images in the genu of the corpus callosum and in the frontoparietal cortex ( fig . diffusion - weighted mri imaging ( dwi ) showed an abnormal signal only in the cortex . a follow - up mri taken 30 h after admission newly revealed hyperintensity in the splenium on a flair image ( fig . on the basis of the clinical history and characteristic mri findings , we diagnosed the patient as having mbd and started administration of thiamine and other vitamins of the b complex before the second mri . the patient was given 1,000 mg / day thiamine intravenously for 2 weeks and 200 mg / day thiamine for the next 5 weeks , but he did not show recovery and was discharged 7 weeks after onset . as he was in a persistent stuporous state with severe cognitive decline , neuropsychological signs , including disconnection syndromes , could not be evaluated . mri taken 45 days after admission showed cystic necrosis in the central layer of the genu and linear necrosis in the splenium on flair images ( fig . chronic alcoholism and acute consciousness disturbance following a suspected seizure , along with characteristic lesions of the corpus callosum , confirmed the diagnosis of mbd in our patient . the serial mri findings in the acute state in our patient disclosed progression of the callosal lesions in mbd : the first mri revealed a hyperintense lesion in the genu on flair images , and the follow - up mri revealed a new hyperintense lesion in the splenium of the corpus callosum . it has been reported that the first change on mri is diffuse swelling of the corpus callosum , followed by a genu lesion , and finally by a splenium lesion . the mode of progression of the callosal lesion in our patient was in accordance with the reports , except for a lack of diffuse swelling of the corpus callosum . the first mri change in the genu of the corpus callosum was not associated with an apparent change in diffusion on dwi , and hyperintense signals on dwi appeared in the lesion 30 h after the first mri . these findings suggest that the initial change in the corpus callosum was partly vasogenic edema and that the lesion was then converted into cytotoxic edema . the necrotic lesions in the corpus callosum in the chronic stage in our patient confirm the cytotoxic process . it has been suggested that cortical lesions on mri are occasionally associated with mbd , especially in cases with poor prognosis and severe cognitive decline ; our patient also had a poor prognosis . cortical lesions have frequently been found in pathological studies in mbd and have been speculated to have morel 's laminar sclerosis as their pathology . the cortical lesions already existed when the initial vasogenic changes appeared in the genu of the callosum in our patient , which suggests that they resulted from the primary pathological process induced by alcoholic intoxication and malnutrition in mbd . in conclusion , the serial mri findings in the acute stage of mbd demonstrate that the callosal lesions progress from the genu to the splenium , and that the cortical lesions appear at the initial stage of the pathological process in mbd .\noutput:\n" }, { "from": "agent", "value": "we report on serial mri findings of cerebral lesions in a 55 - year - old man with severe marchiafava - bignami disease ( mbd ) . the first mri change on fluid - attenuated inversion recovery images was hyperintensity in the genu of the corpus callosum and in the frontoparietal cortex . following this change , a splenial lesion appeared . the first mri change in the genu of the corpus callosum was not associated with a change in diffusion on diffusion - weighted mri imaging , suggesting a pathological change involving vasogenic edema . development of cortical lesions in the initial stage confirms that cortical lesions result from the primary pathogenetic process induced by alcoholic intoxication and malnutrition in mbd ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the evidence in evidence - based medicine might be based on scientific principles and not exclusively on probability - based statistics . although probability - based statistics has a role in the evidence structure of clinical epidemiology , it need not dominate the evidence structure of medical practice . the hard - won principles of pathophysiology developed by clinical medicine and laboratory research constitute the core principles of medical evidence . probability - based statistics now masquerades as the foundation of medical research , but clinical decisions are made with regard to the individual patient , who is a unique microcosm of physiologic , genetic , and biochemical processes . evidence - based medicine must be liberated from bondage to probability - based statistics , which is founded on the notion of chance and random processes , and instead become established on the determinate processes of molecular biology , based on the universal principles of biological science . the current bondage of evidence - based medicine to probability - based statistics has led to a mindset on the part of the physician that leads to the misapplication of statistics to the diagnosis and treatment of the individual patient and to the definition of standard of care . the diagnosis and treatment of stroke traditionally have been based on the principles of pathophysiology , biology , histology , anatomy , neuropharmacology , and individual patient context . medical education requires a foundation in these basic sciences , because the physician s perception regarding the disease process unfolding before him / her depends on the individual features of that one patient he / she is engaging . principles of these basic disciplines apply to the clinical behavior of the patient s disease and healing process . the changing state of the patient demands active monitoring and an adaptive response from the physician ; it is a dynamic process of interaction . probability - based evidence - based medicine demands the physician s detachment from the dynamic principles of the disease and healing process , and thus from the individual patient , because the physician is required to apply statistical findings from population - based clinical trials to the diagnosis and treatment of each patient with stroke . the diagnosis and treatment of stroke traditionallyhave been based on the principles of pathophysiology , biology , histology , anatomy , neuropharmacology , and individual patient context . medical education requires a foundation in these basic sciences , because the physician s perception regarding the disease process unfolding before him / her depends on the individual features of that one patient he / she is engaging . principles of these basic disciplines apply to the clinical behavior of the patient s disease and healing process . the changing state of the patient demands active monitoring and an adaptive response from the physician ; it is a dynamic process of interaction . probability - based evidence - based medicine demands the physician s detachment from the dynamic principles of the disease and healing process , and thus from the individual patient , because the physician is required to apply statistical findings from population - based clinical trials to the diagnosis and treatment of each patient with stroke . when a physician is faced with a patient in the throes of an acute stroke , the situation is dynamic . the principles of virchow s triad suggest a continuum of vascular integrity . currently , there is a classification of stroke diagnosis that conforms to the binary logic of probability , requiring a rounding off of diagnosis to the ischemic or the hemorrhagic type in order to generalize the situation to facts that can be applied to any group of stroke patients.these generalized categories of patients are the object of large clinical trials . it is at the bedside where evidence - based medicine founded on these trials is now practiced . to apply any scientific ( statistical probability ) result from these trials , the physician must round the patient off , regardless of his / her specifics , to one of the categories.the most common questions asked of any treatment choice or diagnosis in this context are , what is the most common thing that could be wrong with the patient ? and in how many patients does this or that treatment work ? the answers to these questions become the diagnosis and treatment choices.the science of clinical trials is based on probability theory . clinical guidelines for evidence - based medicinethe intended result is a statistical approach to medicine.when a physician is faced with a patient , he / she has the notion that the patient has a diagnosis of x with probability 0.3 ( for example ) , a number pulled from a large clinical trial . because of this probability - based approach to diagnosis , the physician imagines 10 hypothetical patients in front of him / her , one of whom is the indicated real patient . thus , he / she says that given the probability of diagnosis x , seven of the hypothetical patients in our example do not have x and three must have x. he / she considers it his / her duty to guess or bet which one of the hypothetical patients matches the real patient . the guess is a conclusion based on what most patients must have according to the probabilities . taking a bet or chance on being right is justified because of the basic belief in a random universe in which truth is not based on principle but on statistical probability.the clinical consequence of betting on the match between the patient and the known statistics , once this matching occurs , is that the tendency to go further with diagnostic testing to refute or confirm the diagnosis or to search for other diagnoses becomes more difficult to justify because the scientific basis for all medical decisions is the known probabilities . thus , the probability - based mindset of the physician who must practice probability - based evidence - based medicine turns the one - on - one patientphysician interface into an imaginary , but false , statistical situation.the application of statistics to the individual , unique patient becomes necessary only because of and through probability theory . when a physician is faced with a patient in the throes of an acute stroke , the situation is dynamic . the principles of virchow s triad suggest a continuum of vascular integrity . currently , there is a classification of stroke diagnosis that conforms to the binary logic of probability , requiring a rounding off of diagnosis to the ischemic or the hemorrhagic type in order to generalize the situation to facts that can be applied to any group of stroke patients . it is at the bedside where evidence - based medicine founded on these trials is now practiced . to apply any scientific ( statistical probability ) result from these trials , the physician must round the patient off , regardless of his / her specifics , to one of the categories . the most common questions asked of any treatment choice or diagnosis in this context are , what is the most common thing that could be wrong with the patient ? and in how many patientsclinical guidelines for evidence - based medicine require the physician to reason from a probability standpoint . when a physician is faced with a patient , he / she has the notion that the patient has a diagnosis of x with probability 0.3 ( for example ) , a number pulled from a large clinical trial . because of this probability - based approach to diagnosis , the physician imagines 10 hypothetical patients in front of him / her , one of whom is the indicated real patient . thus , he / she says that given the probability of diagnosis x , seven of the hypothetical patients in our example do not have x and three must have x. he / she considers it his / her duty to guess or bet which one of the hypothetical patients matches the real patient . the guess is a conclusion based on what most patients must have according to the probabilities . taking a bet or chance on being right is justified because of the basic belief in a random universe in which truth is not based on principle but on statistical probability . the clinical consequence of betting on the match between the patient and the known statistics , once this matching occurs , is that the tendency to go further with diagnostic testing to refute or confirm the diagnosis or to search for other diagnoses becomes more difficult to justify because the scientific basis for all medical decisions is the known probabilities . thus , the probability - based mindset of the physician who must practice probability - based evidence - based medicine turns the one - on - one patient physician interface into an imaginary , but false , statistical situation . the application of statistics to the individual , unique patient becomes necessary only because of and through probability theory . if one abandons the requirement of probabilities , then it is not necessary to apply statistics to the clinical encounter . the physician is free to think about the clinical situation in terms of principles of basic science , physiology , biology , chemistry , pharmacology , anatomy , and pathology.the principles of these basic sciences are the cornerstones of diagnosis and treatment of the individual patient . each physician has his / her perception of their dynamic in any single patient . because their interaction is ever changing , the physician perceives new interactions and can discover what is specific and special to that patient . no probabilities are necessary , because each process can be measured as a clinical impression , by constant monitoring , and by laboratory results . the bedside question is , what is the process , disease dynamic , and specifics that apply to this patient ? although each of these elements applies to any patient to a certain degree , any individual patient has the opportunity to have his / her unique clinical situation properly diagnosed and appropriately treated . if one abandons the requirement of probabilities , then it is not necessary to apply statistics to the clinical encounter . the physician is free to think about the clinical situation in terms of principles of basic science , physiology , biology , chemistry , pharmacology , anatomy , and pathology . the principles of these basic sciences are the cornerstones of diagnosis and treatment of the individual patient . because their interaction is ever changing , the physician perceives new interactions and can discover what is specific and special to that patient . no probabilities are necessary , because each process can be measured as a clinical impression , by constant monitoring , and by laboratory results . the bedside question is , what is the process , disease dynamic , and specifics that apply to this patient ? although each of these elements applies to any patient to a certain degree , any individual patient has the opportunity to have his / her unique clinical situation properly diagnosed and appropriately treated . the previously reported incidence of an unusual cause , pheochromocytoma , is a small percentage . the statistical mindset bases this patient s diagnosis on prior probabilities that the patient has pheochromocytoma . this leads to a tendency not to test for this condition , as the probability is less than 0.5 . that is , there is a 51 % percent chance the patient does not have pheochromocytomascience - based medicine of probability - based statistical medicine , evidence - based medicine based on probabilities.probability theory reinforces the physician s tendency to think in terms of legal liability and to use the legal formulamore likely than not or 51 % probability regarding the correctness of his / her judgment rather than asking what is actually wrong with this patient and applying physiologic principles . probability - based thinking also leads to the excessive ordering of unnecessary tests rather than ordering the correct tests required by physiology - based thinking . the decision not to order frivolous tests is based on the confidence that comes with physiology - based thinking . intimate knowledge of neuroanatomy and neurophysiology is the only source of confidence that can safeguard the neurologist against the urge to order frivolous tests but also gives him / her the confidence to request tests that may be relatively arcane and experimental when necessary . the solution to the malpractice crisis lies in emphasizing physiology - based thinking at both the medical and legal levels of understanding and freeing both areas from relying on the 18th century mathematical model of probability - based statistics . the previously reported incidence of an unusual cause , pheochromocytoma , is a small percentage . the statistical mindset bases this patient s diagnosis on prior probabilities that the patient has pheochromocytoma . this leads to a tendency not to test for this condition , as the probability is less than 0.5 . that is , there is a 51 % percent chance the patient does not have pheochromocytomahe / she is off the hook because he / she has practiced science - based medicine of probability - based statistical medicine , evidence - based medicine based on probabilities . probability theory reinforces the physician s tendency to think in terms of legal liability and to use the legal formulamore likely than not or 51 % probability regarding the correctness of his / her judgment rather than asking what is actually wrong with this patient and applying physiologic principles . probability - based thinking also leads to the excessive ordering of unnecessary tests rather than ordering the correct tests required by physiology - based thinking . the decision not to order frivolous tests is based on the confidence that comes with physiology - based thinking . intimate knowledge of neuroanatomy and neurophysiology is the only source of confidence that can safeguard the neurologist against the urge to order frivolous tests but also gives him / her the confidence to request tests that may be relatively arcane and experimental when necessary . the solution to the malpractice crisis lies in emphasizing physiology - based thinking at both the medical and legal levels of understanding and freeing both areas from relying on the 18th century mathematical model of probability - based statistics . the requirement of evidence - based medicine to apply probabilities to the individual patient leads necessarily to underdiagnosis , undertreatment , and missed diagnoses . the word evidence implies truth , but once the false image of a statistical situation is applied to an individual clinical situation , truth has been abandoned . independent , knowledgeable , principled diagnosis and treatment are required for each patient because the physician s expertise and the patient s specific disease state are what bring that patient to that physician in a unique , historical moment . the requirement of evidence - based medicine to apply probabilities to the individual patient leads necessarily to underdiagnosis , undertreatment , and missed diagnoses . the word evidence implies truth , but once the false image of a statistical situation is applied to an individual clinical situation , truth has been abandoned . independent , knowledgeable , principled diagnosis and treatment are required for each patient because the physician s expertise and the patient s specific disease state are what bring that patient to that physician in a unique , historical moment . when a physician is faced with a patient in the throes of an acute stroke , the situation is dynamic . the principles of virchow s triad suggest a continuum of vascular integrity . currently , there is a classification of stroke diagnosis that conforms to the binary logic of probability , requiring a rounding off of diagnosis to the ischemic or the hemorrhagic type in order to generalize the situation to facts that can be applied to any group of stroke patients.these generalized categories of patients are the object of large clinical trials . it is at the bedside where evidence - based medicine founded on these trials is now practiced . to apply any scientific ( statistical probability ) result from these trials , the physician must round the patient off , regardless of his / her specifics , to one of the categories.the most common questions asked of any treatment choice or diagnosis in this context are , what is the most common thing that could be wrong with the patient ? and in how many patients does this or that treatment work ? the answers to these questions become the diagnosis and treatment choices.the science of clinical trials is based on probability theory . clinical guidelines for evidence - based medicine require the physician to reason from a probability standpoint . the intended result is a statistical approach to medicine.when a physician is faced with a patient , he / she has the notion that the patient has a diagnosis of x with probability 0.3 ( for example ) , a number pulled from a large clinical trial . because of this probability - based approach to diagnosis , the physician imagines 10 hypothetical patients in front of him / her , one of whom is the indicated real patient . thus , he / she says that given the probability of diagnosis x , seven of the hypothetical patients in our example do not have x and three must have x. he / she considers it his / her duty to guess or bet which one of the hypothetical patients matches the real patient . the guess is a conclusion based on what most patients must have according to the probabilities . taking a bet or chance on being right is justified because of the basic belief in a random universe in which truth is not based on principle but on statistical probability.the clinical consequence of betting on the match between the patient and the known statistics , once this matching occurs , is that the tendency to go further with diagnostic testing to refute or confirm the diagnosis or to search for other diagnoses becomes more difficult to justify because the scientific basis for all medical decisions is the known probabilities . thus , the probability - based mindset of the physician who must practice probability - based evidence - based medicine turns the one - on - one patient physician interface into an imaginary , but false , statistical situation.the application of statistics to the individual , unique patient becomes necessary only because of and through probability theory . when a physician is faced with a patient in the throes of an acute stroke , currently , there is a classification of stroke diagnosis that conforms to the binary logic of probability , requiring a rounding off of diagnosis to the ischemic or the hemorrhagic type in order to generalize the situation to facts that can be applied to any group of stroke patients . these generalized categories of patients are the object of large clinical trials . it is at the bedside where evidence - based medicine founded on these trials is now practiced . to apply any scientific ( statistical probability ) result from these trials , the physician must round the patient off , regardless of his / her specifics , to one of the categories . the most common questions asked of any treatment choice or diagnosis in this context are , what is the most common thing that could be wrong with the patient ? and in how many patientsclinical guidelines for evidence - based medicine require the physician to reason from a probability standpoint . when a physician is faced with a patient , he / she has the notion that the patient has a diagnosis of x with probability 0.3 ( for example ) , a number pulled from a large clinical trial . because of this probability - based approach to diagnosis , the physician imagines 10 hypothetical patients in front of him / her , one of whom is the indicated real patient . thus , he / she says that given the probability of diagnosis x , seven of the hypothetical patients in our example do not have x and three must have x. he / she considers it his / her duty to guess or bet which one of the hypothetical patients matches the real patient . the guess is a conclusion based on what most patients must have according to the probabilities . taking a bet or chance on being right is justified because of the basic belief in a random universe in which truth is not based on principle but on statistical probability . the clinical consequence of betting on the match between the patient and the known statistics , once this matching occurs , is that the tendency to go further with diagnostic testing to refute or confirm the diagnosis or to search for other diagnoses becomes more difficult to justify because the scientific basis for all medical decisions is the known probabilities . thus , the probability - based mindset of the physician who must practice probability - based evidence - based medicine turns the one - on - one patient physician interface into an imaginary , but false , statistical situation . the application of statistics to the individual , unique patient becomes necessary only because of and through probability theory . if one abandons the requirement of probabilities , then it is not necessary to apply statistics to the clinical encounter . the physician is free to think about the clinical situation in terms of principles of basic science , physiology , biology , chemistry , pharmacology , anatomy , and pathology.the principles of these basic sciences are the cornerstones of diagnosis and treatment of the individual patient . each physician has his / her perception of their dynamic in any single patient . because their interaction is ever changing , the physician perceives new interactions and can discover what is specific and special to that patient . no probabilities are necessary , because each process can be measured as a clinical impression , by constant monitoring , and by laboratory results . the bedside question is , what is the process , disease dynamic , and specifics that apply to this patient ? although each of these elements applies to any patient to a certain degree , any individual patient has the opportunity to have his / her unique clinical situation properly diagnosed and appropriately treated . if one abandons the requirement of probabilities , then it is not necessary to apply statistics to the clinical encounter . the physician is free to think about the clinical situation in terms of principles of basic science , physiology , biology , chemistry , pharmacology , anatomy , and pathology . the principles of these basic sciences are the cornerstones of diagnosis and treatment of the individual patient . each physician has his / her perception of their dynamic in any single patient . because their interaction is ever changing , the physician perceives new interactions and can discover what is specific and special to that patient . no probabilities are necessary , because each process can be measured as a clinical impression , by constant monitoring , and by laboratory results . the bedside question is , what is the process , disease dynamic , and specifics that apply to this patient ? although each of these elements applies to any patient to a certain degree , any individual patient has the opportunity to have his / her unique clinical situation properly diagnosed and appropriately treated . the previously reported incidence of an unusual cause , pheochromocytoma , is a small percentage . the statistical mindset bases this patient s diagnosis on prior probabilities that the patient has pheochromocytoma . this leads to a tendency not to test for this condition , as the probability is less than 0.5 . that is , there is a 51 % percent chance the patient does not have pheochromocytomascience - based medicine of probability - based statistical medicine , evidence - based medicine based on probabilities.probability theory reinforces the physician s tendency to think in terms of legal liability and to use the legal formulamore likely than not or 51 % probability regarding the correctness of his / her judgment rather than asking what is actually wrong with this patient and applying physiologic principles . probability - based thinking also leads to the excessive ordering of unnecessary tests rather than ordering the correct tests required by physiology - based thinking . the decision not to order frivolous tests is based on the confidence that comes with physiology - based thinking . intimate knowledge of neuroanatomy and neurophysiology is the only source of confidence that can safeguard the neurologist against the urge to order frivolous tests but also gives him / her the confidence to request tests that may be relatively arcane and experimental when necessary . the solution to the malpractice crisis lies in emphasizing physiology - based thinking at both the medical and legal levels of understanding and freeing both areas from relying on the 18th century mathematical model of probability - based statistics . the previously reported incidence of an unusual cause , pheochromocytoma , is a small percentage . the statistical mindset bases this patient s diagnosis on prior probabilities that the patient has pheochromocytoma . this leads to a tendency not to test for this condition , as the probability is less than 0.5 . that is , there is a 51 % percent chance the patient does not have pheochromocytomahe / she is off the hook because he / she has practiced science - based medicine of probability - based statistical medicine , evidence - based medicine based on probabilities . probability theory reinforces the physician s tendency to think in terms of legal liability and to use the legal formulamore likely than not or 51 % probability regarding the correctness of his / her judgment rather than asking what is actually wrong with this patient and applying physiologic principles . probability - based thinking also leads to the excessive ordering of unnecessary tests rather than ordering the correct tests required by physiology - based thinking . the decision not to order frivolous tests is based on the confidence that comes with physiology - based thinking . intimate knowledge of neuroanatomy and neurophysiology is the only source of confidence that can safeguard the neurologist against the urge to order frivolous tests but also gives him / her the confidence to request tests that may be relatively arcane and experimental when necessary . the solution to the malpractice crisis lies in emphasizing physiology - based thinking at both the medical and legal levels of understanding and freeing both areas from relying on the 18th century mathematical model of probability - based statistics . the previously reported incidence of an unusual cause , pheochromocytoma , is a small percentage . the statistical mindset bases this patient s diagnosis on prior probabilities that the patient has pheochromocytoma . this leads to a tendency not to test for this condition , as the probability is less than 0.5 . that is , there is a 51 % percent chance the patient does not have pheochromocytomascience - based medicine of probability - based statistical medicine , evidence - based medicine based on probabilities.probability theory reinforces the physician s tendency to think in terms of legal liability and to use the legal formulamore likely than not or 51 % probability regarding the correctness of his / her judgment rather than asking what is actually wrong with this patient and applying physiologic principles . probability - based thinking also leads to the excessive ordering of unnecessary tests rather than ordering the correct tests required by physiology - based thinking . the decision not to order frivolous tests is based on the confidence that comes with physiology - based thinking . intimate knowledge of neuroanatomy and neurophysiology is the only source of confidence that can safeguard the neurologist against the urge to order frivolous tests but also gives him / her the confidence to request tests that may be relatively arcane and experimental when necessary . the solution to the malpractice crisis lies in emphasizing physiology - based thinking at both the medical and legal levels of understanding and freeing both areas from relying on the 18th century mathematical model of probability - based statistics . the previously reported incidence of an unusual cause , pheochromocytoma , is a small percentage . the statistical mindset bases this patient s diagnosis on prior probabilities that the patient has pheochromocytoma . this leads to a tendency not to test for this condition , as the probability is less than 0.5 . that is , there is a 51 % percent chance the patient does not have pheochromocytomascience - based medicine of probability - based statistical medicine , evidence - based medicine based on probabilities . probability theory reinforces the physician s tendency to think in terms of legal liability and to use the legal formula more likely than not or 51 % probability regarding the correctness of his / her judgment rather than asking what is actually wrong with this patient and applying physiologic principles . probability - based thinking also leads to the excessive ordering of unnecessary tests rather than ordering the correct tests required by physiology - based thinking . the decision not to order frivolous tests is based on the confidence that comes with physiology - based thinking . intimate knowledge of neuroanatomy and neurophysiology is the only source of confidence that can safeguard the neurologist against the urge to order frivolous tests but also gives him / her the confidence to request tests that may be relatively arcane and experimental when necessary . the solution to the malpractice crisis lies in emphasizing physiology - based thinking at both the medical and legal levels of understanding and freeing both areas from relying on the 18th century mathematical model of probability - based statistics . the requirement of evidence - based medicine to apply probabilities to the individual patient leads necessarily to underdiagnosis , undertreatment , and missed diagnoses . the word evidence implies truth , but once the false image of a statistical situation is applied to an individual clinical situation , truth has been abandoned . independent , knowledgeable , principled diagnosis and treatmentare required for each patient because the physician s expertise and the patient s specific disease state are what bring that patient to that physician in a unique , historical moment . the requirement of evidence - based medicine to apply probabilities to the individual patient leads necessarily to underdiagnosis , undertreatment , and missed diagnoses . the word evidence implies truth , but once the false image of a statistical situation is applied to an individual clinical situation , truth has been abandoned . independent , knowledgeable , principled diagnosis and treatment are required for each patient because the physician s expertise and the patient s specific disease state are what bring that patient to that physician in a unique , historical moment .\noutput:\n" }, { "from": "agent", "value": "opinion statementmedical science is now synonymous with probability - based statistics . statistics deals with a group ; it does not need probability theory . probability theory is consistent with the worldview that the universe is infinite , bounded , random , and governed by chance . its logic is binary , its geometry is cartesian , its rules offer a scientific method by which hypotheses may be tested . clinical trials and even hypothesis testing at the bedside have nestled into the probability foundation . as a result , scientific evidence now appears only through the lens of probability theory . because there is no definitive truth in the worldview of probability theory , the truth of evidence lies in probabilities only . the probabilistic view of science has a firm impact on the practice of medicine and implications for medical legal decisions ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: bacterial biofilm refers to aggregates of microorganisms embedded in a self - made protective matrix of exopolymers . the bacteria within the biofilms are resistant to antibiotics ; in some cases , the resistance may increase a thousand fold .1 therefore , conventional antibiotic therapy is frequently ineffective in eradicating bacteria in the biofilm . it is generally believed that biofilm is a common cause of persistent infections and chronic inflammatory diseases that are difficult to be cured .2,3 in recent years , biofilms have been consistently detected on the nasal mucosa of patients with chronic rhinosinusitis ( crs ) .411 these are typically associated with more severe disease and with poor outcomes of endoscopic sinus surgery .12,13 staphylococcus aureus biofilm is increasingly implicated in the pathogenesis of crs .11,1416 evaluation of therapeutic interventions that specifically target s. aureus biofilms in patients with crs is a key imperative .17,18 given that the mucosa of the sinus cavities is accessible to topical therapy , it is intuitive to evaluate the effect of topical antibiotics for treatment of biofilm infections . earlier , the efficacy of silk fibroin nano silver ( sf - ns ) solution in disrupting s. aureus biofilms has been demonstrated in vitro .19 this study tested the use of topical sf - ns solution in a rabbit model of s. aureus biofilm - associated sinusitis . the stable existence of s. aureus biofilms on the maxillary sinus mucosa was verified after 4 weeks of bacterial inoculation ,20 which gave an opportunity to test this novel therapeutic agent against biofilm under in vivo conditions . twenty - four new zealand white rabbits ( weight : 2.53.5 kg ) were obtained from the laboratory animal center at the fudan university ( shanghai , china ) . all the experimental protocols were approved by the animal care and use committee of fudan university , and the animal study was carried out in accordance with the ethical guidelines for animal experiments established by fudan university . the sf - ns solution used in this studywas supplied by the state key laboratory of molecular engineering of polymers and was made by in situ reduction reaction between natural polymer bombyx mori silk fibroin and silver nitrate under light . the principles of synthesis of sf - ns and its key characteristics are shown in figure 1 ; a more detailed description is available in a previous study .19 the average size of the silver nanoparticle was 12.02.1 nm . the minimum bactericidal concentration ( mbc ) for s. aureus strain ( clinical isolate sa006 ) was 76.8 mg / l , which was determined according to the clinical & laboratory standards institute ( clsi , 2011 ) guidelines for macrodilution in broth .19 the biofilm - forming sa006 , determined by the traditional crystal violet biofilm assay ,21,22 was chosen owing to its relatively strong biofilm formation capacity . the night before the modeling surgery , a single colony of sa006 was inoculated in tryptic soy broth supplemented with 0.5 % glucose ( tsbg ) and incubated overnight at 37c with shaking . then the bacterial suspension was diluted 200-fold with tsbg to achieve a concentration of ~ 110 colony - forming units ( cfu ) / ml and kept on ice for further use . a rabbit model of s. aureus biofilm - associated sinusitiswas established surgically as previously described by our group .20 briefly , under adequate anesthesia , the skin was incised vertically along the median line of the dorsum . a laterally based flap of periosteum was elevated from the midline to the right side , and then a small hole ( diameter : 1.5 mm ) was drilled to enter the right maxillary sinus . a piece of compressed absorbable gelatin sponge was inserted into the maxillary sinus , and subsequently inoculated with 0.5 ml of bacterial suspension through the hole . then , the periosteal and skin incisions were closed with interrupted suture , and the rabbits were caged individually in an air - conditioned room with 12 - hour dark light cycles and free access to water and food . four weeks after modeling surgery , indwelling maxillary sinus irrigation catheters were placed into the right maxillary sinus as described by chiu et al23 with some modification . briefly , a plastic catheter connected with an end - enlarged stainless steel needle was used as the irrigating catheter and tunneled under the skin from the vertex to the dorsum incision ( figure 2a ) . the hub of the metal needle was exposed outside the vertex and secured to the skin with a purse string suture , to avoid its displacement by the animals . the enlarged end of the metal needle under the skin was fixed between the skin and periosteum with interrupted suture to secure the catheter ( figure 2b ) . approximately 4 mm of the plastic end was inserted into the maxillary sinus through the hole made in the modeling process ( figure 2c ) . the rabbits were randomly divided into four groups ( six animals in each group ) : a blank control group ( animal models without irrigation ) , a negative control group ( treated with saline ) , and two experimental groups ( treated with 153.6 and 384 mg / l of sf - ns solution [ 2 mbc and 5 mbc , respectively ] ) . the right maxillary sinus was irrigated at a slow pace with test solution , sf - ns solution or normal saline via the indwelling catheter ( 2 ml twice a day ; flow rate : 0.2 ml / s ) , starting at 1 day after implantation of the indwelling catheter . after 7 days of irrigation , the rabbits were anesthetized with intraperitoneal administration of 10 % chloral hydrate ( 350 mg / kg ) and sacrificed with air injection through ear vein . the sinus mucosa was carefully removed , washed thoroughly with saline , and placed in 2.5 % glutaraldehyde for scanning electron microscopy ( sem ) specimen preparation . the specimens were initially fixed for 24 hours in 2.5 % glutaraldehyde at 4c , then rinsed three times with 1 phosphate - buffered saline ( pbs ) and fixed with 1 % osmium tetroxide for 2 hours . they were then rinsed again three times with pbs , and dehydrated through a graded ethanol series ( 50 % , 70 % , 90 % , 100 % , 15 minutes each ) . the specimens were then immersed in a mixture of 100 % ethanol and isoamyl acetate ( 2:1 ) , and then in pure isoamyl acetate , for 15 minutes each solution . all specimens were dried in carbon dioxide critical point dryer , sputter coated with gold , and examined with an su8010 sem ( hitachi , tokyo , japan ) at an accelerating voltage of 10 kv . structures characterized by water channels , 3d structure , and matrix - embedded spherical bodies were evaluated for evidence of bacterial biofilms .9 for quantitative analysis of biofilm formation on the sinus mucosa in each rabbit , three fields of vision were randomly selected for each specimen . each field of view ( 2,000 ) was equally divided into nine regions and graded according to the number of biofilm affected regions ( average of the three visual fields ) : lack of involvement of any region was recorded as 0 , involvement of 13 regions as 1 , involvement of 46 regions as 2 , and involvement of 79 regions as 3 . statistical analysis was performed using kruskal wallis rank sum test , and p - value 0.05 was considered as statistically significant . twenty - four new zealand white rabbits ( weight : 2.53.5 kg ) were obtained from the laboratory animal center at the fudan university ( shanghai , china ) . all the experimental protocols were approved by the animal care and use committee of fudan university , and the animal study was carried out in accordance with the ethical guidelines for animal experiments established by fudan university . the sf - ns solution used in this study was supplied by the state key laboratory of molecular engineering of polymers and was made by in situ reduction reaction between natural polymer bombyx mori silk fibroin and silver nitrate under light . the principles of synthesis of sf - ns and its key characteristics are shown in figure 1 ; a more detailed description is available in a previous study .19 the average size of the silver nanoparticle was 12.02.1 nm . the minimum bactericidal concentration ( mbc ) for s. aureus strain ( clinical isolate sa006 ) was 76.8 mg / l , which was determined according to the clinical & laboratory standards institute ( clsi , 2011 ) guidelines for macrodilution in broth .19 the biofilm - forming sa006 , determined by the traditional crystal violet biofilm assay ,21,22 was chosen owing to its relatively strong biofilm formation capacity . the night before the modeling surgery , a single colony of sa006 was inoculated in tryptic soy broth supplemented with 0.5 % glucose ( tsbg ) and incubated overnight at 37c with shaking . then the bacterial suspension was diluted 200-fold with tsbg to achieve a concentration of ~ 110 colony - forming units ( cfu ) / ml and kept on ice for further use . a rabbit model of s. aureus biofilm - associated sinusitis was established surgically as previously described by our group .20 briefly , under adequate anesthesia , the skin was incised vertically along the median line of the dorsum . a laterally based flap of periosteum was elevated from the midline to the right side , and then a small hole ( diameter : 1.5 mm ) was drilled to enter the right maxillary sinus . a piece of compressed absorbable gelatin sponge was inserted into the maxillary sinus , and subsequently inoculated with 0.5 ml of bacterial suspension through the hole . then , the periosteal and skin incisions were closed with interrupted suture , and the rabbits were caged individually in an air - conditioned room with 12 - hour dark light cycles and free access to water and food . four weeks after modeling surgery , indwelling maxillary sinus irrigation catheters were placed into the right maxillary sinus as described by chiu et al23 with some modification . briefly , a plastic catheter connected with an end - enlarged stainless steel needle was used as the irrigating catheter and tunneled under the skin from the vertex to the dorsum incision ( figure 2a ) . the hub of the metal needle was exposed outside the vertex and secured to the skin with a purse string suture , to avoid its displacement by the animals . the enlarged end of the metal needle under the skin was fixed between the skin and periosteum with interrupted suture to secure the catheter ( figure 2b ) . approximately 4 mm of the plastic end was inserted into the maxillary sinus through the hole made in the modeling process ( figure 2c ) . the rabbits were randomly divided into four groups ( six animals in each group ) : a blank control group ( animal models without irrigation ) , a negative control group ( treated with saline ) , and two experimental groups ( treated with 153.6 and 384 mg / l of sf - ns solution [ 2 mbc and 5 mbc , respectively ] ) . the right maxillary sinus was irrigated at a slow pace with test solution , sf - ns solution or normal saline via the indwelling catheter ( 2 ml twice a day ; flow rate : 0.2 ml / s ) , starting at 1 day after implantation of the indwelling catheter . after 7 days of irrigation , the rabbits were anesthetized with intraperitoneal administration of 10 % chloral hydrate ( 350 mg / kg ) and sacrificed with air injection through ear vein . the sinus mucosa was carefully removed , washed thoroughly with saline , and placed in 2.5 % glutaraldehyde for scanning electron microscopy ( sem ) specimen preparation . the specimens were initially fixed for 24 hours in 2.5 % glutaraldehyde at 4c , then rinsed three times with 1 phosphate - buffered saline ( pbs ) and fixed with 1 % osmium tetroxide for 2 hours . they were then rinsed again three times with pbs , and dehydrated through a graded ethanol series ( 50 % , 70 % , 90 % , 100 % , 15 minutes each ) . the specimens were then immersed in a mixture of 100 % ethanol and isoamyl acetate ( 2:1 ) , and then in pure isoamyl acetate , for 15 minutes each solution . all specimens were dried in carbon dioxide critical point dryer , sputter coated with gold , and examined with an su8010 sem ( hitachi , tokyo , japan ) at an accelerating voltage of 10 kv . structures characterized by water channels , 3d structure , and matrix - embedded spherical bodies were evaluated for evidence of bacterial biofilms .9 for quantitative analysis of biofilm formation on the sinus mucosa in each rabbit , three fields of vision were randomly selected for each specimen . each field of view ( 2,000 ) was equally divided into nine regions and graded according to the number of biofilm affected regions ( average of the three visual fields ) : lack of involvement of any region was recorded as 0 , involvement of 13 regions as 1 , involvement of 46 regions as 2 , and involvement of 79 regions as 3 . wallis rank sum test , and p - value 0.05 was considered as statistically significant . the irrigation solutions were dripping out of the right nares of all rabbits ( figure 2d ) . two of the 24 animals died prematurely during the period of nasal irrigation ( one each in the saline group and the 5 mbc group ) of pneumonia with empyema , presumably caused by aspiration of the test solutions into the lower respiratory tract . none of the other animals showed signs of systemic illness during the course of the experiment . the sinuses of the model rabbits in the blank control group were filled with thick mucopurulent secretions , and the mucosa was friable and swollen . the sinuses in the negative control and 153.6 mg / l sf - ns experimental group showed mild to moderate edema of the mucosal linings with mild pus formation . l sf - ns experimental group was very thin and smooth , with no pus in the sinuses . on sem , significant differences were observed between specimens from the different groups . for the rabbits without topical irrigation , sem showed destruction of cilia of the sinus mucosa and clusters of organisms attached to the mucosa with morphological features of biofilms , such as water channels , 3d structure , and matrix - embedded spherical bodies ( figure 3a1 and a2 ) . saline irrigation in the negative control group reduced the bacterial biofilms of the sinus mucosa to a certain extent . a considerable portion of the biofilm still existed between the epithelial cells ( figure 3b1 and b2 ) . for the experimental group treated with 153.6 mg / l sf - ns solution , the epithelium was found to have partially repaired with some ciliary buds and short cilia . however , the cell damage was still visible and a small portion of biofilms still existed ; some damaged epithelial cells were observable at high magnification ( figure 3c2 ) . in the experimental group treated with 384 mg / l sf - ns solution , the integrity of the epithelium was almost completely restored with relatively normal cilia ; however , some naked epithelial cells were still present , and there was no evidence of bacterial biofilm on the mucosal surface ( figure 3d1 and d2 ) , which was significantly lower than that in the negative control group or 153.6 mg / l of sf - ns - treated experimental group . quantitative analysis of bacterial biofilm revealed statistically significant between - group differences ( table 1 ) . although the bacterial biofilms on the sinus mucosa of the negative control group were reduced to a certain extent , statistical analysis showed that there was no significant difference in the range of biofilm involvement when compared with that in the blank control group . although the bacterial biofilm involvement in the 153.6 mg / l sf - ns experimental group was significantly lower than that in blank control group , no significant difference was observed when compared with the saline group . however , the 384 mg / l sf - ns group showed the least biofilm involvement ; the between - group difference with each of the other three groups was statistically significant . the obvious advantage of topical administration is the higher local concentration of the therapeutic agent with minimal systemic side effects . in recent years , management of biofilm - associated crs has largely been confined to topical administration of antimicrobials .2427 this study evaluated the efficacy of sf - ns solution as a topical anti - biofilm agent in a rabbit model of sinusitis . the results showed that topical nasal irrigation , even with saline , has certain benefits in decreasing the biomass of the s. aureus biofilm in the sinuses of the rabbits . however , although the saline irrigation is beneficial in reducing the microorganisms attached to the mucosal surface , yet a significant portion of the biofilms still persisted between the epithelial cells along with severe epithelial injury . this suggests that the saline might just remove the superficial and loose structure of the biofilms . this could be attributed to the lack of nutrients in the superficial layers of the biofilm , which results in fall off of the dead or dormant microorganisms . however , the viable biofilms located in deep sites or between the epithelial cells , which directly damaged the epithelium , were not eliminated by saline irrigation alone . in vitro experiments found that sf - ns solution at 2 mbc level destroyed s. aureus biofilms partially , and when the concentration increased to 5 mbc , the biofilms were totally destroyed .19 although in vitro and in vivo conditions are not the same , yet the purpose is the same , which is to observe biofilm - disrupting properties of sf - ns after direct contact with the biofilms . hence , sf - ns solution was used at the concentrations of 153.6 and 384 mg / l ( 2 mbc and 5 mbc , respectively ) as anti - biofilm agents in this study . results showed that sf - ns solution at 2 mbc level is more effective in reducing the biofilm biomass when compared with saline . although a small amount of biofilm still existed in some damaged epithelial cells , the injured epithelium exhibited signs of restoration , which indicated that it was the sf - ns component of the solution which acted against the biofilm and that the biofilm was not removed solely by the flushing action . this suggested that better results may be achieved if the duration of treatment is further extended . topical application of sf - ns solution at the 5 mbc level eliminated s. aureus biofilms in the sinuses of the rabbits after irrigation for 7 days . furthermore , the integrity of epithelium had been recovered and most of the epithelial cells were normal with regeneration of cilia , which indicates that the repair of the epithelial cells had been in progress for some time . the association of ciliary beat defect with crs is well acknowledged . as noted in the experiment , a marked destruction of the sinonasal epithelium was observed with a complete absence of cilia , when the sinonasal mucosa was colonized by bacterial biofilms . thus , as stated by galli et al , biofilm formation represents the later phase of the inflammatory process that leads to complete epithelial destruction .28 the results of the present study clearly showed restoration of epithelium and cilia after treatment with sf - ns solutions . thus , although the mechanism of nasal epithelial restoration is still poorly understood , treatment of bacterial biofilms may be a key factor for ciliary recovery in biofilm - affected nasal mucosa . although studies have found that silk fibroin has a role in promoting reepithelialization ,29,30 the role of silk fibroin in epithelial restoration in this severe inflammatory condition needs to be studied further . the antibacterial property of silver nanoparticles against a broad spectrum of bacteria has been increasingly used in various fields .31 nonetheless , individual silver nanoparticles are easily oxidized and / or aggregated in air , which hampers their practical application .32 this study used green product sf - ns synthesized by the reaction of silk fibroin and silver nitrate , detailed information on which can be found in our previously published literature .19 the silk fibroin acted as a soluble template for biomineralization and the tyrosine residues in the silk fibroin backbone were thought to be responsible for the reduction of ag into silver nanoparticles in situ . silk fibroin is a natural nonionic surfactant that enhances the stability of silver nanoparticles in aqueous dispersion .33 therefore , silk fibroin acts simultaneously as a reducing , dispersing , and stabilizing agent of the synthesized silver nanoparticles . in a previous study ,19 it was found that synthesized sf - ns retained the antimicrobial properties of silver nanoparticles and could dissolve in water without aggregation , which makes it suitable for use as a solution for treatment . this study demonstrated that sf - ns solution is effective against mature biofilms formed by s. aureus in vivo in a concentration - dependent manner . although 2 mbc and 5 mbc levels of sf - ns solutions showed no negative impact on the morphology of epithelial cells and cilia , for clinical use the other characteristics of silver nanoparticles still need to be considered , such as whether they can be easily taken up in the cells , and their potential toxic effects . sf - ns solution at concentrations of 153.6 and 384 mg / l was found to be an effective topical nasal antimicrobial agent , which reduced the biomass of s. aureus biofilms in the rabbit model of sinusitis . the clinical utility of sf - ns solution for patients with biofilm - associated crs is yet to be determined . however , the anti - biofilm properties of sf - ns solution provide another option for future therapeutic interventions for biofilm - associated sinusitis .\noutput:\n" }, { "from": "agent", "value": "backgroundstaphylococcus aureus biofilms contribute significantly to the recalcitrant nature of chronic rhinosinusitis . in previous studies , it has been shown that silk fibroin nano silver solution can eliminate s. aureus biofilms in vitro , which suggests a potential role of this novel agent in the treatment of biofilm - associated diseases , such as sinusitis.objectivethe aim of this study was to investigate the efficacy of silk fibroin nano silver solution as a topical anti - biofilm agent in a rabbit model of sinusitis.methodsbiofilm - associated sinusitis models were established in 24 new zealand white rabbits by gelatin sponge placement and s. aureus inoculation through a hole drilled into the anterolateral wall of the right maxillary sinus . after 4 weeks , indwelling catheters were placed into the maxillary sinus . different concentrations of silk fibroin nano silver solution or normal saline were irrigated slowly into the maxillary sinus via the indwelling catheters . after 7 days of irrigation , the rabbits were sacrificed . the sinus mucosa was harvested and examined for biofilm biomass as well as morphological integrity of the epithelium by scanning electron microscopy.resultssilk fibroin nano silver solution was found to be most effective in reducing the biomass of the s. aureus biofilms at a concentration of 384 mg / l , followed by the concentration of 153.6 mg / l , when compared with saline . after treatment with 384 mg / l silk fibroin nano silver solution , the biofilms were completely eliminated and the injured epithelium was almost restored with regenerated cilia on the surface.conclusionsilk fibroin nano silver solution was found to be an effective topical agent against s. aureus biofilms in the rabbit model of sinusitis , and its effect was concentration - dependent ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: encephalocele is a rare lesion , with embryological mesodermal anomaly resulting in a defect in the calvarium and dura associated with herniation of meninges , cerebrospinal fluid ( csf ) , and \\ or brain tissues through a defect that is usually covered by the scalp . however , an increase in pressure inside the sac may lead to stretching of the overlying skin , ulceration , and csf discharge . depending on the content of the sac it may be meningocele which contains csf and meninges or meningoencephalocele which contains meninges , csf and neural tissue as sac contents . the incidence of encephalocele is approximately 1 per 5,000 live births ; occipital encephalocele is more common in females than males . occipital encephalocele occurs between the lambda and foramen magnum , typically in the midline , and is divided into supratorcular and infratorcular types . a 9 - month - old infant presented with a large swelling in the occipital region , which was gradually increasing in size since birth and was associated with delayed developmental motor milestones in the form of delayed neck holding and sitting with support . he was the first born child of nonconsanguineous parents , and was delivered at full term . examination upon admission revealed the size of swelling at approximately 91010 cm , which became prominent on coughing , and was cystic , fluctuant , and transilluminant in most parts . pre - operative hematological and biochemistry results were within normal limits . computed tomography ( ct ) scan head showed occipital encephalocele with hypoplasia of the corpus callosum and mild ventriculomegaly [ figure 1 ] . bone window of ct scan of brain revealed a defect 3 cm in diameter in the occipital bone abutting the foramen magnum . magnetic resonance image ( mri ) brain with mr angiography ( mra ) showed herniation of the occipital lobe , cerebellar vermis , and torcular herophili . pre - operative axial t1 - weighted mri brain pre - operative sagittal t2 - weighted mri brain pre - operative coronal t2 - weighted mri brain surgical planning was discussed with the parent . the patient was operated upon in the prone position , and care was taken to maintain the fluid and electrolytes balance and normothermia . the sac content included gliosed occipital lobe , both occipital horns of ventricles , cerebellar hemisphere , and torcular herophili . the gliosed neural tissue with torcula was not resected but reposited into the cranial cavity along with the torcula and ventricle . at the last follow up 3 months following surgery , he was doing well and had improved developmental milestones . post operative axial ct brain a 6 - month - old infant was brought with a complaint of discharge of clear fluid following the rupture of occipital encephalocele suggestive of csf leakage . size of the encephalocele sac was about 1518 cm , with excoriation of the skin over the encephalocele . mri brain after birth revealed a giant occipital encephalocele , with the content including occipital lobe and torcula ; however , there was no gross ventricular dilatation . the patient was taken up for surgery on an emergent basis , and exploration and repair of the ruptured encephalocele sac was done . a part of the occipital lobe was herniating into the sac ; hence , the torcula was carefully reposited into the cranial cavity . postoperative ct scan showed no increase in ventriculomegaly he tolerated the surgery well and was discharged 14 days following surgery . at the last follow - up at 6 months , he was doing well . a 9 - month - old infant presented with a large swelling in the occipital region , which was gradually increasing in size since birth and was associated with delayed developmental motor milestones in the form of delayed neck holding and sitting with support . he was the first born child of nonconsanguineous parents , and was delivered at full term . examination upon admission revealed the size of swelling at approximately 91010 cm , which became prominent on coughing , and was cystic , fluctuant , and transilluminant in most parts . pre - operative hematological and biochemistry results were within normal limits . computed tomography ( ct ) scan head showed occipital encephalocele with hypoplasia of the corpus callosum and mild ventriculomegaly [ figure 1 ] . bone window of ct scan of brain revealed a defect 3 cm in diameter in the occipital bone abutting the foramen magnum . magnetic resonance image ( mri ) brain with mr angiography ( mra ) showed herniation of the occipital lobe , cerebellar vermis , and torcular herophili . pre - operative axial t1 - weighted mri brain pre - operative sagittal t2 - weighted mri brain pre - operative coronal t2 - weighted mri brain surgical planning was discussed with the parent . the patient was operated upon in the prone position , and care was taken to maintain the fluid and electrolytes balance and normothermia . the sac content included gliosed occipital lobe , both occipital horns of ventricles , cerebellar hemisphere , and torcular herophili . the gliosed neural tissue with torcula was not resected but reposited into the cranial cavity along with the torcula and ventricle . at the last follow up 3 months following surgery , he was doing well and had improved developmental milestones . a 6 - month - old infant was brought with a complaint of discharge of clear fluid following the rupture of occipital encephalocele suggestive of csf leakage . size of the encephalocele sac was about 1518 cm , with excoriation of the skin over the encephalocele . mri brain after birth revealed a giant occipital encephalocele , with the content including occipital lobe and torcula ; however , there was no gross ventricular dilatation . the patient was taken up for surgery on an emergent basis , and exploration and repair of the ruptured encephalocele sac was done . a part of the occipital lobe was herniating into the sac ; hence , the torcula was carefully reposited into the cranial cavity . postoperative ct scan showed no increase in ventriculomegaly he tolerated the surgery well and was discharged 14 days following surgery . at the last follow - up at 6 months , he was doing well . occipital encephalocele is more common than anterior encephalocele in the western hemisphere , accounting for about 85 % . typically , the bony defect may be confined only to the occipital bone or may descend to involve the posterior lip of foramen magnum , and even up to the posterior arch of the atlas and , accordingly , may be divided into supratorcular and infratorcular types . the contents of encephalocele may be occipital lobe , cerebellum , brainstem , or , rarely , torcula . torcula as one of the contents of encephalocele poses a great challenge as its injury may lead to cerebral deep venous system thrombosis and its associated consequences of assault to the already compromised brain ; therefore , prognosis in such cases depends on the mass of herniated neural tissue , associated occipital lobe , torcula , and the content of posterior fossa . the presence of microcephaly causes difficulty in repositioning of the herniated neural tissue and sinus , with a probability of aggravation of hydrocephalus after surgery . coexistent hydrocephalus may occur due to torsion of the aqueduct of sylvius or aqueduct stenosis . hydrocephalus may also occur after excision of the encephalocele due to changes in the csf dynamics . management of occipital encephalocele presents a challenge for neurosurgeons , especially if the contents form a significant part of the cerebellum , brainstem , or torcula . in our case , mri head detects the content of sac , associated anatomy , and hydrocephalus , as well as their relationships with the adjoining sinus . the optimal investigation is to visualize the contents of the sac and its relationship with venous sinuses . magnetic resonance venography ( mrv ) may show dilated venous sinuses and torcula , and it aids proper surgical planning . visual evoked response ( ver ) is used in case of giant occipital encephalocele to find out whether the sac contains functional tissue from the visual cortex . surgery is advocated taking into consideration the cosmesis , risk of rupture , csf leak and meningitis , content of herniated neural tissue , presence of sinus , associated hydrocephalus , and associated brain and bone anomalies . the patient was positioned prone with care to avoid hypothermia and blood loss ; monitoring of electrolytes was of paramount importance . aspiration of csf prior to incision may aid the dissection of sac , especially in large or giant encephalocele . however , vertical incision is safer in encephalocele extending above and below the posterior fossa if the sac is separated from the flap . identification of the content through a detailed study of mri and mrv may help avoid mishap , as the brainstem and torcula may be present as sac contents rarely . both the cases presented here had torcula as the sac content , so the aim was to preserve the torcula . suggested that although gliosed and ischemic herniated neural tissue can be excised , great caution is required to preserve venous sinuses that may course through it . during surgery , careful dissection andsince duramater is osteogenic , it helps in significant bone growth , which can eliminate or reduce the size of bone defect ; moreover , cranioplasty is rarely required . accordingly , there is no need to cover the bone defect with a cortical bone in infants and neonates . in the postoperative period , the possibility of aggravation of hydrocephalus should be kept in mind , and if it occurs , it may need shunt surgery . torcula as one of the contents of the encephalocele is a rare occurrence and is a surgical challenge . however , pre - operative evaluation with mri / mrv and ver may clearly demonstrate the contents and venous structures and torcula must be identified to ensure careful management during surgery and avoid the damage caused by it , and hence , the associated consequent morbidity and mortality .\noutput:\n" }, { "from": "agent", "value": "the presence of torcula or sinus in the occipital encephalocele presents a challenge during surgery . however , a detailed study of magnetic resonance image and magnetic resonance venography can aid in preoperative localization of the torcula . knowing the encephalocele 's contents , its relationship with falx cerebri and falx cerebelli , and vigilance during surgery is a sure way to protect neural tissue . visual evoked potential ( vep ) may be indicated in torcular encephalocele . here , authors report two such cases , one presented with ruptured encephalocele with cerebrospinal fluid leak and another case presented six months after birth due to financial constraints . pertinent literature and management is briefly reviewed ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: pancreatic cancer is one of the most malignant tumors , for which it is extremely difficult to make an early diagnosis and surgical resection . and it is also difficult to get the different stages of fresh clinical pancreatic cancer specimens , so the early appearance of pancreatic cancer can not be such easy to diagnose . the histological examination of specimens obtained by endoscopy method not only takes several days for diagnosis but also increases medical expenses . therefore , it seems important to find a fast and simple way to diagnose the human pancreatic cancer . the fourier transform infrared ( ft - ir ) spectroscopy can provide every aspect of compositional system materials . among the different spectroscopic methods that have been evaluated for utilization in distinguishing between normal and neoplastic tissues , ft - ir spectroscopy , as an advanced and promising technique , has shown its huge potential to this area . this ft - ir technique has become a reality with a large amount of information accumulated from clinical studies , trials , and ft - ir spectroscopy instruments developments . such technique , being reagent - free , can rapidly and noninvasively detect changes in the biochemical composition of cells and tissues ( at the molecular level ) , especially during carcinogenesis . some articles have been published about the application of ft - ir spectroscopy in the diagnosis of various human cancer cells so far . but , in some normal conditions , ft - ir analysis can not be such quickly and accurately used to obtain the exact results information . and how to use chemometrics to make the determination and classification of these complex systems change possibly , fast , andaccurately has become a hot research in the instrument analysis . besides , wavelet transform ( wt ) is a much more effective signal processing method than the inheritance of the fourier transform one and also plays an important role in signal analysis and feature extraction . in the multiresolution wavelet analysis , the results of the transformation ( a wavelet factor ) contain more valuable information , and the wt coefficients of each level are different for the same characterization of the signal . therefore the wavelet decomposition coefficients may be considered as the characteristics of the signal , only with a small number of factors can be passed on the absorption spectra for a good reflection , and will be one of the more effective chemical analysis methods . artificial neural networks ( ann ) have a higher intelligence and have been widely used . its calculation is simple and the prediction is accurate for the nonlinear issues . our group has previously reported that normal and abnormal human lung tissues can be fast distinguished using cwt - hatr - ft - ir combined with support vector machine . in this paper , we focus on the classification of normal and abnormal rats pancreatic tissues . the ft - ir is obtained by atr - ftir technique . the feature vectors , which represent spectral characteristics of the ft - ir , are extracted by using dwt multiresolution analysis methods . the discrete wavelet transformation ( dwt ) is the sum of the signal multiplied by the scaled and shifted mother wavelet function . normally wavelet decomposition consists of calculating the resemblance coefficients between the signal and the wavelet located at position b of scale a. if the coefficients are large , the resemblance is strong . the coefficients c ( a , b ) are calculated as ( 1 ) ca , b = rst1atbadtar +0 , br , where is wavelets , s is signal , a is scale , and b is position . pnn is the feed - forward network model of artificial neural network based on the theory of statistics with parzen window function as the activation function . pnn absorbs the advantages of radial basis function neural network ( rbf - nn ) and classical theory of probability density estimation and compares with the traditional feed - forward neural network , which especially has the remarkable advantage in the pattern classification aspect . the first and last layout , respectively , denote input and output layout ; the two middle layouts are hidden layouts . the first hidden layout is the pattern unit layout with parzen window function as the activation function ; the second one is summing unit layout which alternatively sums the output of the first one . the training methods of pnn mostly have recursion orthogonal least square algorithm ( rols ) and recursion least square ( rls ) . both methods have quick convergence rate ; in contrast , the training rate of the second one is quicker and has higher training precision . to the input vectorx , output value y j of the ith nerve cell in the output layout of pnn can be written as ( 2 ) yj = k = 1mwjkhkx , j = 1,2 , , m , hkx = i = 1nkpixckj , where x is input vector with dimension ; h k ( x ) is output of the kth unit in the second hidden layout ; w jk is connected weight between the jth nerve cell in the second hidden layout and the kth nerve cell of output layout ; p ( ) is parzen window function ; c kj is the kth center vector of the jth class in the first hidden layout ; n k is the number of the center vectors of the kth class in the first hidden layout ; is euclidean norm ; m is the number of nerve cells in the output layout . anicolet ( madison , wi , usa ) nexus 670 ftir spectrometer , equipped with a temperature - stabilized deuterated triglycine sulphate ( dtgs ) detector and diamond attenuation total reflection ( atr ) accessory , was used . the spectral range is 4000650 cm with resolution 2 cm and the cumulative number is scan of 64 times . tumor specific antigen ( tsa ) was for laboratory use only from shanghai huayi bio technology co. , ltd .68 - week - old , 160 normal sprague - dawley ( sd ) rats , about 180 g , half male and half female , were used in the experiment . all rats were provided by the department of animals , jinhua institute for drug control , china , and were permitted by animal protection association . then the sd rats were randomly divided into three groups a , b , and c : 70 rats for group a ( dmba group ) , another 70 rats for group b ( dmba + tsa group ) , and last 20 rats for group c ( control group ) . none is fed but water for 24 h before the operation .2 % pentobarbital sodium ( 1.5 ml / kg ) was injected into the sd rats ' abdominal cavity where is about 1 cm incision into the upper middle abdomen for anesthesia after the exposure of the pancreas , the membrane and partial terms of pancreas were cut from the tail of body in deep 1 mm , group a and group b were put into 9 mg dmba , and then the abdomen was stitched after stitching the membrane of pancreas . they were fed in the general environment with free drinking purified water and full price nutrition diet particles . group b was weekly injected into the sd rats ' abdominal cavity with 1 g / ml tsa 1 ml . in addition to natural death , group a ( 7 , 10 , and 20 sd rats ) and group b ( 6 , 10 , and 20 sd rats ) will be killed , respectively , in the third , fourth , and fifth month randomly ; then all group c will be killed in the fifth month . the anatomical pancreatic tissues were washed in physiology salt and then the samples were directly measured to collect their ftir data in three hours ; the specimens were taken at the same time for pathological analysis . the sample tissues included 220 pancreatic normal tissues , 120 early - staged cancerous tissues , and 100 advanced cancerous tissues . the ft - ir spectrum background was recorded before collecting the sample 's ft - ir spectrum.reference spectra were recorded using a blank diamond - atr . single beam spectra were obtained for all the samples and the ratio of the spectra against the background spectra of air was used to present the spectra in absorbance units . after each experiment the diamond - atr was thoroughly washed with absolute ethyl alcohol and dried with nitrogen , and its spectra were examined to ensure that no residue from the previous experiment was retained on the diamond surface . all of the tissue samples were dried with absorbent cotton and further dried with nitrogen . all the experiments were repeated three times and the averaged spectra were used for further analysis . the absorption values from different wave bands based on the characters of the absorption value were obtained by copying data method . matlab software was used for wavelet transition analysis . using daubechies wavelet , which has a good detection capability of the signal singularity , as the analysis wavelet , one - dimensional dwt is done to the ft - ir spectra of samples under different scales . five layers of the samples character variable were picked up by selecting a decomposition level whose difference degree was the most obvious . through a comparative analysis , figure 2 shows the ft - ir spectra of pancreatic normal , early carcinoma , and advanced carcinoma tissues . as shown in figure 2 , the location , intensity , and shape of the absorbance peak change with the normal , early carcinoma , and advanced carcinoma tissues . the hydroxyl absorption peak from protein , nucleic acid , and grease is located at 3327 cm with a similar intensity . the pancreatic normal tissue has three obvious absorption bands , which were 2956 , 2924 , and 2852 cm , respectively , in the range of 3000 ~ 2800 cm of saturated c h bond stretching vibration region . the carbonyl absorption peak from ester of fat is located at 1743 cm , which is also weakened after canceration . the carbonyl group absorption peak from protein is located at 1650 cm ( including water molecules in the hydroxyl in the absorption of 1640 cm ) , and its intensity decreases as the cancerous tissue progresses . absorption peak from amide ii band is located at 1555 cm , and its intensity also decreases as the cancerous tissue progresses . the other spectrum bands , such as symmetrical flexing vibration and asymmetrical flexing vibration of diphosphate ester from nucleic acid , had absorption peaks located at 1084 cm and 1242 cm , respectively . the ft - ir from the normal and early carcinoma tissues has very closed absorbance and it is difficult to distinguish between them only by experience . sowe use one - dimensional discrete wavelet transformation to extract their features for further classification . h stretching bands , c h aliphatic asymmetric and symmetric stretching vibration band and the character is not obvious . appropriate feature description is considered to be one of the most important components of classification procedures . the result of feature extraction is a more concise description that still retains most of the spectrum characteristics . in this paper , we scale the ft - ir data to the range 4000 ~ 650 in order to perform analysis wavelet . extracting features from the ft - ir data can reduce the computational burden and improve results . the proper wavelet base and scale should be determined by analyzing the signal spectra property and the comparison of decomposition results with different wavelet bases and decomposition levels . during the multiresolution wavelet decomposition process , the suitable wavelet basis function and wavelet decomposition level are determined based on the comparison of the ft - ir signals and the signals ' decomposition effects under different resolution . the standard selection is to extrude several characteristic peaks in the original spectra and select a good smoothing wavelet . after comparing haar , daubechies , mexican hat , meyer , morlet , and symlets wavelet decomposition , we choose daubechies wavelet as wavelet analysis . two characteristic peaks in the original ft - ir signal of wavelet domain are used for further extraction of its eigenvalues . the pancreatic normal , early carcinoma , and advanced carcinoma tissues were performed by discrete wavelet transformation separately ; the decomposition level is set as 5 . after analysis we choose the two levels 3 and 4 to extract the features . figure 3 shows preprocessed ft - ir spectra of normal , early carcinoma , and advanced carcinoma tissues ' dwt coefficients , where d1d5 indicates detailed information after decomposition ( fine to coarse ) . from figure 3 , we could see that it is difficult to discern the main features of its spectrum from the wavelet domain if the discrete wavelet transform resolution is fine because of too much detailed information . the detailed information is sensitive to spectrum change , has strong response to characteristic peak of the original various spectra , and is not good for the feature extraction . in order to effectively extract representative characteristics within two scales of discrete wavelet , the spectra in each scalefour feature regions of two details in the dwt domain , whose feature values are the spectra energy in the four feature regions , form the feature vector . after testing , we define the structure of pnn as nine nodes in the input layer , four nodes in the hidden layer , and three nodes in the output layer ; the error is 0.01 . the successful training network studied how to identify pancreatic normal , early carcinoma , and advanced carcinoma tissues . for the training process , we used nine input layer nodes of pnn structure , followed by normalized nine feature vectors . the output layer nodes were divided into category 1 : normal tissues , category 2 : early carcinoma tissues , and category 3 : advanced carcinoma tissues . the input data is the eigenvector extracted from the wavelet transform of the original ftir . based on the results in table 1 , basically , the three different types of samples ( the pancreatic normal , early carcinoma , and advanced carcinoma tissues ) are correctly identified . the eigenvectors of the different samples that were extracted from the wavelet transform of the ft - ir have significant difference so that the high accuracy of the classification can be achieved . it is 100 % for identifying the pancreatic advanced carcinoma tissues because there is significant difference among them . the recognition accuracy rate of normal and early carcinoma tissues is lower than advanced carcinoma tissues because the difference is very small . it is easy to do the ft - ir measurement directly using diamond - atr , which does not need to have the pretreated samples . there is a significant difference between normal pancreas tissue and advanced cancer , but to the early cancer the difference of their ft - ir spectra is not such obvious . some important features were extracted to the ft - ir signals in the dwt domain , and probability artificial neural network pattern for recognition and classification based on their energy was also used . network method for complex and ambiguous and cross information applications has special value and the use of radial basis function neural networks such as scientific evaluation system to avoid identification of the human experience and a number of other methods of complexity are simple , rapid , and accurate . therefore , ft - ir through discrete waveletfeature extraction using probability neural network for early identification of pancreatic cancer has a more wide application prospect .\noutput:\n" }, { "from": "agent", "value": "sprague - dawley ( sd ) rats ' normal and abnormal pancreatic tissues are determined directly by attenuated total reflectance fourier transform infrared ( atr - ft - ir ) spectroscopy method . in order to diagnose earlier stage of sd rats pancreatic cancer rate with ft - ir , a novel method of extraction of ft - ir feature using discrete wavelet transformation ( dwt ) analysis and classification with the probability neural network ( pnn ) was developed . the differences between normal pancreatic and abnormal samples were identified by pnn based on the indices of 4 feature variants . when error goal was 0.01 , the total correct rates of pancreatic early carcinoma and advanced carcinoma were 98 % and 100 % , respectively . it was practical to apply pnn on the basis of atr - ft - ir to identify abnormal tissues . the research result shows the feasibility of establishing the models with ft - ir - dwt - pnn method to identify normal pancreatic tissues , early carcinoma tissues , and advanced carcinoma tissues ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the underlying diseases causing dic include obstetric accidents , intravascular hemolysis , septicemia , viremia , burns , trauma , acute liver disease , and malignant disease1 ) . the incidence of dic was reported on 7 % of the patients with solid tumor and 15 % - 20 % of the patients with acute leukemia34 ) . dic in pediatric solid tumor has been reported with disseminated neuroblastoma , nephroblastoma , infantile fibrosarcoma , and multi - system langerhans cell histiocytosis5 ) . the pediatric patients with rhabdomyosarcoma presenting with dic at diagnosis are rare and are mainly seen with the widespread alveolar rhabdomyosarcoma metastatic to bone marrow ( bm ) 3 ) . clinically , dic in cancer is less fulminant than the types of dic seen in sepsis and trauma . also , chronic and systemic activation of coagulation can progress subclinically , and this progression may lead to exhaustion of coagulation factors and platelets . therefore , bleeding may be the first clinical symptom of dic in a patient with cancer2 ) . here , we describe an unusual case with acute bleeding and dic , which were severe and very difficult to control , with the presenting manifestation of alveolar rhabdomyosarcoma metastatic to bm . early administration of chemotherapy and vigorous supportive care could control the massive bleeding and dic . a 13 - year - old boy was admitted in january 2011 , due to an uncontrolled bleeding at the operation site of the right thenar muscle . the swelling of the right thenar muscle developed after a fall on august 2010 ( fig . however , no treatment was given under the impression that the swelling was a hematoma . after showing no improvement for over 5 months , excision of this lesion was attempted at a private orthopedic surgery clinic . before marginal excision , he underwent two additional operations at different hospitals for the control of bleeding , but the bleeding at the operation site continued . when a pathologic finding of the mass suggested a diagnosis of malignancy , he was transferred to our hospital for further management . at the admission , the patient 's general state was poor with signs of pallor , weakness , bruising at the intravenous site , and purpura on the operation site over the right thenar muscle with continuous bleeding ( fig . , there was a 22 cm - sized lymph node ( ln ) in the right axillary area and 1 cm - sized hepatosplenomegaly . laboratory tests revealed markedly decreased platelet and hemoglobin levels and features suggestive of dic ( white blood cell , 9,900 / l ; hemoglobin , 4.8 g / dl ; platelets , 28,000 / l ; prothrombin time , 1.47 international normalized ratio ; activated partial thromboplastin time , 45.4 sec ; fibrinogen , 87 mg / dl ; fibrin / fibrinogen degeneration product , 656.4 g / ml ; and d - dimer , 16.17 mg / l ) . the coagulation factors ii , the factors v and viii were 30 % ( normal , 60 % - 140 % ) and 40 % ( normal , 50 % - 150 % ) , respectively .18 - fluoro -2-deoxy - d - glucose positron emission tomography scan showed hypermetabolic lesions ( maximum standardized uptake value [ suvmax ] , 2.7 ) along the rim of a previous mass in the right thenar muscle and conglomerated hypermetabolic lesions ( suvmax , 5.3 ) in the right axillary space . it suggested post - operative inflammation in the right thenar muscle and metastatic lymphadenopathy in the right axillary space ( fig . despite of the repeated blood product transfusions , the massive bleeding from the operation site and the intravenous access site worsened , and a gross hematuria developed . on the 4th hd , the pathologic findings of the mass were reported as alveolar rhabdomyosarcoma with positive immnunohistochemical stains of myognesin , desmin , and myod and with negative resection margin . the patient was transferred to the intensive care unit , and chemotherapy consisting of vincristine , doxorubicin , and cyclophosphamide ( vac ) was administered . also , repeated transfusions , synthetic protease inhibitor , and substitution of antithrombin - iii were administered . on the 10th hd , a massive epistaxis led to hematemesis of approximately 1.5 l of blood , and it required transfusions of 4 units of red blood cells ( rbcs ) , 9 units of platelet concentrates ( pcs ) , 1 unit of fresh frozen plasma ( ffp ) , and 8 units of cryoprecipitate , with two times of cauterization . two weeks after the chemotherapy was started , the laboratory findings of dic showed improvement ( fig .2 ) , so a bm section biopsy and an axillary ln biopsy were performed .1 e ) and axillary ln revealed involvement of rhabdomyosarcoma . during the initial 20 days of admission , the patient received total blood transfusions of 311 units ( 26 units of rbc , 26 units of ffp , 74 units of pc , 17 units of single donor platelets , and 168 units of cryoprecipitate ) for the control of the dic and bleeding . on the 28th hd or three weeks after the start of chemotherapy , the patient was discharged . the patient received a combination chemotherapy consisting of vac every 3 weeks . at 9th week after the start of chemotherapy , the size of right axillary ln decreased from 3.6 cm to 2.1 cm . at 21st week after the start of chemotherapy , the bm showed disappearance of rhabodyosarcoma and negative immunostaining for desmin or myogenin . for the planned high - dose chemotherapy with autologous peripheral blood stem cell ( apbsc ) transplantation , two rounds of apbsc collections were performed . unfortunately , however , at the 27th week of chemotherapy , the patient was found to have a nodule in the right forearm that was increasing in size for over 2 weeks , and the biopsy revealed it as an alveolar rhabdomyosarcoma . despite of the salvage chemotherapy consisting of ifosfamide , carboplatin , etoposide , and palliative radiation therapy ( right axilla , arm , thenar muscle , and liver , 36 gy ) , the patient died 5 months later from the disease progression to the liver and the brain . recent studies show that the solid tumors express different procoagulant molecules including tissue factor ( tf ) , which binds to factor vii ( a ) to activate the factors ix and x , and to the cancer procoagulant , which is a cysteine protease with factor x - activating properties . alternatively , most tumors induce a hypofibrinolytic state , due to high levels of fibrinolytic inhibitor such as plasminogen activator inhibitor type 1 . virtually , all pathways that lead to the occurrence of dic are driven by proinflammatory cytokines , such as interleukin - 6 , interleukin - 1 , interleukin - 8 , and tumor necrosis factor - 2 ) . these cases were found in the review5 ) of 13 cases , published from 1978 to 2010 . out of 11 patients with the involvement of bm , 10 casesin which the patients have recovered from the dic received multiagent chemotherapy , and the recovery time from the dic varied from 6 days to after 3 cycles of chemotherapy . multivariate analysis revealed that the older age , male sex , primary tumor necrosis , and advanced tumor stage are the risk factors for dic3 ) . the prognosis of alveolar rhabdomyosarcoma stage iv with the involvement of bm is very poor , especially in the cases complicated by massive dic5 ) . it is very important to administer chemotherapy early , with the aim of diminishing tumor - triggered procoagulant activity . there is a dilemma associated with this practice , because cytotoxic agents may aggravate dic and may also suppress the bm . however , in an inoperable situation , administration of multidrug chemotherapy revealed to have an immediate beneficial effect , even if a measurable antitumor effect is not observed6 ) . in the case reported here , despite of the continuous bleeding at the postoperative site , administration of vac chemotherapy at 4th hd was undertaken and the dic showed signs of improvement after the 2nd week of chemotherapy . in the cancer patients complicated with dic , once the treatment directed at the primary disorder is initiated , the additional supportive therapy may be required in order to correct the coagulation abnormalities . although the low levels of platelet and coagulation factors may increase the risk of bleeding , the plasma or platelet substitution therapy is not indicated on the basis of the laboratory findings alone , unless an active bleeding is present or the invasive procedures are required7 ) . in our patient , the massive bleeding required as many as 311 units of blood component replacement ( 26 units of rbc , 26 units of ffp , 74 units of pc , 17 units of single donor platelets , and 168 units of cryoprecipitate ) . based on the concept that dic is characterized by systemic activation of coagulation , anticoagulant therapy may be a principle approach in therapy . however , the safety and efficacy of this strategy in malignancy - associated dic have never been studied in proper clinical settings2 ) . according to an experimental study , heparin therapy showed hopeful results in inhibiting the activation of coagulation in dic8 ) . in the cases with obvious thromboembolic disease or where fibrin deposition predominateshowever , our patient did not receive heparin therapy and only received repeated transfusions , synthetic protease inhibitor , and substitution of antithrombin - iii . clinically , dic in malignancy has a less fulminant course than the types of dic in sepsis and trauma . particularly , solid tumors are the most common cause of chronic dic . however , our case was unusual because of its acute presentation of severe dic which was very difficult to control . the coagulopathy may be triggered by direct surgical manipulation of the tumor . by surgical trauma to the tumor blood vessels , this can lead to the complication of acute dic after the trauma to malignant cells910 ) . in our case , early administration of chemotherapy and vigorous supportive care , including repeated transfusions , controlled the massive bleeding and dic at the initial diagnosis . in conclusion , for the patients with rhabdomyosarcoma complicated with dic , the early start of systemic chemotherapy to diminish the malignancy triggered procoagulant activity is important .\noutput:\n" }, { "from": "agent", "value": "it is uncommon for pediatric patients with rhabdomyosarcoma to present with clinical and / or laboratory features of disseminated intravascular coagulation ( dic ) . we report a case of metastatic alveolar rhabdomyosarcoma with severe bleeding because of dic in a 13 - year - old boy . he experienced persistent oozing at the site of a previous operation , gross hematuria , and massive epistaxis . two weeks after initiating combination chemotherapy consisting of vincristine , doxorubicin , and cyclophosphamide , the patients ' laboratory indications of dic began to resolve . during this period , the patient received massive blood transfusion of a total of 311 units ( 26 units of red blood cells , 26 units of fresh frozen plasma , 74 units of platelet concentrates , 17 units of single donor platelets , and 168 units of cryoprecipitate ) , antithrombin - iii and a synthetic protease inhibitor . despite chemotherapy and radiation therapy , he died 1 year later because of disease progression . in children with metastatic rhabdomyosarcoma and massive dic , prompt chemotherapy and aggressive supportive care is important to decrease malignancy - triggered procoagulant activities ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: salivary duct carcinoma is a distinctive primary neoplasm of the major salivary gland first described by kleinsasser et al . in 1968 . it is characterized by an aggressive behavior , early metastasis , local recurrence and significant mortality . nearly 85 % of the cases occur in the parotid gland followed by the submandibular gland . the tumor has predilection for older men in the sixth to seventh decades of life . a number of patients experience facial nerve palsy and / or pain , and have cervical lymphadenopathy at presentation . familiarity with this entity is necessary to avoid false interpretation . on account of its apocrine features and a high nuclear grade , several primary and metastatic neoplasms enter the differential diagnosis , particularly on fine needle aspiration cytology.a 40 - year - old male presented with a painless swelling below the right ear lobule , since five years , with a history of a rapid increase in the size of the swelling since three months . on examination , there was a right parotid swelling of 74 cm , which was hard in consistency . the patient underwent superficial parotidectomy based on the fnac report of adenocarcinoma [ not otherwise specified ] [ figures 1 and 2 ] . cuboidal to columnar epithelial cells with pleomorphic , vesicular nuclei , mildly acidophilic cytoplasm attempting acinar structures ( h and e , 2010 ) f.n.a.c . cuboidal to columnar neoplastic cells having abundant delicate cytoplasm , round - to - oval nuclei attempting acinar / ductal structures ( h and e , 4010 ) grossly the specimen consisted of a roughly ovoid , nodular mass of 743 cm with a bosselated surface and the adjacent remnant of normal salivary gland parenchyma . the cut surface showed a well - encapsulated , gray - white tumor , predominantly solid , with areas of necrosis and small cystic spaces containing mucoid material [ figure 3 ] . salivary duct carcinoma cut section gray - white homogeneous surface with foci of necrosis and tiny cystic spaces histologically , it was a salivary duct carcinoma infiltrating , as evidenced by the pleomorphic cuboidal epithelial cells forming solid nests , cribriform and comedone patterns , papillary epithelial projections into duct - like structures , and densely sclerotic hyalinized stroma [ figures 49 ] . salivary duct carcinoma cribriform growth pattern of the neoplastic cells with surrounding hyaline sclerosis of the stroma ( h and e , 1010 ) salivary duct carcinoma cribriform growth pattern of neoplastic cells ( h and e , 2010 ) salivary duct carcinoma multiple comedones surrounded by hyalinized , sclerotic stroma ( h and e , 1010 ) salivary duct carcinoma large comedones surrounded by stroma showing dense hyaline sclerosis ( h and e , 2010 ) salivary duct carcinoma hyalinized sclerotic stroma with duct cell proliferation ( h and e , 410 ) salivary duct carcinoma papillary epithelial projections into duct - like structures ( h and e , 410 ) the h and e stained slides were subjected for review . the smears were moderately cellular comprising of cuboidal - to - columnar epithelial cells with pleomorphic vesicular nuclei exhibiting anisonucleosis , open chromatin , and mildly acidophilic cytoplasm attempting acinar structures , with inflammatory necrotic debris . grossly the specimen consisted of a roughly ovoid , nodular mass of 743 cm with a bosselated surface and the adjacent remnant of normal salivary gland parenchyma . the cut surface showed a well - encapsulated , gray - white tumor , predominantly solid , with areas of necrosis and small cystic spaces containing mucoid material [ figure 3 ] . salivary duct carcinoma cut section gray - white homogeneous surface with foci of necrosis and tiny cystic spaces histologically , it was a salivary duct carcinoma infiltrating , as evidenced by the pleomorphic cuboidal epithelial cells forming solid nests , cribriform and comedone patterns , papillary epithelial projections into duct - like structures , and densely sclerotic hyalinized stroma [ figures 49 ] . salivary duct carcinoma cribriform growth pattern of the neoplastic cells with surrounding hyaline sclerosis of the stroma ( h and e , 1010 ) salivary duct carcinoma cribriform growth pattern of neoplastic cells ( h and e , 2010 ) salivary duct carcinoma multiple comedones surrounded by hyalinized , sclerotic stroma ( h and e , 1010 ) salivary duct carcinoma large comedones surrounded by stroma showing dense hyaline sclerosis ( h and e , 2010 ) salivary duct carcinoma hyalinized sclerotic stroma with duct cell proliferation ( h and e , 410 ) salivary duct carcinoma papillary epithelial projections into duct - like structures ( h and e , 410 ) the smears were moderately cellular comprising of cuboidal - to - columnar epithelial cells with pleomorphic vesicular nuclei exhibiting anisonucleosis , open chromatin , and mildly acidophilic cytoplasm attempting acinar structures , with inflammatory necrotic debris . salivary duct carcinoma is regarded as a high - grade aggressive tumor with morphologic resemblance to ductal carcinoma of the breast . there have been several reports describing the cytologic features of salivary duct carcinoma ; however , accurate diagnosis by fnac can still be difficult due to its nonspecific , high - grade nuclear features . the cellular yield on fnac of salivary duct carcinoma can vary from low to high , depending on the degree of desmoplasia and necrosis . the tumor cells are large cuboidal or polygonal - to - round in shape with moderate amount of finely granular to finely vacuolated , intact - to - fragile cytoplasm some of the cells have plasmacytoid appearence with mild or moderate degree of nuclear pleomorphism and hyperchromasia . the cells are arranged singly , in loosely cohesive groups , three - dimensional clusters or flat sheets . cribriform and comedo necrosis patterns are most obvious in cell block material . it is important to exclude metastatic carcinoma particularly from breast , prostate and lung . although immunohistochemical staining for prostate specific antigen ( psa ) and prostatic acid phosphates ( pap ) may be useful to identify metastasis from prostatic carcinoma , psa secreting salivary duct carcinoma with elevated serum levels of psa , but pap negative has been reported . exclusion of primary in the breast and lung must be made largely on clinical grounds , as their cytological appearance may be identical . expression of the oestrogen receptor is stated to be useful in the definitive diagnosis of these tumors , on cytology . it has been suggested that a negative estrogen receptor together with diffuse intense staining for carcinoembryonic antigen , favor a diagnosis of salivary duct carcinoma over breast carcinoma . at the time of fnac , the differential diagnosis offered are high - grade mucoepidermoid carcinoma , adenocarcinoma not otherwise specified ( adc - nos ) , oncocytic neoplasms , warthin 's tumor ( wt ) with nuclear atypia and acinic cell carcinoma . confusion with high - grade mucoepidermoid carcinoma may arise due to the possibility of finding cells with vacuolated and dense cytoplasm resembling mucous and squamoid cells . the cytologic features of adc - nos may be indistinguishable from salivary duct carcinoma . the apocrine features of salivary duct carcinoma may mislead to a diagnosis of oncocytic neoplasms . salivary duct carcinoma shows a higher nuclearcytoplasmic ratio , less granular cytoplasm , and many three - dimensional clusters . warthin 's tumor , with nuclear atypia , and paucity of lymphoid cells in the background may be mistaken for salivary duct carcinoma . the presence of cribriform , papillary , and comedo patterns , which are best seen on cell block should alert the pathologist to the possibility of salivary duct carcinoma . the papillary cystic variant of acinic cell carcinoma ( acc ) may exhibit a papillary pattern . the variability of cell cytoplasm and absence of nuclear atypia and comedo necrosis in acc helps in differentiating these lesions from salivary duct carcinoma . salivary duct carcinoma usually demonstrates a moderate - to - severe degree of nuclear atypia . of late , low - grade salivary duct carcinoma , exhibiting a mild degree of nuclear atypia is described . a false negative diagnosis of pleomorphic adenoma has been made in these cases . by fnac , given the known difficulty in making an accurate diagnosis of salivary duct carcinoma , the identification of a tumor exhibiting a variable nuclear grade , with cribriform , papillary , and comedo patterns , in the appropriate clinical setting of elderly patients with parotid mass and facial palsy , should suggest the diagnosis of this uncommon tumor after excluding metastatic carcinoma , although the present case is relatively younger and without the usual features suggestive of malignancy . this case is being reported because of its rarity and also to add one more case to the existing literature .\noutput:\n" }, { "from": "agent", "value": "a 40 - year old male presented with rapidly growing swelling in the right parotid region . based on the fine needle aspiration cytology report of adenocarcinoma not otherwise specified , superficial parotidectomy was performed , which showed the features of salivary duct carcinoma by histopathological examination . the smears were reviewed to identify the potential pitfalls in the cytological diagnosis of salivary duct carcinoma ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: carotid body tumors ( cbts ) are the most common tumors of extra - adrenal chromaffin tissue and represent more than 50 % of head and neck paragangliomas . however , their incidence is low , reaching only 1 : 30000 . although these tumors are mostly benign ,530 % of cases present with a clinical malignant behaviour or increased functionality . furthermore , due to a potentially infiltrating and disseminating growth , cbts should be regarded as semimalignant . therefore , early detection , proper investigation , and effective treatment are imperative . aim of this retrospective study is to present a small but significant cohort of cbts that were managed and treated in our institution . epidemiologic data , diagnostic investigation , and therapeutic management was recorded and presented . finally , data are compared to international literature in order to produce useful conclusions . we retrospectively evaluated all patients treated for a cbt during a period of almost 2.5 years ( 03 / 201309 / 2015 ) in our institution . all patients were treated in the vascular surgery department of a tertiary urban general hospital . all patients with a known cbt before surgery underwent ultrasound and magnetic resonance ( mr ) imaging in order to classify the type of cbt and plan the proper treatment . the classification was further verified during the postoperative histopathological examination , based on the shamblin classification . this system classifies the tumors into three groups : group i ( tumors are too small and do not involve the surrounding vessels ) , group ii ( tumors are adherent or partially surround and compress the carotid vessels without being problematic for resection ) , and group iii ( tumors show an intimate adherent relationship to the entire circumference of the carotid bifurcation , requiring partial or complete vessel resection and reconstruction ) . before surgery , all patients were examined by an otolaryngologist and anesthesiologist as part of a multidisciplinary preoperative management . finally , in casessuspicious for functional tumours ( typical symptoms such as flushing , palpitations , or headaches ) , the patients underwent a full blood testing for levels of catecholamines , thyroid hormone , and other types of hormones . primary goal of the surgery was to extract the cbt without further manipulating the carotid vessels , unless it was warranted . resection was performed through a longitudinal cervical incision made along the anterior border of the sternocleidomastoid muscle . cutting into the tumor was sometimes reserved for the advanced shamblin classes to free the carotid vessels of the encircling tumor and finally secure the feeders . the hypoglossal nerve , the vagus nerve , and sometimes the glossopharyngeal nerve were identified away from the tumor and , if infiltrated , gradually and meticulously dissected and freed if possible . major outcomes included mortality , stroke , and cranial nerve injury as well as late recurrences . during the overall period of 2.5 years , nine patients with a total of 10 cbts were treated by surgical excision in our institution . there were 5 women ( 55 % ) and 4 men ( 45 % ) treated , with an overall age ranging from 19 to 78 years ( mean age : 59.516.3 years ) . regarding clinical presentation , only one ( 11 % ) patient had presented with bilaterally located cbts . out of 9 patients , three ( 33 % ) patients had complaints of a painless mass in the lateral cervical region , five ( 55 % ) patients had an incidental diagnosis by an ultrasound evaluation during investigation for other reasons , and finally , in one patient , the cbt was accidentally discovered during an endarterectomy for carotid artery stenosis . the latter patient had undergone only ultrasound and digital angiography before cea that had not identified the presence of a small cbt . all other cases with a known cbt before surgery underwent a mr examination to classify the tumor ( figure 1 ) . no other complications such as nerve palsy , dysphagia / dysphonia , flushing , or palpitations were reported before excision . finally there were no familial cases reported when medical history of patients was obtained ( table 1 ) . according to the shamblin classification , there were 4 ( 40 % ) cbts of type i , 4 ( 40 % ) cbts of type ii , and 2 ( 20 % ) cbts of type iii identified . half of the cbts were located on the left side and half of them on the right side . there was no preoperative embolization of cbts performed , even in the cases of larger size . in one case of bilateral cbts , the tumors were removed in staged procedures , with the repair of the smaller cbt scheduled three months after the excision of the larger cbt . only in the two cases with type iii cbt , a partial resection of internal carotid artery was needed to be performed in order to remove the firmly adhered cbt , and an interposition of a great saphenous vein graft ( end - to - end anastomoses ) followed ( table 2 ) . no severe hypotension was recorded ( table 3 ) ( figures 2 and 3 ) . regarding major outcomes , there was no operative mortality , the perioperative stroke rate was null , and no revision was needed for bleeding . no midterm complications or tumor recurrence was observed during follow - up either ( table 3 ) . in this retrospective study , we have presented a small but significant series of cbts treated in a multidisciplinary manner with satisfying results . perioperative mortality was null , with no postoperative complications observed , both in the early and in the late setting . the usual age onset is 20 to 60 years , except when there is a genetic predisposition . in such cases , indeed , paraganglioma patients have been associated lately with succinate dehydrogenase - ( sdh - ) gene mutations and , thus , all of them should undergo screening testing in order to design further treatment . however , in our series , there was only one 19 - year - old patient , with no familial history of cbts being reported . moreover , the prevalence of cbts showed no gender difference in our cohort , concurring with the literature . in general , the most frequent clinical presentation reported is a palpable painless cervical mass although only one - third of our cases reported such a symptom and the diagnosis was incidental in more than a half of our patients . other less frequent symptoms include flushing , palpitations , or headaches suggestive of a functionally active tumor . the patient may present with symptoms of dysphagia , choking , or hoarseness depending upon the cranial nerve involvement . concerning preoperative diagnostic evaluation , duplex ultrasound scan is able to provide information such as tumor size , its position and relationship with adjacent structures , and intralesional blood flow signals . given that this is a noninvasive and readily available examination , it remains the first - line imaging modality for the assessment of cbts . for further investigation , computed tomography or mr studies provide details concerning the tumor characterization and the regional extension of cbts and allow for tumor volume assessment . the classic salt and pepper imaging appearance of these lesions is observed on t2 weighted images , where the pepper refers to the low signal flow voids and the salt refers to high signal foci of hemorrhage and / or slow flow . moreover , both modalities can predict the shamblin classification , according to several authors . therefore , both ultrasound and mr imaging were ordered for all our patients . finally , selective digital angiography can identify the feeding vessels of the tumor , usually originating from the external carotid artery . although it is considered to be the golden standard for diagnosis by some authors , no cbt was detected on the digital angiography performed in our patient who underwent cea . additionally , an invasive examination such as digital angiography should be recommended only when embolization is planned to be performed . finally , several authors have recently highlighted the promising results of 68 - gallium -1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid -1-nal3-octreotide ( ( 68 ) ga - dota - noc ) positron emission ct tomography ( pet - ct ) in detection and characterization of paragangliomas , although larger studies are needed to verify its performance . the selection of treatment depends on the size , location , and biologic activity of the tumor as well as the overall fitness of the patient . surgical excision remains the golden standard of therapy due to the risk of local complications related to tumor size and the risk of malignancy . concerning postoperative outcomes , surgery has been associated with several complications such as stroke , cranial nerve injury , and bleeding . cranial nerve injury occurs usually in 19 % to 49 % of patients although none of our cases presented any such symptom . speech and swallowing difficulties could be produced in the immediate postoperative period , and most of these deficits are compensated with rehabilitation . when a malignancy is suspected , tumor resection should be accompanied by lymphadenectomy and eventual radiotherapy which seems to be effective for isolated metastasis , although no malignancy was diagnosed in our series . finally , when the tumor is considered functional , careful evaluation before surgery , measurement of serum catecholamine , treatment with adrenergic blockers , and gentle manipulations during the excision are essential for optimal results . several techniques have been proposed to reduce adverse outcomes and to achieve optimal results as well . visualization and careful dissection of the principal regional nerves ( vagus nerve , hypoglossal nerve , and the superior laryngeal nerve ) are mandatory . careful and accurate dissection of the tumor should be performed along the subadventitial plane orwhite line suggested by gordon - taylor in order to separate the tumor through a relatively avascular plane . however , as shown in our study , excision of larger tumors could necessitate carotid segment resection and graft interpositioning . early external carotid artery division intraoperatively seems to reduce the stroke rate as well as bleeding rate , although this was not performed in our patients with satisfying results . zeng et al . have also recommended standardized shunting during cbt excision in order to exclude the vascular supply of external carotid artery , reduce the size of the tumor , and guide the resection in difficult cases . as recommended by many authors and applied in our institution as well , multidisciplinary approach of diagnosis and treatment including radiologists , vascular surgeons , otolaryngologists , and anesthesiologists is imperative for optimal results . in bilateral cases , the goal of treatment should be the preservation of life quality rather than the cure of the disease itself . the main reason is that if the patient sustains a cranial nerve injury after the first procedure , the contralateral tumor of the other side could be monitored closely without resection or it could be treated by alternative means such as radiotherapy . however , kruger et al . conclude that the smaller tumor should be resected first , followed by the staged resection of the larger cbt . finally , baroreflex failure syndrome is a rare but significant complication after bilateral cbt excision including severe fluctuations of blood pressure . in our study , only one case had bilateral cbts and staged excision was performed without any early or late adverse events . the classic shamblin classification has been proposed over 40 years ago ; however , it remains a highly subjective system according to many authors . however , as the definition itself implies , this classification is mainly useful for predicting vascular morbidity rather than major neurological outcomes after surgery . assessment of tumor size , volume , and anatomic relationships to structures , such as the angle of the jaw and the vertebral bodies , may provide a more objective way to predict perioperative morbidity as well . furthermore , there has been a debate during the last decades regarding the indication of preoperative embolization of cbts . the aim of such procedure includes preoperative tumor shrinking , reducing vascularization , and intraoperative bleeding risk , especially for cbts of larger size ( shamblin types ii and iii ) . such procedure should be undertaken only in those vessels that can be subselectively catheterized and determined not to allow free reflux of contrast medium into the internal carotid artery . in a recent meta - analysis , the authors conclude that surgical resection combined with preoperative embolization decreases blood loss and operative time as well . a large retrospective review of more than 2,000 patients found significantly lower risk for hematoma and transfusion after endovascular treatment , although the cost outweighed open surgery by far . recommend performing embolization the day before the surgical procedure in order to avoid any inflammatory reaction around the lesion and to achieve optimal bleeding risk reduction . however , several authors advocate that large cbts could be equally resected safely both with and without preoperative embolization . have shown that preoperative embolization does not reduce neurological complications , although the rates of stroke and nerve palsy after surgery are acceptable even in large tumors . this concurs with our results where no patient in our cohort underwent any endovascular procedure although the outcome was optimalhowever , taking into consideration the number of cases per year , this rate is similar to the ratio of most of the published studies . additionally , the follow - up period after surgery does not permit long - term conclusions regarding the recurrence of such tumors . finally , the small number of patients did not allow for subanalysis among the shamblin groups to be performed . multidisciplinary management of patients with cbts is necessary to ensure satisfying results and avoid complications , even in demanding cases . after careful treatment planning and intraoperative manipulations , outcomes are optimal even without preoperative embolization .\noutput:\n" }, { "from": "agent", "value": "objective . aim of this study is to present the experience of our institution in carotid body tumors ( cbts ) treatment . methods . all cases treated in a vascular surgery department within 2.5 years ( 03 / 201309 / 2015 ) were retrospectively evaluated . demographics , diagnostic , and treatment strategy were recorded . all patients with known cbt underwent ultrasound and magnetic resonance imaging preoperatively . all cases were classified according to the shamblin type and evaluated by a radiologist , otolaryngologist , and anesthesiologist before and after surgery . major outcomes included mortality , stroke , cranial nerve injury , and recurrence . results . overall , nine patients ( mean age : 59.5 16.3 years ) with a total of ten cbts were treated . there was no gender prevalence and most of the cases ( 55 % ) were asymptomatic . there were no functional or familial cases . there was only one bilateral case treated in a staged manner . no preoperative embolization of cbts was performed . mortality and stroke rates were null . no severe complication was observed in the early and late setting . no malignancy was recorded . mean follow - up was 15.6 7.8 months . conclusions . multidisciplinary management of patients with cbts is imperative for optimal results , especially in type iii tumors , bilateral or functional cases . after careful treatment planning and intraoperative manipulations , complications could be avoided even without preoperative embolization ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: clinical scoring systems stratify patients on a population basis , but they do not have sufficient sensitivity and specificity to answer fundamental questions about individuals . for instance , is the patient infected , responding to therapy , or likely to recover ? in this issue , monserrat and coworkers report their examination of surface marker expression on peripheral t cells over a 28 - day period ( intensive care unit [ icu ] admission through follow up ) in 52 patients with septic shock and 36 age - matched and sex - matched healthy control individuals . consistent with previous reports , this cohort of septic patients had significantly depressed t - cell numbers on icu admission that persisted for weeks . monserrat and coworkers retrospectively classified patients as either survivors or nonsurvivors and showed that , with the exception of injury severity assessments ( acute physiology and chronic health evaluation ii , multiple organ dysfunction score , sepsis - related organ failure assessment ) , these two groups of patients were similar on enrollment . although all septic patients had similarly depressed numbers of cd4and cd8lymphocytes , serial profiling of the absolute abundance of nave lymphocytes with different phenotypic markers revealed significant differences between survivors and nonsurvivors . the number of cells expressing surface markers of the nave phenotype was significantly higher in nonsurvivors than in survivors . other biomarker studies of icu populations have examined additional patient populations ( critically ill nonseptic patients , and patients with sepsis and severe sepsis ) as well as healthy control individuals and patients with septic shock . the comparison between septic shock and health reveals the most profound differences , and it is easiest to power a study with just those two groups . however , it would be valuable to know whether monserrat and coworkers ' leukocyte phenotype has utility outside the diagnosis of septic shock . no standard critical care protocol was followed for this study , and it is possible that current patient management regimens do not effectively treat the nonsurvivor patient cohort . these findings add to the body of leukocyte phenotyping studies that aim to differentiate patients with syndromic diagnoses that are common in the icu setting [ 2 - 9 ] . results from single - center studies have illustrated that there are multiple leukocyte phenotypes with potential clinical utility for either diagnosis or prognostication . monserrat and coworkers found that the best receiver operator characteristic ( roc ) curve based on a single variable was obtained with data obtained from icu admission , and a cut - off of 136 cd8cd28t - cells per microliter exhibited 70 % sensitivity and 100 % specificity for predicting death ( area under the curve [ auc ] = 0.84 ) . in earlier work , saenz and coworkers identified a monocyte phenotype ( total number of monocytes per microliter [ = 445 ] + percentage of monocytes that were cd13 / hla - dr positive [ 32 % ] ) that distinguished survivors from non - survivors in patients with severe sepsis ( auc = 0.918 ) . by combining two informative variables , those investigators extracted additional power from their data . tschaikowsky and coworkers have already shown that lymphocyte and monocyte markers exhibit concordant changes in a cohort of patients with severe sepsis . it would be valuable to know whether combining the positive predictors from the study by monserrat and coworkers , or whether combining lymphocyte and monocyte phenotyping in the same study , would improve the roc . this study raises numerous questions . if survivors are responding to therapy and recovering , then why was the roc performance best at icu admission ? is it because of loss of individuals from the nonsurvivor cohort , reducing statistical power at subsequent time points , or is the immune compartment in nonsurvivors responding to therapy even though these patients die ? additional demographic information would be valuable to assist in interpreting these data , especially regarding existing co - morbid conditions and the admitting diagnosis . based on the results of interventional trials , it is clear that the type of patient and icu can influence the efficacy or utility of a test or intervention ( for example , intensive insulin therapy has different effects on outcome depending on whether it is instituted in a surgical or medical icu setting ) . if leukocyte phenotyping conclusively identifies a group of patients who can not be rescued by current care , then how should physicians use this information ? from a mechanistic standpoint , these data add support to the hypothesis that failure of the innate immune system to engage the t - cell compartment plays a significant role in sepsis mortality and suggest that immune - supportive or immunostimulatory therapies may be of value in the management of the septic patient . further development of a leukocyte phenotyping - based test for icu patient stratification beyond clinical scoring could aid in both diagnosis and prognosis and , if validated in a prospective patient cohort , could be incorporated into both clinical practice and clinical trial design . auc : area under the curve ; icu : intensive care unit ; roc : receiver operating characteristic .\noutput:\n" }, { "from": "agent", "value": "in a recent study conducted in a cohort of 52 septic patients , monserrat and coworkers found that profound failure of peripheral t cells to convert from a nave phenotype to an activated phenotype has positive predictive value in identifying patients who do not recover . these data support the hypothesis that failure of the innate immune system to engage the t - cell compartment contributes to sepsis mortality and provides motivation for the development and clinical evaluation of immunostimulatory therapies for patients with sepsis ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: a decade ago the discovery of a novel class of evolutionarily conserved small ( 1824 nucleotides ) non - coding rna molecules , mirnas , has revolutionized our view of gene regulation in almost all biological processes . mirnas emerged as counterparts of transcription factors acting at the post - transcriptional level where they target mostly the 3 untranslated region ( utr ) of gene transcripts ( mrnas ) , promoting their degradation or suppressing their translation into proteins , thereby silencing genes . mirna genes are located either as individual or clustered genes in intergenic or intronic regions . they are transcribed by rna polymerase ii as primary transcripts , the so - called pri - mirs . these pri - mirs are cleaved from a length of hundreds to thousands of nucleotides to hairpin - shaped precursors , the pre - mirnas a process that is mediated by a ribonuclease iii called drosha and the double - stranded dna binding protein dgcr8 / pasha . the pre - mirnas are transported to the cytoplasm via the nuclear export factor exportin 5 and further processed into ~ 22 nucleotide mirna duplexes by the ribonuclease iii dicer and its cofactors ( pact and trbp ) . after dissociation one strand of the rna molecule is incorporated into the rna induced silencing complex ( risc ) . the risc - linked mirna is capable of binding to the target mrna leading either to degradation or to translational repression . the pairing specificity of the mirna to the 3 utr of a target mrna is considered to be based on the 5 proximal seed region ( nucleotides 28 ) and the secondary structure of the surrounding region 48 . apart from the watson - crick base pairing , the number and configuration of mismatches between the mirna and the target mrna as well as the number of target sequences on the mrna determine the efficiency of transcriptional repression . moreover , the ability of a single mirna to regulate multiple functionally related mrnas potentiates the strength of mirna - based regulation . this has been repeatedly demonstrated for the liver - specific mir - 122 , which regulates numerous metabolic genes . notably , an inhibitor of mir - 122 ( miravirsen or spc3649 ) is currently tested in a phase 2a clinical trial to assess safety and tolerability in treatment - naive patients with chronic hepatitis c. although remarkable progress has been made in our understanding of mirna biogenesis and function over the past years , the regulatory mechanisms that orchestrate the complex network of mirnas and the mechanisms mirnas use to regulate gene expression are not fully understood . likewise , information on upstream regulators of mirnas that managegenes encoding mirnas are transcribed by rna polymerase ii similar to most of their target mrnas suggesting that transcription factors such as stat3 fine - tune mirna expression resulting in complex regulatory circuits involving positive and negative feedback loops . stat3 belongs to the family of stat proteins , which are activated in response to extracellular signaling proteins including the interleukin ( il ) - 6 family [ il - 5 , il - 6 , il - 11 , leukemia inhibitory factor ( lif ) , oncostatin m ( osm ) , ciliary neurotrophic factor ( cntf ) and cardiotrophin - 1 ( ct - 1 ) ] , erythropoietin and leptin , prolactin and angiotensin ii ( angii ) . upon activation , i.e. , phosphorylation of tyrosine and serine residues , stat3 forms homo - or heterodimers with other stat proteins and translocates to the nucleus where it activates the transcription of downstream target genes by binding to specific dna elements ( gas - motives ) in their promoter . in addition , and as outlined in the present review several mirnas are also transcriptionally regulated by stat3 . the goal of the present review is to highlight regulatory circuits involving stat3 and mirnas in the context of development and pathophysiological conditions related to inflammation , infection , cancer , cardiovascular disease and pulmonary hypertension ( table 1 ) . a better understanding of the complex regulatory networks between stat3 and mirnas may lead to novel specific therapeutic approaches in various disease settings . soon after the recognition of mirnas as fundamental regulators of gene expression , it became clear that mirnas have important regulatory functions during embryonic development . for example , foshay et al . provided evidence that mirna ( mir ) - 17 family members , mir - 17 - 5p , mir - 20a , mir - 93 and mir - 106a , are differentially expressed in developing mouse embryos and function to control differentiation of stem cells . particularly , mir - 93 appears to promote the differentiation of primitive endoderm and trophectoderm in the blastocyst . high expression of mir - 93 and mir - 17 - 5p were also found within the mesoderm of gastrulating embryos acting to delay or enhance differentiation into the different germ layers . notably , one major target gene responsible for the effects of these mirnas on cellular differentiation was stat3 that is known to act as an embryonic stem ( es ) cell regulator . using stat3 - 3utr - luciferase constructs , a regulatory property was particularly shown for mir - 93 and to a lesser extent for mir - 20a but not for the other members of the mir - 17 family . regulatory circuits of stat3 and mirnas play important roles in the neural lineage differentiation of es cells . neural stem cells differentiate into the three main neural lineages : neurons , astrocytes and oligodendrocytes . in the developing central nervous system , activation of stat3is known to direct the differentiation of neural stem cells toward astrocytes and to suppress neurogenesis . two putative brain - specific mirnas , mir - 124a and mir - 9 , appear to be essential for this process since they appear to modulate neuronal differentiation by downregulating canonical stat3 signaling by targeting the gp130 , the lifr and the cntfr . this mirna - mediated suppression of stat3 - mediated effects may promote differentiation of neural stem cells toward neuronal lineage a feature that could be of therapeutic value for potential stem cell therapy in neurodegenerative diseases such as parkinson or alzheimer disease . the branching morphogenesis of the lung is a third example where regulatory circuits between stat3 and mirna may participate in embryonic development . here , particularly the mir - 17 family seems essential for maintaining the homeostasis of epithelial structures in the developing lung since mir - 17 , mir - 20a , and mir - 106b were identified as fine - regulators of both mitogen - activated protein kinase - 14 ( mapk14 ) and stat3 , which in turn regulate cadherin - 1 ( cdh1 ) expression . asa key adhesion receptor cdh1 is essential for epithelial cell identification and grouping during development and mediates the interaction between extracellular matrix , cytoplasmic plaques , and other adhesion molecules . however , detailed molecular links between stat3 and the observed alteration of cdh1 expression remain to be further evaluated . in summary , regulatory circuits involving stat3 and mirnas play important roles during stem cell differentiation and early organogenesis . a better understanding of these interactions may help to improve stem cell based regenerative therapy concepts in the future . in the past decade , numerous mirna - based key regulatory functions in the innate and adaptive immunity have been identified including immune cell lineage commitment , differentiation , maturation and maintenance of immune homeostasis . for example , in primary lineage - negative cells , mir - 125b overexpression enhances colony - formation in vitro and promotes myelopoiesis in mouse bone marrow chimeras . in this process mir - 125b coordinated the regulation of several signaling pathways involving also stat3 to direct distinct phenotypes in myeloid cells , i.e. , blocking granulocyte colony - stimulating factor ( g - csf ) - dependent differentiation of primary lineage - negative cells and at the same time enhancing colony formation in the presence of g - csf indicating that mir - 125b confers a proliferative or survival advantage to myeloid cells . mir - 125b overexpression reduced dna - binding , and transcriptional activity but not induction of tyrosine - phosphorylation and nuclear translocation of stat3 suggesting that mir125b is not interfering with canonical stat3 activation pathways but seems to affect one or more stat3 cofactors . the activator protein 1 ( ap - 1 ) transcription factors c - jun and jund were identified as novel mir - 125b targets , but only gene - specific silencing of jund and not c - jun mimicked to some extend the mir - 125b overexpression phenotype with regard to myelopoiesis and stat3 silencing . thus , mir - 125b , stat3 and jund are interconnected in a novel circuit regulating the differentiation and survival of specific inflammatory cell types from myeloid precursors . additional mirnas , such as mir - 17 - 5p and mir - 20a , exert also suppressive potential on so - called myeloid - derived suppressor cells ( mdscs ) by modulating stat3 expression . mdscs are considered as important components of the immune suppressive network that particularly affects t cell function and are critical factors for tumor - associated immune suppression . importantly , mdscs transfected with mir - 17 - 5p or mir - 20a display reduced ability to suppress antigen - specific cd4 and cd8 t cells . similar to mir - 125b , mir - 17 - 5p and mir - 20a are directly regulating stat3 via seed sequence binding thereby affecting the activity of mdscs . interestingly , the expression of both mir - 17 - 5p and mir - 20a in mdscs was found to be lower in tumor bearing mice than in disease - free animals , which may trigger the suppression of t cell mediated immunity under cancerous condition . it becomes increasingly evident that many mirnas play important roles for the innate immune response . in the context of viral infections , mirnas are regulators of both viral and host cell gene expression , and therefore , can benefit either the virus or the host . consequently , the particular interaction determines the degree to which hosts are able to restrict viral replication and infection and finally the viral pathogenesis and outcome . notably , viruses may use cellular mirnas for their replication machinery , and furthermore , may influence the expression of cellular mirnas and thereby the cellular gene expression for the benefit of their own survival . . reported on a protective role of mir - 155 for the innate antiviral immunity through targeting suppressor of cytokine signaling 1 ( socs - 1 ) , and thus , promoting janus kinase ( jak ) - stat signaling pathway in response to current anti - hepatitis b virus ( hbv ) treatment with interferon ( ifn ) - , which consequently inhibits hbv replication in human hepatoma cells . the contrary situation was shown in a study demonstrating how mirna expression in host cells is dysregulated by viral proteins . the authors showed that the pleiotropic hbv x protein ( hbx ) , which is associated with hepatocellular carcinoma ( hcc ) , induces an alteration of the mirna expression pattern in hepatoma cells . among others , the let - 7 family , in particular let - 7a , was downregulated . further characterization of let - 7a in hepatoma cells implied that it negatively regulates cellular proliferation through direct targeting of stat3 . thus , hbx - mediated downregulation of let - 7a and upregulation of stat3 would promote cell proliferation in hbx transfected cells and induce tumor formation and development of hcc . thus , these studies demonstrate a potential mirna - controlled stat3 axis in the regulation of the innate immunity . in thisregard , modulating mir - 17 - 5p and mir - 20a may lead to immunotherapeutic approaches in the treatment of cancer diseases . in addition , mirna modulation of the stat3 pathway may have the potential to be incorporated into therapeutic control of inflammation and infectious diseases affecting the immunity ranging from viral infections to virus - induced cancer diseases . enhanced activation of stat3 is present in many human cancer types and numerous tumor cell lines and is therefore considered a molecular abnormality that supports the tumor phenotype . recently , the analysis of gene expression data in glioblastoma in combination with matched mirna profiles , uncovered a post - transcriptional regulation layer of surprising magnitude , comprising more than 248,000 mirna - mediated interactions . these include about 7,000 genes , whose transcripts act as mirna sponges and 148 genes that act through alternative , non - sponge interactions . biochemical analyses in cell lines confirmed that this network regulates established drivers of tumor initiation and subtype implementation , including phosphatase and tensin homolog ( pten ) , platelet derived growth factor receptor a ( pdgfra ) , retinoblastoma protein 1 ( rb1 ) , vascular endothelial growth factor a ( vegfa ) , stat3 and runt - related transcription factor 1 ( runx1 ) , suggesting that these interactions mediate crosstalk between canonical oncogenic pathways . in line with this observation , it has been reported that stat3 is constitutively activated in 60 % of primary high - grade malignant gliomas and the extent of activation correlates positively with the glioma grade . interestingly , several mirnas such as mir - 9 , mir - 17 and mir - 20a that assumedly target stat3 were found to be dysregulated . it was suggested that these mirnas serve as potent modulators of glioma subclass - specific gene expression networks and may be useful for subclassification of gliomas such as oligodendrogliomas and glioblastomas . this is an important notion since these disease types have different clinical outcomes and require distinct treatments . the negative regulation of stat3 by mir - 20a via binding to the 3 - utr of stat3 mrna was also demonstrated in pancreatic carcinoma cells , which reveal reduced expression of mir - 20a and in turn enhanced de - repressed stat3 expression and activation , boosting proliferation and invasion pathways in pancreatic carcinomas . therefore , applying mirna - 20a is discussed as a novel approach to treat various carcinomas as an alternative or additional option to current cancer therapies targeting stat3 . for example , the upregulation of mir - 19a / b in multiple myeloma negatively regulates socs - 1 , which is a factor that terminates stat3 activation . likewise , mir - 155 exerts its oncogenic effects in breast cancer , at least in part , by negatively regulating socs - 1 . notably , a point mutation in the mir - 155 binding site of the socs -13-utr was identified in a breast tumor that affects mir - 155 mediated repression and , thus , promotes the proliferation of breast cancer cells . conclusively , by de - suppression of stat3 mir - 19a / b and mir - 155 contribute to oncogenic processes in multiple myeloma . in turn , stat3 - induced mirnas promote the oncogenic potential of stat3 by downregulating tumor suppressor genes . for example , pten has been long known as a suppressor of tumor growth by de - activating akt signaling . interestingly , pten expression variability induced by mirna - mediated regulators was predictive for tumor cell growth rates . mir - 21 has been identified as a negative regulator of pten expression and it has been demonstrated that stat3 acts as a transcription factor for mir - 21 expression in various tumor cell lines ( myeloma , prostate cancer cells ) in response to il - 6 and ifn - . meanwhile , mir - 21 is considered as an oncomir with numerous anti - apoptotic features in various carcinomas . interestingly , mir - 21 initiates the transformation of a non - neoplastic cell into a cancer cell by inducing a complex epigenetic switch . this mechanism involves a direct upregulation of mir - 21 and also mir - 181b in an il - 6 / stat3 - dependent manner . mir - 21 and mir - 181b inhibit pten and cylindromatosis ( cyld ) tumor suppressors , leading to increase nuclear factor b ( nfb ) activity that is required to maintain the transformed state . these stat3 - mediated regulatory circuits appear to be crucial for the neoplastic transformation in tumor cells such as in colon adenocarcinomas . the role of the stat3 - mir - 21 axis in cancerous cells was further demonstrated by yang et al . who suggested a stat3 and nfb co - regulation of mir - 21 at the level of the mir - 21 promoter in response to ifn , thereby counteracting as a key feedback regulator of ifn - induced apoptotic mechanisms . furthermore , evidence exists that the stat3 - mir - 21 circuit also plays a role in tumor metastasis since mir - 21 downregulates beside pten and ifn - induced apoptosis additional tumor suppressors ( programmed cell death protein 4 , pcdp4 ) and anti - proliferative proteins ( b cell translocation gene 2 , btg2 ) thereby promoting cell proliferation , migration and survival in metastatic tumor cells such as b16 melanoma cells . thus , stat3 is interconnected with mirnas at multiple levels in complex regulatory circuits ( fig .1 ) that are involved in positive feedback loops of oncogenic transformation mechanisms , proliferation , survival and migration of tumor cells and the epigenetic switch that links inflammation to cancer . figure 1 . examples of stat3 involvement in mirna based regulatory mechanisms in cancer disease . activated stat3 acts as a transcription factor for mir - 181b and mir - 21 expression in various tumor cells . in turn , mir - 21 reduces expression of tumor suppressor genes such as pten and cyld , which ultimately promote tumor transformation and growth through activation of akt and nfb signaling . note the positive feedback loop of nfb as a co - regulator of mir - 21 at the level of the mir - 21 promoter in response to ifn . other tumor suppressors regulated by mir - 21 are pcdp4 and anti - proliferative proteins like btg2 , which , when downregulated , lead to enhanced cell proliferation , migration and survival in metastatic tumor cells . in recent years , mirnas have emerged as fundamental regulators of cardiovascular development , physiology and pathology , such as myocardial infarction , fibrosis , hypertrophy and vascular dysfunction . this recognition has emerged from numerous studies with genetically modified animal models , by systemic administration of mirna silencers , the so - called antagomirs , in small animal models , as well as from studies on circulating extracellular mirnas in the serum or plasma of patients with cardiovascular diseases . we recently demonstrated a pathophysiological circuit in the heart between reduced stat3 protein levels , increased mir - 199a expression and subsequent impairment of the ubiquitin - proteasome system ( ups ) that disrupts the sarcomere structure of cardiomyocytes and impacts on the cardiomyocyte secretome impairing endothelial cell function . we found that failure - prone hearts of mice with a cardiomyocyte - specific deletion of stat3 ( stat3 - ko ) displayed upregulated cardiac expression of mir - 199a before the onset of heart failure . further analysis revealed that stat3 protein acts as a potent suppressor of mir - 199a transcription in postnatal cardiomyocytes . in turn , upregulated mir - 199a expression in stat3 - ko resulted in disturbance of the ups because mir - 199a suppressed the ubiquitin - conjugating enzymes ( ube ) ube2i and ube2g1 . suppression of ube2i and ube2g1 in cardiomyocytes in vivo and in vitro was associated with marked downregulation of specific sarcomeric proteins , i.e. , - and - myosin heavy chain , derangement of the sarcomeric ultrastructure and an eccentric hypertrophy phenotype of the cardiomyocytes . in addition , the mir - 199a - mediated impairment of the ups caused an accumulation of asymmetric dimethylarginine ( adma ) that was released by cardiomyocytes in concentrations able to impair endothelial cell function suggesting that the regulatory circuit between stat3 and mir - 199a impacts on cardiomyocyte and endothelial function in the heart . the potential clinical importance of our findings were underscored by observations in the terminal failing human heart , where low stat3 protein levels were associated with increased mir - 199a levels and reduced ube2g1 expression . another study reported on a potential role of stat3 for cardiac stem cell therapy using a rodent model of myocardial infarction . here it was demonstrated that ischemic preconditioning would improve the survival of bone marrow - derived mesenchymal stem cells ( mscs ) prior to engraftment and promote their paracrine activity as well as their differentiation in a way that involves a stat3 - dependent upregulation of mir - 21 . thus , regulatory circuits involving stat3 and mirnas play important roles in normal cardiac function by maintaining sarcomere homeostasis and endothelial function and seem to be important for protective and regenerative mechanisms during pathophysiological insults such as myocardial ischemia . pulmonary hypertension ( ph ) is a severe disease with high morbidity and mortality that results from an increased pulmonary arterial pressure . symptoms include shortness of breath , dizziness , fainting , markedly decreased exercise tolerance and right ventricular heart failure . mutations in the bone morphogenetic protein ( bmp ) type ii receptor ( bmpr2 ) downregulated expression of bmpr2 in idiopathic ph suggest that dysfunctional bmp signaling plays a crucial role in the pathophysiology of ph . bmpr2 is known to be crucial for differentiation , proliferation , and the fibrous matrix production of both endothelial and smooth muscle cells . brock et al . identified bmpr2 as a direct target of mir - 17 - 5p and mir - 20a , two mirnas in the mir - 17/92 cluster . furthermore they demonstrated that il - 6 upregulates the expression of the mir - 17/92 cluster in human pulmonary arterial endothelial cells via the gp130 - stat3 signaling cascade and showed that a highly conserved stat3 - binding site is present in the promoter region of the mir - 17/92 gene ( c13orf25 ) . in particular , they showed that persistent activation of stat3 via mir - 17 - 5p and mir - 20a reduces the expression of bmpr2 protein through conserved seed matches within the 3 - utr of its mrna . thereby , chronic activation of il -6-gp130-stat3 signaling leads to a downregulation of bmpr2 , which in turn could promote vascular remodeling in the arterial vessels of patients with ph . the pathophysiology of ph appears to include enhanced proliferation and reduced apoptosis of pulmonary artery smooth muscle cells ( pasmcs ) . stat3 seems to promote proliferation and survival of pasmcs by downregulating the expression of mir - 204 . mir - 204 directly targets the expression of protein - tyrosine phosphatase sh2 domain - containing cytoplasmic protein ( shp2 ) , therefore stat3 - dependent downregulation of mir - 204 subsequently leads to shp2 upregulation that via activation of the src kinase and the nuclear factor of activated t cells promotes pasmcs proliferation and resistance to apoptosis , a feature that may promote ph progression . taken together , these studies uncover novel regulatory pathway involving stat3 as transcriptional activator or repressor of mirnas that are critically involved in the etiology of ph and indicate that targeting mirnas should be explored as a potential new therapeutic strategy for this disease . while at the beginning of the mirna era the main research focus was put on genomic alterations of mirna expression pattern that would affect the respective target gene or a functional group of genes , recent studies have identified upstream regulators of mirnas , such as stat3 , and broadened our understanding of how these upstream regulators are interconnected with mirnas to regulate many physiological and pathophysiological processes ( fig . 2 ) . mirna - mediated targeting of stat3 as well as key steps in the stat3 signaling pathways illustrate new positive and negative feedback loops that can control the outcome of stat3 mediated actions and opens up an exciting new avenue in stat3 research ( fig . 2 ) . scheme illustrating stat3 mediated processing of individual mirnas and contrariwise , the modulation of the stat3 pathway by mirnas at different levels . stat3 mediates positive and negative regulation of various mirnas at the transcriptional level . on the other hand , this signaling pathway is controlled by numerous mirnas at the receptor level , by modulating its activators and suppressors and by direct regulation of stat3 mrna . approximately 50 mirnas are predicted to bind the 3 - utr of stat3 , of which let - 7 , mir - 20a and mir - 93 were directly validated using stat3 - 3 - utr - reporter constructs . in view of the versatility of the studies illustrated here , it becomes apparent that a mirna - stat3 axis plays a major role in development , in adult organ systems and in various pathophysiologies ( table 1 ) . consequently , a strict tissue - specificity for targeting the mirna - stat3 interaction has to be provided since persistent modification of stat3 in other organs could evoke off - target effects with severe complications . a mirna - based approach to modifythe stat3 pathway may offer novel options to confine the off - target effects , as some mirnas seem to be predominantly expressed in a tissue - specific manner . at the same timethis approach would imply new challenges , as modification of a given mirna would affect other targets beyond the stat3 signaling pathway . in conclusion , with mirnas as new players in the complex biological networks it remains to be carefully evaluated whether future investigatory efforts will implement sustained translation of experimental mirna data into the clinical arena or whether it gets lost in translation .\noutput:\n" }, { "from": "agent", "value": "micrornas ( mirnas ) are endogenously expressed small non - coding rnas acting at the post - transcriptional level where they promote mrna degradation and block protein translation . recent findings suggest that complex transcriptional and post - transcriptional circuits control mirnas . stat3 has emerged as an important regulator of their expression and biogenesis and , in turn , stat3 signaling pathways are controlled by distinct mirnas . we summarize the current knowledge on stat3 mediated processing of individual mirnas and contrariwise , the modulation of the stat3 pathway by mirnas in development and in pathophysiological conditions such as immune processes , infection , cancer , cardiovascular disease and pulmonary hypertension ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: it can affect any age , but primarily involves children aged less than 5 years and causes paralysis in one out of every 200 to 1000 infected individuals . eradication of poliomyelitis is attained through widespread immunization , and vigilant surveillance for acute flaccid paralysis ( afp ) , reinforced with laboratory implementation . surveillance should be performed not only for paralytic poliomyelitis , but also for other conditions including guillain - barr syndrome ( gbs ) , among children aged less than 15 years . therefore , the surveillance system was organized to identify the clinically suspected cases of poliomyelitis , and then to track them using laboratory investigations to either rule in or rule out the diagnosis of poliomyelitis caused by the wild poliovirus . afp surveillance is a key strategy for monitoring the progress of polio eradication and is a sensitive measure for detecting the potential cases of poliomyelitis and poliovirus infection . the world health organization ( who ) has devised a set of performance indicators to ensure that afp surveillance is properly maintained . an active surveillance program for afp was established by the iranian government based on new indictors recommended by who guidelines . kurdistan is one of the largest provinces in west iran , with a population of about 1.5 million . kurdistan has the largest common border with iraq and may be the portal tray of poliomyelitis from this country . on the other hand , afghanistan and pakistan represent a common epidemiological reservoir of poliovirus . the long border of iran with these two countries requires continuous and vigilant surveillance system to timely detect poliomyelitis cases . we aimed to describe the characteristics of patients reported with afp , and to evaluate the performance of the afp surveillance system using indicators recommended by the who . our study summarizes the findings of the afp surveillance conducted in kurdistan during 2000 - 2010 . this observational study was conducted at the kurdistan center for diseases control and the department of pediatrics , kurdistan university of medical sciences . the four steps of afp surveillance recommended by who were followed as : finding and reporting children with afptransporting stool samples for analysisisolating and identifying poliovirus in the laboratorymapping the virus to determine the origin of the virus strain . finding and reporting children with afp transporting stool samples for analysis isolating and identifying poliovirus in the laboratory mapping the virus to determine the origin of the virus strain . the who has defined afp as any child under 15 years of age with acute onset of focal weakness or paralysis ( including gbs ) or any person with paralytic illness at any age when polio suspected , characterized by flaccid ( reduced tone ) , without other obvious causes ( e.g. trauma ) . data regarding the demographic characteristics of the patients , dates of evaluation , diagnosis , follow - up , and laboratory findings were included in the questionnaire . all documents including copies of the patients charts , laboratory findings , imaging and electrodiagnostic evaluations ( electromyography [ emg ] and nerve conduction velocity studies [ ncs ] ) even if performed in other hospitals were collected in an exclusive file . the staffs in all health facilities from district health centers to large hospitals were educated to promptly report every case of acute flaccid paralysis ( afp ) in any child less than 15 years of age . our public health staff made regular weekly visits to hospitals and all private medical clinics to search for afp cases which may have been overlooked or misdiagnosed . a specially designed form had to be signed by attending physicians in the health care centers for any suspicious case or \" zero reporting \" of afp . all children with afp were reported and tested for wild poliovirus within 48 hours of onset , even if the physicians were confident on clinical grounds that the child did not have polio . close contacts of the patients were traced to ensure that they had been fully immunized . according to the who guidelines , which require that adequate stool samples be collected within 14 days of the onset of paralysis , two specimens taken 2448 hours apart were gathered . stool specimens were sealed in containers and stored immediately inside a refrigerator or packed between frozen ice packs at 48c in a cold box , and shipped to the national laboratory in tehran within 72 hours of collection . the national polio laboratory ( nlp ) is located at the school of public health affiliated to tehran university of medical sciences and has been integrated into the network of polio laboratories run by the world health organization since 1996 . it is also a who - accredited laboratory to perform intra - typic differentiation of polioviruses . more recently , the iran national polio intratypic differentiation ( it d ) laboratory has been accredited again by who from may 2010 to april 2011 based on the overall review for 12 months . the laboratory had passed the proficiency test . from january 2000 to december 2010 , all children who fulfilled the who definition for afp were included in our study . all the patients were evaluated for 60 days after the onset of symptoms to identify the signs of residual weakness . the afp committee of the kurdistan university of medical sciences formed an expert panel consisting of three consultants including a pediatric infectious diseases sub - specialist , a neurologist , and an infectious diseases specialist to classify the afp cases according to the who recommendations . the who protocol for case classification was followed to determine which patients should undergo review by the expert panel ( fig . this group included patients whose stool specimens were insufficient for laboratory diagnosis , who still suffered from residual weakness , or who had not been followed up . a detailed case report was given to each panel member who independently evaluated each case . the panel members views and comments were documented and a consensus was reached for the final classification of each patient . the diagnosis was made following a complete review of the clinical and epidemiological data , emg and ncs studies follow up outcome and laboratory results of stool cultures for polio and non - polio enteroviruses provided by npl . these forms were filled up and signed by members of the provincial committee every 3 months and faxed to the national expert committee ( nec ) in tehran . if the cause of a case of afp could not be determined at the provincial level , the case was referred to the nec , which was responsible for the final diagnosis . this committee consists of eight experts ( a pediatrician , virologist , infectious diseases specialist , neurologist , and an epidemiologist ) . ncc convenes several times per year , reviews reports , interacts with the provincial committee and the nlp , and prepares an annual report of the situation for the who eastern mediterranean regional office ( emro ) . after final approval of the data by ncc , feedback was provided to the provincial committee . ( the permission citing this figure was obtained from the who , with the permission i d : 102317 ) the detected cases were divided into four different age groups . then in order to estimate the annual incidence rate of afp in population aged less than 15 , we used the poisson regression . the data were analyzed using r software , version 2.15 to generate statistics based on the who performance indicators . one - hundred thirty nine children with acute flaccid paralysis aged from 2 months to 14 years were reported to the center for diseases control during 20002010 periods . table 1 shows the incidence of afp by age and sex . according to the poisson regression analysis , the incidence of diseases manifesting as afp such as gbs were highest in early years of age , 66 % of patients were less than 6 years old [ relative risk ( rr ) = 5.93 , 95 % confidence interval ( ci ) : 3.2 , 10.7 , p 0.001 ] . maleshowever this difference was not statistically significant [ rr = 0.93 , 95 % ci : 0.77 , 1.12 , ( p = 0.5 ) ] . sixty percent of children were from urban areas . in 139 ( 100 % ) of the cases stool samplesstool examination was adequate in all cases and was sufficient to exclude poliomyelitis . in 138 ( 99 % ) stool samples no poliovirus was isolated ( table 2 ) . in one stool sample , this child was vaccinated one week after the occurrence of paralysis and therefore paralysis was not related to polio vaccination . the major clinical causes of afp were gbs ( 56.8 % ) , central nervous system ( cns ) infection ( 4.3 % ) , cns tumors ( 5.1 % ) , transverse myelitis ( 5 % ) , myasthenia gravis ( 2 cases ) , hypokalemic paralysis ( 2 cases ) , and botulism ( one case ) . the diagnosis of gbs was based on the classic clinical feature of symmetric ascending paralysis . in the 37 % of the cases emg and ncswere performed but cerebrospinal fluid analysis data were available for only 13 % of the cases . in some cases with dominant cns manifestation , mri or ct scan of the brain or spinal cord was performed to rule out mass occupying lesions . most children had an uneventful recovery , but residual weakness persisted in 28 ( 20 % ) patients . four children with the final diagnosis of gbs ( 1 case ) , encephalitis ( 1 case ) , congenital myopathy ( 1 case ) and metabolic encephalopathy ( 1 case ) expired . eleven cases that were primarily reported as afp by primary care physicians were discarded by the afp provincial committee because their clinical pictures were not compatible with the definition of acute flaccid paralysis . the stool cultures for all of them were negative and all had an uneventful recovery . the results of these cases were not counted in the final report to avoid over diagnosis and over - counting the afp cases . all of these cases with their classification were reported to nec and feedback was provided by nec . mean annual incidence rate of afp per 100,000 under 15 year old children by age and gender using poisson regression analysis the overall incidence of afp was calculated as 1.3 to 3.6 ( mean 3.2 ) per 100000 population in kurdistan during the study period ( table 2 ) . the incidence was lowest in the early years of the study and received highest ( 6.1 ) in 2006 . the mean incidence of gbs was calculated as 1.7 . during the study , a high coverage rate for poliovirus vaccination was maintained . based on several studies with cluster sampling , the coverage rate for 3 doses of oral poliovirus vaccine remained well high at about 100 % ( table 2 ) . the peak incidences of afp occurred during may ( 14 patients ) and june ( 17 patients ) , which coincides with the higher enterovirus activity associated with summer months ( fig . afp surveillance indicator statistics in kurdistan province comparing with iran and emro in total no . of acute flaccid paralysis ( afp ) gbs was the most common cause of afp in our study , which is consistent with the findings of other studies . this syndrome occurs throughout the world with an annual incidence of 0.44 ( mean 1.3 ) cases per 100000 population . our surveillance data suggest that about seven cases of gbs per year will be diagnosed with paralytic presentations in kurdistan . considering the population in kurdistan , this figure for individuals under 15 years of age gives a mean incidence of 1.7 per 100000 . the diversity of end diagnosis of afp patients was similar to other reports with some differences ( table 3 ) . myositis and toxic synovitis of the hip were among the less frequent diagnoses in other series . notably , in a few reports trauma or posttraumatic lesions had been reported as afp . in some cases , the underlying mechanism initially had been obscure so necessitated investigation of the cases to rule out poliomyelitis . however when the trauma is clear mechanism of the paralysis , it should not be reported as afp in the final report . the diagnoses of afp is very diverse because many diseases can mimic symptoms and signs of poliomyelitis . accordingly , the diagnosis reports should be mostly based on symptoms and signs of a specific involved organ system . etiological diagnosis should be reserved for the specific diagnosis of poliomyelitis . using both organ specific and etiological agents for reporting diagnoses other than poliomyelitis may be misleading in developing countries . in many developing countries , diagnosis by etiological agent has only been possible in remote specialized reference laboratories for poliovirus using specific culture media . the afp surveillance system should be based on a unique guideline for reporting specific diagnoses to be able to compare results of many locations and countries . the who has defined the target of detecting at least one afp case per 100000 in children under15 years of age per year as a measure to evaluate the effectiveness of afp surveillance . this ratio was increased to two cases per 100000 because iran is near polio - endemic countries such as afghanistan , pakistan and iraq . by detecting 1.3 to 3.6 ( mean 3.2 ) cases per 100000 population in kurdistan comparing 3.1 to 3.3 rate for iran and 4.4 to 5.6 for eastern mediterranean region of who during the study periodthe number of reported cases of afp was relatively higher during the summer months because of higher enterovirus activity . adequate virological examination was performed for more than 90 % of patients ( table 2 ) . virus isolation from feces or throat swabs was successful for only a minimum of 5 % of the patients . who target for non - polio enterovirus isolation rate is 10 % . this indicator remained regularly below the acceptable rate in recent years in our country ( table 2 ) . according to polio laboratory network update \" a major change in 2000 is the substitution of poliovirus - specific l20b cells for npev - sensitive hep2 cells in national reference polio laboratories . because isolation of npev now depends solely on rd cells , annual rates for most laboratories are expected to be lower than in previous years . \" the npev rate is no longer a strict criterion for accreditation of reference laboratories because the isolation rate is affected by various factors such as the season of the year , altitude , or population hygiene levels . consequently , there is a need to improve the virological culture technique of patients with afp in our country . other performance indicators have met who criteria with regard to afp rate , timeliness of reporting , and adequate epidemiological investigations ( table 2 ) . number of cases ( % ) with neurological diagnoses of acute flaccid paralysis ( afp ) from 2000 to 2010 comparing to other reports our report shows that improvements are needed , particularly with regard to laboratory investigation of afp cases . \" satisfactory afp surveillance programs rely on three factors : detection , investigation , and timely reporting of cases . \" afp surveillance results in our region indicate that vigilance in case detection and reporting meet the who standards . the completeness and accuracy of reporting was further improved by reviewing hospital discharge records as secondary data sources . our study was disadvantageous for the some disorganization of data collected during early years of the study . another limitation of our study is that the data collection using questionnaires was done by health care workers and therefore , some answers could be subject to error and may be less reliable . the surveillance system for afp was effective in kurdistan province and compares well in most aspects with other systems in the eastern mediterranean region . the surveillance system and its evaluation may serve as a model for surveillance of other infectious diseases . conception and design , acquisition of data , analysis and interpretation of data : j. soltani , n. esmailnasab , d. roshani acquisition of data , patient selection and follow up : m karimi , m.j .\noutput:\n" }, { "from": "agent", "value": "abstractobjectivethe surveillance of acute flaccid paralysis ( afp ) is a key strategy for monitoring the progress of poliomyelitis eradication and is a sensitive measure for detecting potential cases of poliomyelitis and poliovirus infection . this study was conducted to describe the characteristics of patients reported with afp , and to evaluate the performance of the surveillance system in kurdistan province , western iran , using indicators recommended by the world health organization ( who ) . methodsthis observational study was conducted from january 2000 to december 2010 at the kurdistan center for disease control and the department of pediatrics . all children who fulfilled the who definition for afp were included in our study . the stool samples of all the children were sent for poliovirus isolation . all the patients were evaluated for 60 days after the onset of symptoms to identify the signs of residual weakness.findingsone - hundred thirty nine children aged < 15 years were reported to the center for diseases control with afp . in 138 ( 99 % ) stool samples no poliovirus was isolated . none of the patients was diagnosed as having acute poliomyelitis or polio - compatible paralysis . guillain - barr syndrome was the most frequent final diagnosis ( 79 cases ) followed by transverse myelitis ( 7 cases ) and encephalitis ( 6 cases ) . by detecting 1.3 to 3.6 ( mean 3.2 ) afp cases per 100 000 population in kurdistan during the study period , we achieved the who target for afp surveillance . all performance indicators but one consistently met the who requirements and therefore demonstrated the effectiveness of the afp surveillance program in kurdistan.conclusionthe effective surveillance system in kurdistan and its evaluation may serve as a model for the surveillance of other infectious diseases ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: carboxylic acids are pervasive in nature and are produced industrially on a large scale . therefore , methods of employing them in organic preparations have received a lot of attention . hard uv ( 250 nm ) irradiations generate carbon - centered radicals but also induce much degradation . conventionally , decarboxylative alkylations have relied on preparations of unappealing precursors such as peroxides , barton esters , or hunsdieker salts . recently attention shifted toward discovering catalytic systems capable of utilizing them in target - oriented syntheses . decarboxylative copper - catalyzed reactions of carboxylic acids with carbonyls and with aldimines , and of amino acids with alkynes have been reported . photoredox methods have also been used for this purpose but can suffer from difficulties in removing the catalyst . interest in heterogeneous photoredox methods for carboxylates dates back to the 1970s and the photo - kolb reaction . the chosen semiconductor can be nontoxic and can easily be removed by filtration , and when visible or soft uva light is used , the procedure can be convenient and benign . most applications of tio2 scpc have utilized aerobic conditions , resulting in selective oxidations of organic substrates or more complete substrate mineralizations . under anhydrous , anaerobic conditions and with certain substrates , tio2 scpc can lead to the generation of specific radicals adapted for molecular assembly applications . to date , however , only a modest number of such processes have been identified and developed . notably , scpc additions of enol ethers to various acceptors have been investigated , and successful additions of tertiary amines to electron - deficient alkenes , some bearing chiral auxiliaries , have been described . we recently discovered that under dry , anaerobic conditions , tio2 mediation with carboxylic acid precursors could result in carbonalkylations and annulations were achieved when photolyses of certain acid precursors were carried out in the presence of suitable electron - deficient alkenes . this paper reports advances in crucial aspects of this process in the following areas : ( 1 ) structural features in the carboxylic acids that are necessary and sufficient ; ( 2 ) the range of functionality in the alkene acceptors that can be tolerated ; ( 3 ) how the reactions respond to modifications to the catalyst form and the catalyst support ; and ( 4 ) the mechanism followed by the reaction . in our preliminary study , we discovered an experimental protocol with reasonably wide applicability utilizing degussa ( evonik ) p25 as a 15 mg ml dispersion in dried acetonitrile . this dispersion , with added carboxylic acid and substrate , in an oven - dried pyrex tube was purged with argon and then irradiated by two face - to - face sunlamp arrays ( uva ) at ambient temperature . after photolysis , the catalyst was removed by filtration and the products were isolated by conventional organic techniques . during initial investigations , n - phenylmaleimide ( 2 ) was found to be an ideal radical acceptor in this system , as it is symmetrical and photostable , its photodimerization is negligible ( under our experimental conditions ) , and its electron - withdrawing character favors addition by weakly nucleophilic radicals . this alkene was therefore chosen to test the applicabliity of our process with simple aliphatic carboxylic acids 1 . standard unoptimized conditions were adopted so a clear comparison of behavior from acid to acid could be obtained ( table 1 ) . in all instances ,0.1 mmol of 1 and 0.2 mmol of 2 were photolyzed in a suspension of the p25 catalyst ( 12 mg , 0.15 mmol ) in ch3cn ( 12 ml ) for 18 h. the reactions did indeed lead to the formation of adducts 3 incorporating the r moiety of the carboxylic acid and an additional h atom , together with significant amounts of succinimide 4 ( scheme 1 ) . for acids that decarboxylated to give methyl ( entry 1 ) or primary radicals ( entries 2 and 3 ) , the yields were low ; however , increased yields were obtained with secondary and tertiary radicals ( entries 4 and 5 ) . negligible adduct was detected for the destabilized , - type cf3 radical ( entry 6 ) . the efficiency of the process evidently increased as the stabilization energy of the released radical increased ( see the supporting information for a plot of radical stabilization energy vs yield ) . the observation of a significant amount of 4 in each case suggested that alkene 2 plays the role of an electron sink , consuming electrons in two sequential reduction protonations . we next examined a set of addition reactions with n - phenylmaleimide involving more diverse carboxylic acids ( scheme 2 ) . primary alkyl radicals stabilized by - alkoxy groups proved to be a good deal more reactive than the simple alkyl radicals . methoxy - and tert - butoxyacetic acids gave the corresponding adducts ( 3 g and 3h ) in reasonable yields of 54 % and 57 % , respectively , while 2 - tetrahydrofuroic acid furnished a 1:1 mixture of the two diastereomers of 3i in a very pleasing yield of 75 % . however , methylthioacetic acid returned only a disappointing 34 % yield of the desired product 3j . moderate and poor yields were obtained with benzyl ( 57 % ) and 2 - thienylmethyl acids ( 22 % ) , but these adducts ( 3k and 3l ) were accompanied by the dimers bibenzyl ( 18 % ) and 1,2 - bis ( thiophen -2-yl ) ethane ( 27 % ) , respectively . accompanied by dimers ( see the text ) . decarboxylative additions also worked with boc - protected - amino acids , and the bottom row in scheme 2 displays the adducts and the useful yields obtained . while boc - proline was transformed into adduct 3n in a fine yield of 75 % , boc - alanine and the unnatural - amino acid boc - piperidinecarboxylic acid gave much more modest yields of 38 % and 29 % , respectively . no retention of chirality was observed when optically pure amino acids were employed because the released radicals have planar , or close to planar , configurations at their reactive centers . surprisingly , vinylacetic , ethynylacetic , and cyanoacetic acids failed to react , even though the released radicals would be strongly stabilized . to compare the efficiencies of different forms of the titania catalyst , the reaction of phenoxyacetic acid with acrylamide , which was clean and efficient ( 82 % adduct isolated ) was chosen . for each photolysis , suboptimum conditions of phenoxyacetic acid ( 0.1 mmol ) and acrylamide ( 0.2 mmol ) with irradiation for 17 h in anhydrous ch3cn ( 12 ml ) were employed . where applicable , tio2 ( 12 mg ) was employed in a 1 mg ml dispersion ( see the supporting information for full details ) . with p25 itself ( table 2 , entry 1 ) , a 47 % yield of the 4 - phenoxybutanamide adduct was recorded . with millenium pc500 titania , having about 6 times the surface area , the yield dropped slightly ( entry 2 ) . reactions were also carried out in schlenk tubes coated with a fine internal layer of tio2 by a sol gel process ( see the supporting information for details ) . these proved to be very efficient and led to the best yield ( entry 3 ) . tio2 photospheres consisting of hollow pyrex beads coated externally with rutile titania delivered lower conversion and adduct yields ( entry 4 ) . this was attributed to difficulties in dispersing the photospheres satisfactorily throughout the reaction flask . because of their buoyancy , they tended to accumulate at the top , and this was compounded by the fact that the high rate of magnetic stirring used in attempts to overcome this tended to result in their becoming damaged . an isolated yield of 68 % was achieved upon scale - up of the reaction in the coated tube ( entry 3 ) . incorporation of 4 - tert - butyl and 4 - trifluoromethyl substituents in the aryl ring of the acid component furnished the corresponding adducts in similarly pleasing yields of 68 % and 66 % , respectively . although the sol gel - coated tubes gave the best yields and conversions , the coatings tended to detach , so they could only be used about three times . we therefore concluded that for ease of handling with conventional organic techniques , scale - up , and efficient product formation , the orthodox p25 catalyst was the best compromise . isolated yield from 5:1 acid / acrylamide irradiated for 62 h. millenium pc500 ( anatase , surface area 300 m g , particle size 510 nm ) . hollow glass spheres ( mean diameter 45 m , density 0.22 g / ml ) coated with tio2 , from microsphere technology . the reaction of aryloxyacetic acids ( 5 ) with n - substituted maleimides ( 2 ) led to n - substituted -3,4-dihydrochromenopyrrole-1,3-dione derivatives 6 , each accompanied by a significant amount of the expected adduct 7 ( scheme 3 ) . tricyclics 6 presumably resulted from cyclization of the initial adduct radical onto the aryl ring followed by rearomatization . good to excellent overall yields were obtained under all conditions ( table 3 ) . a moderate amount of succinimide ( 1143 % yield ) was also formed in each case . dispersion of 1 mg ml except for dd = dense dispersion of 5 mg ml . table 3 shows that the process worked well with both electron - releasing and electron - withdrawing substituents in the aromatic ring and for methyl - and phenyl - substituted maleimides . the reactions with just p25 generally gave a slight excess of the chromenopyrrole 6 ( entries 1 , 4 , 6 , 8 , and 10 ) , except in the case of the cf3 substituent ( entry 12 ) , for which an excess of adduct 7 was observed . the selectivity for chromenopyrroles 6 was improved by using a more dense dispersion of p25 ( entries 2 , 7 , and 11 ) . on the other hand , gel tio2 - coated tubes ( entries 3 , 5 , 9 , and 13 ) led to a reversal in selectivity with predominant formation of adduct 7 . the possibility to tuneh coupling constants between the two protons at the junction of the pyran and dihydropyrrole rings within the range of 9.29.3 hz . this indicated a cis arrangement , in agreement with the conclusion that the reaction selectively formed the cis isomer in every case . very few syntheses of dihydrochromenopyrrole -1,3-diones 6 have been reported , but compounds with the corresponding reduced ring system , chromenopyrrolidines , are well - known biologically active species . three types of acid framework with different acceptor groups were prepared to test the applicability of p25 - mediated ring closures .2 - ( 2 - vinylphenoxy ) acetic acids having alkene acceptors with ester ( 8a ) , nitrile ( 8b ) , and ketone ( 8c ) substituents ( scheme 4 ) were obtained by treatment of 2 - formylphenoxyacetic acid with the appropriate phosphorane ( see the experimental section ) . c having aromatic acceptors were prepared by coupling of the appropriate 1,1 - biphenyl -2-ol with methyl bromoacetate and subsequent hydrolysis of the ester with lioh in meoh / h2o . acids 13a and 13b having oxime ether acceptor groups were prepared by condensation of 2 - formylphenoxyacetic acid with the appropriate alkoxylamine hydrochloride . the second used 1 ml aliquots of acid solutions ( 10 mm ) in cd3cn ( 5 ml ) in sol gel - coated nmr tubes . the tubes were purged with argon and then placed in an overhead stirrer ( turned on its side ) , which was then spun at 250 rpm . the tube was held at a slight angle with respect to horizontal in the chuck of the overhead stirrer so that , when rotated , it described a small ( ca .2 cm ) circle at its non - chuck - held end so as to agitate the reaction solution . irradiation was performed using a photoreactor with twelve 8 w black light blue ( blb ) uv lamps ( max = 365 nm ) ( see the supporting information for a graphic ) . periodically the tube was removed for nmr analysis . this was repeated until all of the starting material had been consumed or the product concentration plateaued . for acids 8a c with alkene acceptors , control photolyses in the absence of tio2 showed that e / z isomerization was significant ( 5279 % ) . in conventional p25 - mediated reactions , 8ac all gave rather complex product mixtures containing unreacted alkene as a mixture of e and z isomers ( 8/9 ) as well as the 5 - exo ring - closed dihydrobenzofurans 10 . nmr and gc ms analyses showed complex product mixtures containing possible trace amounts of the cyclized 6h - benzo [ c ] chromenes 12a c . the 2,3 - dihydrobenzofuran core of 10 is found in many natural products and pharmaceutically relevant molecules and has generated much interest . yields in brackets are maximum yields from nmr monitoring of sol gel tube reactions . the reaction profile from irradiation of acid 8a in a sol gel - coated tube obtained by nmr monitoring ( figure 1 ) shows the sharp decrease in 8a ( the e isomer ) , which was all consumed in 150 min . the z isomer 9a initially increased , passed through a maximum at about 25 min , and then steadily decreased as it too was converted to cyclic product 10a . analogous reaction profiles were obtained for the sol gel tube reactions of 8a c , 11b , and 13a . gel tube reactions of 11a and 11b . a significant yield ( 28 % ) of the cyclized product n - ( 2,3 - dihydrobenzofuranyl ) - o - methylhydroxylamine ( 14a ) was found in the sol gel tube reaction of oxime ether - functionalized acid 13a ( scheme 4 ) . however , attempts to isolate and fully characterize this alkoxyamine were not successful . reaction profile for acid 8a obtained by nmr monitoring . hole capture at the tio2 surface by a carboxylate creates the corresponding acyloxyl radical . radicals of this type were directly observed by cw x - band epr spectroscopy of frozen suspensions of p25 and t - buco2h in ch3cn . transient t - bu radicals and phoch2 radicals were observed during uv irradiation of the acids t - buco2h and phoch2co2h , respectively , with pc - 500 in fluid phh at 300 k. in similar epr experiments with vinylacetic acid and 2,2,2 - triphenylacetic acid , we were also able to detect and characterize allyl and triphenylmethyl radicals , respectively ( see the supporting information ) . the isotropic character of the solution epr spectra of all the rxch2 radicals established that in the main they were freely tumbling and not attached to the tio2 surface ( scheme 5 ) . literature precedents imply that weakly nucleophilic rxch2 radicals should add rapidly to the electron - deficient double bonds of maleimides ( and similar acceptors ) . most likely the resulting adduct radicals 15 will be converted to enolates 16 by electron transfer from the tio2 particles . , addition produces electrophilic imidoalkyl radicals 15 , for which a competition exists between reduction to adducts 7 or homolytic closure ( 6 - endo - trig ) onto the aryl ring . as radicals 15 are weakly electrophilic in character , this annulation should be favored by increasing the electron density in the ring and , conversely , disfavored by decreasing it . in agreement with this , the proportion of 6 increased when an electron - releasing tert - butyl group was introduced to the ring , whereas it decreased when an electron - withdrawing trifluoromethyl group was introduced . the resonance - stabilized cyclohexadienyl - type radicals 17 will rearomatize to yield the functionalized chromenes 6 . this aromatization could result from hole capture from tio2 by the radicals 17 and subsequent proton loss as shown . alternatively , electron transfer to maleimide might take place , as suggested in related work by hoffmann . protonation of the resulting maleimide radical anions , followed by further electron capture and protonation steps , would explain the significant yields of succinimides obtained in our reactions . however , as greater amounts of succinimides than cyclized products 6 were generally formed , it is thought that direct reduction of the maleimide acceptor by the conduction band of the p25 also initiates this process . from the results described in schemes 1 and 2 and table 1 , it can be deduced that the stability of the initial radicals is an important factor in this system . carboxylic acids dissociate on the tio2 surface to give the corresponding surface - bound carboxylate and a proton . hole pair , which can migrate through the bulk of the semiconductor to the surface . the tio2 surface is extensively hydroxylated , and it is thought that these species act as surface trapping sites for the valence - band holes . electron transfer from the system of the carboxylate to a hole trap site furnishes the surface - bound rxch2co2 radical . we propose that a competition exists between - scission of this surface - bound species to yield the desired free rxch2 radical and back transfer of the electron , either from the trap site or from trapped conduction - band electrons , to the carboxylate . for acid precursors that generate stabilized rxch2 radicals , such as those depicted in scheme 2 , the decarboxylation step is more favorable , thus explaining the improved yields and conversions recorded . conversely , for the simple aliphatic acids of table 1 , the radical stabilization energy from the rx groups is minimal , so back transfer of an electron to the tio2 will take precedence over the loss of co2 . it should be noted that while we believe radical stability to be a key aspect in this system , it is clear that there are other factors at play as well and that these take precedence in deciding the reaction outcome in a few instances . for example , vinylacetic acid would be expected to generate the allyl radical very readily in the presence of photoexcited tio2 . while we did observe the allyl radical in our epr experiments , no products at allwere observed in the preparative photolysis involving vinylacetic acid and 2 . in this case , other as yet unknown factors at the tio2 surface must come into play . a crucial feature of the process is that in the formation of adducts 3 and 7 a hydrogen atom is gained from some source within the dispersion . this is not the proton lost from the aromatic ring because reduced adducts were formed equally well from acids lacking aromatic rings . the reaction of phenoxyacetic acid with acrylamide was again chosen as a test - bed process ( scheme 7 ) because it was clean and practically quantitative . when this reaction was carried out in d3 - ch3cn solvent , the isolated adduct was screened for d incorporation by h and h nmr spectroscopy and gc ms . reaction with d1 - phenoxyacetic acid also yielded adduct with no detectable d incorporation . thus , unless the acidic d atom of 5a rapidly and completely exchanges , the source of the additional h atom is neither the acid nor the solvent . however , it is well - established that h2o molecules and ho groups are attached to the surface of the tio2 particles . drying p25 in a vacuum at 150c removes a significant amount of the surface h2o while leaving the chemically attached ho groups . when p25 dried in this way was used , the yield of 18 was scarcely reduced , suggesting that the oh groups were likely the proton donors . attempts were made to deuterate the h2o and oh groups on the p25 surface by refluxing in degassed d2o in a glovebox . however , it was found that back exchange occurred immediately upon exposure to air and rapidly with any moisture traces in solvents or on surfaces . when the partly deuterated p25d was photolyzed with the undeuterated acid , the phenoxybutanamide product contained no deuterium . it seemed possible , however , that p25 surface od groups could have rapidly exchanged with protons from the cooh groups of 5a . experiments with partly deuterated p25d and 5a - cood were also carried out , but deuterated 19d was again not found . in view of the partially deuterated nature of the p25d andthe ease with which it reverts to the protiated form , making handling difficult , our tentative conclusion is still that the p25 is the source of the h atoms . we have found that photochemical reactions employing p25 and carboxylic acids under dry anaerobic conditions generate c - centered radicals that can be deployed in several types of c c bond - forming processes . acids that yielded alkoxyalkyl , alkylthioalkyl , and benzyl radicals alkylated electron - deficient alkenes in moderate to good yields . boc - protected amino acids furnished aminoalkyl radicals that alkylated n - phenylmaleimide in useful yields . the reactions of aryloxyacetic acids with maleimides resulted in a cascade process in which a pyrrolochromene derivative accompanied the alkylated succinimide . selectivity for one or other of these products could be tuned to some extent by employing the tio2 catalyst under different conditions . aryloxyacetic acids adapted for intramolecular ring closures by the inclusion of 2 - alkenyl , 2 - aryl , or 2 - oximinyl functionality reacted rather poorly , especially the 2 - aryl acceptor types . the mechanism ( scheme 5 ) is supported by epr spectroscopic evidence of the intermediates . experiments with deuterium - labeled solvent and reactants implied that this was the hydroxyl groups on the surface of the p25 . it appears that the titania supplies electrons and holes upon photostimulation but also donates protons from surface hydroxyl groups , thus acting as both a catalyst and a reaction partner . these photoredox reactions are cleanly , safely , and cheaply carried out in the laboratory , and the heterogeneous catalyst is simply filtered off during workup . thus , with the exception mentioned above , they constitute a useful synthetic protocol . to a suspension of semiconductor ( 15 mg ml ) in mecn ( freshly distilled over cah2 ) in an oven - dried pyrex tube were added known amounts of the desired carboxylic acid and alkene . the mixture was then irradiated with eight 29 cm 15 w philips cleo tubes ( = 350 nm ) for the desired reaction time at ambient temperature . following irradiation , the solvent was removed under reduced pressure , and the reaction mixture was purified by chromatography . yields were determined from the amounts of isolated products and / or from the h nmr spectra by reference to ch2br2 as an internal standard . a photoreactor consisting of two lots of six 8 w blb uv lamps ( emission max = 365 nm ) , each arranged in a semicylinder with an aluminum reflector , was used to irradiate the contents of the nmr tube . the two photoreactor semicylinders were brought together to surround the nmr tube ( see the supporting information for a graphic ) . for a typical reaction , a stock solution comprising acid ( 10 mm ) in d3 - ch3cn was prepared . this solution was purged with argon for 5 min , and then 1 ml was pipetted into an argon - flushed sol gel - coated nmr tube . the loaded nmr tube was placed in an overhead stirrer ( turned on its side ) , which was spun at 250 rpm . the tube was held at a slight angle with respect to horizontal in the chuck of the overhead stirrer so that , when rotated , it described a small ( ca . 2 cm ) circle at its non - chuck - held end so as to agitate the reaction solution . once the nmr tube was in place , the irradiation was started , and the tube was periodically removed and analyzed by nmr . these experiments were carried out in a similar fashion to the photoredox experiments outlined above . following photolysis , the reaction mixtures were scrutinized for deuterium incorporation by h and h nmr spectroscopy and gc ms . further details of these experiments are provided in the supporting information . acetic acid ( 6 mg , 0.1 mmol ) , n - phenylmaleimide ( 34.7 mg , 0.2 mmol ) , and tio2 ( 12 mg , 0.15 mmol ) were reacted in accordance with the general procedure to yield 3a ( 24 % by nmr ) as a white solid . h nmr ( 400 mhz , cdcl3 , 296 k ) : 1.44 ( d , j = 7.2 hz , 3h ) , 2.472.54 ( m , 1h ) , 2.973.14 ( m , 2h ) , 7.277.30 ( m , 2h ) , 7.367.42 ( m , 1h ) , 7.447.50 ( m , 2h ) . c nmr ( 100 mhz , cdcl3 , 297 k ) : 16.9 , 34.9 , 36.7 , 126.4 , 128.6 , 129.2 , 132.0 , 175.5 , 179.6 . hr - esims : m / z 190.0861 ( calcd for c11h12no2 , 190.0863 ) . also observed was n - phenylsuccinimide ( 41 % by nmr ) . n - hexanoic acid ( 11.6 mg , 0.1 mmol ) , n - phenylmaleimide ( 34.7 mg , 0.2 mmol ) , and tio2 ( 12 mg , 0.15 mmol ) were reacted in accordance with the general procedure . following irradiation , a yield of 4 % ( 0.04 mmol ) was determined for 3b . yields were determined by assigning peaks a and b by analogy with the previously characterized 3 - ethyl adduct.h nmr ( 500 mhz , cdcl3 , 295 k ) : 2.60 ( dd , j = 3.3 , 17.0 hz , 1h ) , 2.973.07 ( m , 1h ) . also observed were n - phenylsuccinimide ( 4 % by nmr ) and unreacted n - hexanoic acid ( 65 % conversion by nmr ) . tert - butylacetic acid ( 11.6 mg , 0.1 mmol ) , n - phenylmaleimide ( 34.7 mg , 0.2 mmol ) , and tio2 ( 12 mg , 0.15 mmol ) were reacted in accordance with the general procedure to yield 3c ( 18 % by nmr ) as a white solid . h nmr ( 400 mhz , cdcl3 , 296 k ) : 0.94 ( s , 9h ) , 1.36 ( dd , j = 10.7 , 14.0 hz , 1h ) , 2.12 ( dd , j = 2.0 , 13.9 hz , 1h ) , 2.54 ( dd , j = 5.3 , 18.1 hz , 1h ) , 3.03 ( dd , j = 9.1 , 18.1 hz , 1h ) , 2.842.92 ( m , 1h ) , 7.197.22 ( m , 2h ) , 7.297.34 ( m , 1h ) , 7.377.42 ( m , 2h ) . c nmr ( 100 mhz , cdcl3 , 297 k ) : 29.6 , 29.7 , 31.0 , 37.6 , 45.9 , 126.4 , 128.6 , 129.2 , 132.1 , 175.8 , 179.8 . hr - esims : m / z 246.1486 ( calcd for c15h20no2 , 246.1489 ) . also observed was n - phenylsuccinimide ( 40 % by nmr ) . isobutyric acid ( 8.1 mg , 0.1 mmol ) , n - phenylmaleimide ( 34.7 mg , 0.2 mmol ) , and tio2 ( 12 mg , 0.15 mmol ) were reacted in accordance with the general procedure to yield 3d ( 25 % by nmr ) as a white solid . h nmr ( 400 mhz , cdcl3 , 297 k ) : 0.99 ( d , j = 6.8 hz , 3h ) , 1.07 ( d , j = 6.9 hz , 3h ) , 2.322.40 ( m , 1h ) , 2.56 ( dd , j = 4.4 , 18.3 hz , 1h ) , 2.79 ( dd , j = 9.4 , 18.3 hz , 1h ) , 2.872.92 ( m , 1h ) , 7.187.21 ( m , 2h ) , 7.297.34 ( m , 1h ) , 7.377.43 ( m , 2h ) . c nmr ( 100 mhz , cdcl3 , 300 k ) : 17.3 , 20.0 , 29.2 , 30.6 , 45.8 , 126.5 , 128.6 , 129.2 , 131.9 , 175.9 , 178.4 . hr - esims : m / z 218.1178 ( calcd for c13h16no2 , 218.1176 ) . also observed was n - phenylsuccinimide ( 25 % by nmr ) . pivalic acid ( 10.2 mg , 0.1 mmol ) , n - phenylmaleimide ( 34.7 mg , 0.2 mmol ) , and tio2 ( 12 mg , 0.15 mmol ) were reacted in accordance with the general procedure to yield 3e ( 38 % by nmr ) as a white solid . h nmr ( 400 mhz , cdcl3 , 300 k ) : 1.12 ( s , 9h ) , 2.672.80 ( m , 2h ) , 2.89 ( dd , j = 8.8 , 17.6 hz , 1h ) , 7.247.26 ( m , 2h ) , 7.367.41 ( m , 1h ) , 7.457.49 ( m , 2h ) . c nmr ( 100 mhz , cdcl3 , 300 k ) : 27.2 , 32.0 , 33.8 , 49.9 , 126.6 , 128.6 , 129.2 , 132.0 , 175.6 , 177.4 . hr - esims : m / z 232.1326 ( calcd for c14h18no2 , 232.1332 ) . also observed was n - phenylsuccinimide ( 31 % by nmr ) . trifluoroacetic acid ( 11.4 mg , 0.1 mmol ) , n - phenylmaleimide ( 34.7 mg , 0.2 mmol ) , and tio2 ( 12 mg , 0.15 mmol ) were reacted in accordance with the general procedure to yield 3f ( 1 % by nmr ) . h nmr ( 400 mhz , cdcl3 , 295 k ) : 2.86 ( dd , j = 5.5 , 18.6 hz , 1h ) , 2.99 ( dd , j = 9.5 , 18.6 hz , 1h ) , 3.61 ( m , 1h ) , 7.10 ( m , 2h ) , 7.39 ( m , 3h ) . f nmr ( 375 mhz , cdcl3 , 296 k ) : 69.3 ( s , 3f ) methoxyacetic acid ( 54.4 mg , 0.63 mmol ) , n - phenylmaleimide ( 433.6 mg , 2.50 mmol ) , and tio2 ( 75 mg , 0.94 mmol ) were reacted in accordance with the general procedure . following irradiation for 18 h , the reaction mixture was purified by column chromatography on silica gel ( eluent : 30 % etoac in petroleum ether 4060 ) to yield 3 g as a white powder ( 74.4 mg , 54 % ) . h nmr ( 400 mhz , cdcl3 , 299 k ) : 2.862.99 ( m , 2h ) , 3.083.15 ( m , 1h ) , 3.38 ( s , 3h ) , 3.36 ( dd , j = 3.3 , 9.1 hz , 1h ) , 3.91 ( dd , j = 3.9 , 9.1 hz , 1h ) , 7.267.30 ( m , 2h ) , 7.367.41 ( m , 1h ) , 7.447.49 ( m , 2h ) . c nmr ( 75 mhz , cdcl3 , 298 k ) : 31.9 , 41.2 , 59.3 , 70.8 , 126.6 , 128.6 , 129.1 , 132.1 , 175.8 , 177.3 . tert - butoxyacetic acid ( 87.3 mg , 0.66 mmol ) , n - phenylmaleimide ( 462.3 mg , 2.67 mmol ) , and tio2 ( 80 mg , 1.0 mmol ) were reacted in accordance with the general procedure . following irradiation for 17 h , h nmr analysis revealed that n - phenylmaleimide had been consumed entirely while a significant quantity of tert - butoxyacetic acid remained . a further 462.3 mg of n - phenylmaleimide was hence added , and the reaction was photolyzed for another 18 h. the reaction mixture was then purified by column chromatography on silica gel ( eluent : 25 % etoac in pentanes ) to yield 3h as a yellow oil ( 97.8 mg , 57 % ) . h nmr ( 500 mhz , cdcl3 , 295 k ) : 1.18 ( s , 9h ) , 2.852.89 ( m , 2h ) , 3.073.11 ( m , 1h ) , 3.59 ( dd , j = 2.9 , 8.5 hz , 1h ) , 3.91 ( dd , j = 3.5 , 8.5 hz , 1h ) , 7.27 ( d , j = 7.4 hz , 2h ) , 7.39 ( t , j = 7.4 hz , 1h ) , 7.48 ( t , j = 7.4 hz , 2h ) . c nmr ( 75 mhz , cdcl3 , 297 k ) : 27.4 , 32.3 , 41.3 , 60.7 , 73.3 , 126.6 , 128.6 , 129.2 , 134.2 , 176.3 , 178.0 . hr - esims : m / z 262.1440 ( calcd for c15h20no3 , 262.1438 ) . 2 - tetrahydrofuroic acid ( 76.6 mg , 0.66 mmol ) , n - phenylmaleimide ( 462.3 mg , 2.67 mmol ) , and tio2 ( 80 mg , 1.00 mmol ) were reacted in accordance with the general procedure . following irradiation for 18 h , the reaction mixture was purified by column chromatography on silica gel ( eluent : et2o ) to yield a 1:1 mixture of the two diastereoisomers of 3i as a yellow oil ( 121.8 mg , 75 % ) . diastereomer 1 : h nmr ( 400 mhz , cdcl3 , 295 k ) : 1.922.02 ( m , 2h ) , 2.022.12 ( m , 2h ) , 2.792.84 ( m , 1h ) , 2.99 ( dd , j = 9.3 , 18.3 hz , 1h ) , 3.263.30 ( m , 1h ) , 3.763.84 ( m , 2h ) , 4.234.27 ( m , 1h ) , 7.267.32 ( m , 2h ) , 7.377.42 ( m , 1h ) , 7.457.51 ( m , 2h ) . c nmr ( 100 mhz , cdcl3 , 297 k ) : 25.9 , 27.9 , 32.7 , 43.4 , 68.8 , 79.1 , 126.6 , 128.6 , 129.1 , 132.0 , 175.7 , 175.9 . diastereomer 2 : h nmr ( 500 mhz , cdcl3 , 295 k ) : 1.631.71 ( m , 1h ) , 1.922.02 ( m , 2h ) , 2.102.19 ( m , 1h ) , 2.792.84 ( m , 2h ) , 3.083.12 ( m , 1h ) , 3.863.94 ( m , 2h ) , 4.394.44 ( m , 1h ) , 7.267.32 ( m , 2h ) , 7.377.42 ( m , 1h ) , 7.457.51 ( m , 2h ) . c nmr ( 100 mhz , cdcl3 , 297 k ) : 25.9 , 29.7 , 29.8 , 44.4 , 68.8 , 77.3 , 126.6 , 128.6 , 129.1 , 132.0 , 176.5 , 177.4 . gc ms : for tr = 15.75 min , m / z ( % ) 245 ( 38 ) , 217 ( 10 ) , 202 ( 58 ) , 175 ( 100 ) , 147 ( 10 ) , 119 ( 28 ) , 111 ( 11 ) , 71 ( 98 ) ; for tr = 16.20 min , m / z ( % ) 245 ( 51 ) , 217 ( 11 ) , 202 ( 33 ) , 175 ( 81 ) , 147 ( 6 ) , 119 ( 22 ) , 111 ( 12 ) , 71 ( 100 ) . hr - esims : m / z 246.1127 ( calcd for c14h16no3 , 246.1125 ) . methylthioacetic acid ( 70.8 mg , 0.67 mmol ) , n - phenylmaleimide ( 462.3 mg , 2.67 mmol ) , and tio2 ( 80 mg , 1.00 mmol ) were reacted in accordance with the general procedure . following irradiation for 42 h , the reaction mixture was purified by column chromatography on silica gel ( eluent : gradient of 2040 % etoac in petroleum ether 4060 ) to yield 3j as a white powder ( 53.6 mg , 34 % ) . h nmr ( 500 mhz , cdcl3 , 299 k ) : 2.14 ( s , 3h ) , 2.84 ( dd , 1h , j = 5.0 , 18.4 hz ) , 2.92 ( dd , 1h , j = 7.4 , 13.5 hz ) , 3.01 ( dd , 1h , j = 9.2 , 18.4 hz ) , 3.04 ( dd , 1h , j = 4.1 , 13.5 hz ) , 3.213.28 ( m , 1h ) , 7.227.27 ( m , 2h ) , 7.357.39 ( m , 1h ) , 7.427.47 ( m , 2h ) . c nmr ( 75 mhz , cdcl3 , 297 k ) : 16.5 , 33.7 , 35.5 , 40.1 , 126.5 , 128.7 , 129.2 , 131.9 , 175.2 , 177.5 . hr - esims : m / z 236.0741 ( calcd for c12h14no2s , 236.0740 ) .2 - thiopheneacetic acid ( 93.9 mg , 0.66 mmol ) , n - phenylmaleimide ( 462.3 mg , 2.67 mmol ) , and tio2 ( 80 mg , 1.00 mmol ) were reacted in accordance with the general procedure . following irradiation for 17 h , the reaction mixture was purified by column chromatography on silica gel ( eluent : 20 % etoac in pentanes ) to yield 3k as a yellow oil ( 45.9 mg , 26 % ) . h nmr ( 500 mhz , cdcl3 , 295 k ) : 2.72 ( dd , j = 4.8 , 18.4 hz , 1h ) , 2.98 ( dd , j = 9.2 , 18.4 hz , 1h ) , 3.303.35 ( m , 1h ) , 3.373.45 ( m , 2h ) , 6.89 ( m , 1h ) , 6.98 ( m , 1h ) , 7.20 ( m , 2h ) , 7.39 ( m , 1h ) , 7.46 ( m , 2h ) . c nmr ( 75 mhz , cdcl3 , 297 k ) 30.7 , 33.4 , 41.3 , 125.0 , 126.5 , 127.0 , 127.3 , 128.7 , 129.2 , 131.8 , 138.2 , 175.2 , 177.8 , 177.5 . hr - esims : m / z 272.0743 ( calcd for c15h14no2s , 272.0740 ) .1,2 - bis ( thiophen -2-yl ) ethane was also isolated as a clear oil ( 14.1 mg , 22 % ) . h nmr ( 500 mhz , cdcl3 , 295 k ) : 3.20 ( s , 4h ) , 6.80 ( d , j = 3.4 hz , 2h ) , 6.916.94 ( m , 2h ) , 7.14 ( d , j = 5.2 hz , 2h ) . data are consistent with literature values . phenylacetic acid ( 89.9 mg , 0.66 mmol ) , n - phenylmaleimide ( 462.3 mg , 2.67 mmol ) , and tio2 ( 80 mg , 1.00 mmol ) were reacted in accordance with the general procedure . following irradiation for 22 h , the reaction mixture was purified by dry flash chromatography on silica gel ( eluent : gradient of 1020 % etoac in ch2cl2 ) to yield 3l as a white powder ( 99.3 mg , 57 % ) . h nmr ( 500 mhz , cdcl3 , 295 k ) : 2.65 ( dd , j = 4.7 , 18.5 hz , 1h ) , 2.88 ( dd , j = 9.2 , 18.5 hz , 1h ) , 3.08 ( dd , j = 8.0 , 13.8 hz , 1h ) , 3.25 ( dd , j = 4.4 , 13.8 hz , 1h ) , 3.303.35 ( m , 1h ) , 7.17 ( m , 2h ) , 7.22 ( m , 2h ) , 7.29 ( m , 1h ) , 7.34 ( m , 2h ) , 7.39 ( m , 1h ) , 7.46 ( m , 2h ) . c nmr ( 75 mhz , cdcl3 , 297 k ) : 33.5 , 36.7 , 41.4 , 77.2 , 126.6 , 127.4 , 128.8 , 129.0 , 129.3 , 129.4 , 132.0 , 136.8 , 175.4 , 178.4 . data are consistent with literature values . bibenzyl ( 10.9 mg , 18 % ) was observed by nmr prior to purification of the reaction mixture . h nmr ( 500 mhz , cdcl3 , 298 k ) : 2.95 ( s , 4h ) , 7.217.24 ( m , 6h ) , 7.307.33 ( m , 4h ) . n - boc - l - alanine ( 126.2 mg , 0.67 mmol ) , n - phenylmaleimide ( 462.3 mg , 2.67 mmol ) , and tio2 ( 80 mg , 1.00 mmol ) were reacted in accordance with the general procedure . following irradiation for 18 h , the mixture was purified by column chromatography on silica gel ( eluent : gradient of 2040 % etoac in petroleum ether 4060 ) to yield two diastereomers of 3 m . diastereomer 1 was isolated as a white powder ( 36.7 mg , 18 % ) . h nmr ( 400 mhz , cdcl3 , 296 k ) : 1.29 ( d , j = 6.9 hz , 3h ) , 1.38 ( s , 9h ) , 2.78 ( dd , j = 4.8 , 18.6 hz , 1h ) , 2.89 ( dd , j = 9.1 , 18.5 hz , 1h ) , 3.153.20 ( m , 1h ) , 4.084.18 ( m , 1h ) , 4.53 ( bs , 1h ) , 7.187.22 ( m , 2h ) , 7.307.35 ( m , 1h ) , 7.387.43 ( m , 2h ) . c nmr ( 75 mhz , cdcl3 , 297 k ) : 18.7 , 28.3 , 32.2 , 45.3 , 47.7 , 80.2 , 126.5 , 128.7 , 129.2 , 131.8 , 155.5 , 175.3 , 176.6 . hr - esims : m / z 341.1467 ( calcd for c17h22o4n2na , 341.1472 ) . diastereomer 2 ( 20 % wrt ch2br2 standard ) was obtained as a 1:1 mixture with n - phenylsuccinimide . h nmr ( 500 mhz , cdcl3 , 297 k ) : 1.25 ( d , j = 6.8 hz , 3h ) , 1.44 ( s , 9h ) , 2.63 ( dd , j = 4.5 , 18.6 hz , 1h ) , 3.00 ( dd , j = 9.6 , 18.5 hz , 1h ) , 3.173.23 ( m , 1h ) , 4.134.17 ( m , 1h ) , 5.20 ( bs , 1h ) , 7.277.30 ( m , 2h ) , 7.397.42 ( m , 1h ) , 7.467.50 ( m , 2h ) . c nmr ( 75 mhz , cdcl3 , 297 k ) : 17.1 , 28.5 , 31.9 , 45.1 , 47.1 , 80.0 , 126.6 , 128.8 , 129.3 , 131.8 , 155.2 , 175.2 , 177.5 . hr - esims : m / z 341.1475 ( calcd for c17h22o4n2na , 341.1472 ) . n - boc - l - proline ( 144.3 mg , 0.67 mmol ) , n - phenylmaleimide ( 462.3 mg , 2.67 mmol ) , and tio2 ( 80 mg , 1.00 mmol ) were reacted in accordance with the general procedure . following irradiation for 17 h , the crude mixture was purified by dry flash chromatography on silica gel ( eluent : gradient of 2060 % etoac in petroleum ether 4060 ) to yield an inseparable mixture of two diastereomers of 3n ( 171 mg , 75 % , 1:1 ratio ) that also contained 7 % n - phenylsuccinimide . h nmr ( 500 mhz , cdcl3 , 326 k ) : diastereomer 11.44 ( s , 9h ) , 1.941.99 ( m , 2h ) , 2.182.24 ( m , 2h ) , 2.732.75 ( m , 1h ) , 2.83 ( dd , j = 3.8 , 9.4 hz , 1h ) , 3.53 ( dd , j = 7.3 , 11.1 hz , 1h ) , 3.793.85 ( m , 2h ) , 4.344.39 ( m , 2h ) , 7.277.47 ( m , 5h ) ; diastereomer 21.49 ( s , 9h ) , 2.142.17 ( m , 2h ) , 1.661.71 ( m , 2h ) , 2.692.71 ( m , 1h ) , 2.86 ( dd , j = 4.3 , 9.7 hz , 1h ) , 3.30 ( dd , j = 3.4 , 7.8 hz , 1h ) , 3.953.99 ( m , 2h ) , 4.314.35 ( m , 2h ) , 7.277.47 ( m , 5h ) . c nmr ( 75 mhz , cdcl3 , 300 k ) : 23.324.0 , 27.9 , 28.4 , 28.5 , 29.730.1 , 31.8 , 43.744.1 , 47.247.8 , 57.157.8 , 79.980.5 , 126.5126.8 , 128.4129.2 , 131.2132.0 , 155.0156.0 , 174.1177.3 . gc ms : for tr = 19.81 min , m / z ( % ) 344 ( 2 ) , 288 ( 19 ) , 271 ( 17 ) , 243 ( 48 ) , 175 ( 16 ) , 114 ( 50 ) , 70 ( 100 ) 57 ( 41 ) ; for tr = 20.09 min , m / z ( % ) 344 ( 2 ) , 288 ( 19 ) , 271 ( 17 ) , 243 ( 48 ) , 175 ( 16 ) , 114 ( 50 ) , 70 ( 100 ) 57 ( 41 ) . hr - esims : m / z 367.1632 ( calcd for c19h24n2o4na , 367.1628 ) . n - boc - d / l -2-piperidinecarboxylic acid ( 151.4 mg , 0.67 mmol ) , n - phenylmaleimide ( 462.3 mg , 2.67 mmol ) , and tio2 ( 80 mg , 1.00 mmol ) were reacted in accordance with the general procedure . following irradiation for 18 h , the crude mixture was purified by column chromatography on silica gel ( eluent : 30 % etoac in pentanes ) to yield two diastereomers of 3o . diastereomer 1 was isolated as an off - white solid ( 32.7 mg , 14 % ) . h nmr ( 500 mhz , cdcl3 , 295 k ) : 1.39 ( s , 9h ) , 1.461.59 ( bm , 2h ) , 1.671.79 ( bm , 4h ) , 2.52 ( dd , j = 3.0 , 18.2 hz , 1h ) , 2.98 ( dd , j = 8.9 , 18.2 hz , 1h ) , 3.04 ( t , j = 13.2 hz , 1h ) , 3.263.30 ( m , 1h ) , 4.06 ( d , j = 13.2 hz , 1h ) , 4.344.37 ( m , 1h ) , 7.327.36 ( m , 3h ) , 7.417.45 ( m , 2h ) . c nmr ( 75 mhz , cdcl3 , 297 k ) : 18.9 , 24.8 , 27.0 , 28.4 , 34.2 , 38.1 , 40.2 , 53.3 , 79.9 , 126.7 , 128.4 , 128.9 , 132.1 , 155.5 , 174.9 , 176.1 . hr - esims : m / z 381.1787 ( calcd for c20h26n2o4na , 381.1785 ) . diastereomer 2 ( 15 % wrt ch2br2 standard ) was obtained as a 1:2 mixture with n - phenylsuccinimide . h nmr ( 500 mhz , cdcl3 , 295 k ) : 1.42 ( s , 9h ) , 1.53 ( m , 1h ) , 1.681.72 ( m , 1h ) , 1.901.96 ( m , 1h ) , 2.212.23 ( m , 1h ) , 2.402.45 ( m , 1h ) , 2.542.58 ( m , 1h ) , 2.95 ( dd , j = 4.4 , 19.0 hz , 1h ) , 3.05 ( dd , j = 9.6 , 17.6 hz , 1h ) , 3.26 ( dd , j = 9.1 , 19.0 hz , 1h ) , 3.35 ( dd , j = 6.3 , 17.6 hz , 1h ) , 3.373.42 ( m , 1h ) , 3.943.98 ( m , 1h ) , 7.387.42 ( m , 3h ) , 7.447.49 ( m , 2h ) . c nmr ( 125 mhz , cdcl3 , 295 k ) : 19.6 , 24.4 , 24.6 , 28.3 , 33.4 , 37.8 , 39.5 , 46.1 , 82.5 , 126.4 , 128.5 , 129.1 , 131.4 , 152.6 , 175.2 , 175.5 . hr - esims : m / z 381.1787 ( calcd for c20h26n2o4na , 381.1785 ) . cyanoacetic acid ( 56.2 mg , 0.67 mmol ) , n - phenylmaleimide ( 462.3 mg , 2.67 mmol ) , and tio2 ( 80 mg , 1.00 mmol ) were reacted in accordance with the general procedure . following irradiation for 18 h , the reaction mixture was scrutinized by h nmr and gc ms , but none of the desired product was obtained . phenoxyacetic acid ( 100 mg , 0.65 mmol ) , n - methylmaleimide ( 145 mg , 1.3 mmol ) , and tio2 ( 75 mg , 0.98 mmol ) were reacted in accordance with the general procedure . following irradiation for 20 h , the crude mixture was purified by column chromatography on silica gel ( eluent : 20 % etoac in petroleum ether 4060 ) to yield 7a as a colorless oil ( 32.6 mg , 23 % ) . h nmr ( 400 mhz , cdcl3 , 297 k ) : 2.882.90 ( m , 2h ) , 3.04 ( s , 3h ) , 3.173.23 ( m , 1h ) , 4.17 ( dd , j = 3.4 , 9.2 hz , 1h ) , 4.40 ( dd , j = 4.4 , 9.2 hz , 1h ) , 6.87 ( d , j = 8.8 hz , 2h ) , 6.98 ( t , j = 7.4 hz , 1h ) , 7.28 ( t , j = 7.4 hz , 2h ) . c nmr ( 75 mhz , cdcl3 , 297 k ) : 25.4 , 32.1 , 41.1 , 66.4 , 115.1 , 122.0 , 130.0 , 158.5 , 177.0178.0 .6 a was also obtained as a white powder ( 77.8 mg , 55 % ) . h nmr ( 400 mhz , cdcl3 , 296 k ) : 3.00 ( s , 3h ) , 3.363.40 ( m , 1h ) , 4.01 ( dd , j = 4.2 , 11.4 hz , 1h ) , 4.07 ( d , j = 9.2 hz , 1h ) , 4.62 ( dd , j = 2.9 , 11.4 hz , 1h ) , 6.89 ( d , j = 8.2 hz , 1h ) , 7.05 ( t , j = 7.5 hz , 1h ) , 7.21 ( t , j = 7.7 hz , 1h ) , 7.58 ( d , j = 7.4 hz , 1h ) . c nmr ( 75 mhz , cdcl3 , 297 k ) : 27.8 , 40.1 , 42.7 , 64.3 , 118.1 , 118.3 , 123.2 , 129.4 , 130.5 , 155.7 , 176.6 , 177.2 . data are consistent with literature values . phenoxyacetic acid ( 100 mg , 0.65 mmol ) , n - phenylmaleimide ( 230 mg , 1.3 mmol ) , and tio2 ( 75 mg , 0.98 mmol ) were reacted in accordance with the general procedure . following irradiation for 11 h , the crude mixture was purified by column chromatography on silica gel ( eluent : 20 % etoac in petroleum ether 4060 ) to yield 7b as a yellow oil ( 71.5 mg , 39 % ) . h nmr ( 400 mhz , cdcl3 , 297 k ) : 3.013.07 ( m , 2h ) , 3.333.39 ( m , 1h ) , 4.28 ( dd , j = 3.2 , 9.0 hz , 1h ) , 4.55 ( dd , j = 4.1 , 9.1 hz , 1h ) , 6.91 ( d , j = 8.8 hz , 2h ) , 7.00 ( t , j = 7.3 hz , 1h ) , 7.287.33 ( m , 2h ) , 7.41 ( t , j = 7.4 hz , 1h ) , 7.48 ( d , j = 7.2 , 2h ) . c nmr ( 75 mhz , cdcl3 , 297 k ) : 32.4 , 41.1 , 66.9 , 115.1 , 122.1 , 127.0 , 129.2 , 129.7 , 130.0 , 132.4 , 158.5 , 175.9 , 177.1 .6 b was also obtained as a white powder ( 72.8 mg , 40 % ) . h nmr ( 400 mhz , cdcl3 , 297 k ) : 3.543.58 ( m , 1h ) , 4.11 , ( dd , j = 4.4 , 11.4 hz , 1h ) , 4.23 ( d , j = 9.3 hz , 1h ) , 4.7 ( dd , j = 3.3 , 11.4 hz , 1h ) , 6.94 ( d , j = 8.2 hz , 1h ) , 7.07 ( t , j = 7.5 hz , 1h ) , 7.227.27 ( m , 2h ) , 7.37 ( t , j = 7.4 hz , 2h ) , 7.44 ( t , j = 7.1 hz , 1h ) , 7.63 ( d , j = 7.4 hz , 1h ) . c nmr ( 75 mhz , cdcl3 , 297 k ) : 40.2 , 42.6 , 64.4 , 77.1 , 77.5 , 77.9 , 117.7 , 118.3 , 123.3 , 126.7 , 129.2 , 129.5 , 129.6 , 130.7 , 132.1155.7175.5 , 176.1 .4 - ( tert - butyl ) phenoxyacetic acid ( 130.3 mg , 0.62 mmol ) , n - methylmaleimide ( 275.6 mg , 2.48 mmol ) , and tio2 ( 75 mg , 0.98 mmol ) were reacted in accordance with the general procedure . following irradiation for 22 h , the reaction mixture was purified by column chromatography on silica gel ( eluent : 20 % etoac in petroleum ether 4060 ) to yield 7c as a clear oil ( 18.4 mg , 11 % ) . h nmr ( 400 mhz , cdcl3 , 296 k ) : 1.29 ( s , 9h ) , 2.842.89 ( m , 2h ) , 3.03 ( s , 3h ) , 3.213.16 ( m , 1h ) , 4.16 ( dd , j = 3.4 , 9.2 hz , 1h ) , 4.39 ( dd , j = 4.4 , 9.2 hz , 1h ) , 6.81 ( d , j = 8.8 hz , 2h ) , 7.29 ( d , j = 8.8 hz , 2h ) . c nmr ( 100 mhz , cdcl3 , 296 k ) : 25.0 , 29.7 , 31.5 , 34.1 , 40.7 , 66.1 , 114.2 , 126.4 , 144.4 , 155.8 , 176.6 , 177.6 . hr - esims : m / z 276.1599 ( calcd for c16h22no3 , 276.1594 ) .6 c was also obtained as a white powder ( 77.2 mg , 46 % ) . h nmr ( 400 mhz , cdcl3 , 296 k ) : 1.32 ( s , 9h ) , 2.98 ( s , 3h ) , 3.333.37 ( m , 1h ) , 3.98 ( dd , j = 4.1 , 11.3 hz , 1h ) , 4.05 ( d , j = 9.2 hz , 1h ) , 4.59 ( dd , j = 3.0 , 11.3 hz , 1h ) , 6.82 ( d , j = 8.6 hz , 1h ) , 7.23 ( dd , j = 2.4 , 8.6 hz , 1h ) , 7.58 ( d , j = 2.4 hz , 1h ) . c nmr ( 75 mhz , cdcl3 , 296 k ) : 25.8 , 31.9 , 34.8 , 40.3 , 42.7 , 64.3 , 117.1 , 117.6 , 126.5 , 127.3 , 146.0 , 153.3 , 176.7 , 177.3 . hr - esims : m / z 274.1442 ( calcd for c16h20no3 , 274.1438 ) .4 - ( tert - butyl ) phenoxyacetic acid ( 70 mg , 0.33 mmol ) , n - phenylmaleimide ( 117 mg , 0.66 mmol ) , and tio2 ( 40 mg , 0.5 mmol ) were reacted in accordance with the general procedure . following irradiation for 19 h , the crude mixture was purified by column chromatography on silica gel ( eluent : 20 % etoac in petroleum ether 4060 ) to yield 7d as a clear oil ( 31.2 mg , 28 % ) . h nmr ( 300 mhz , cdcl3 , 295 k ) : 1.30 ( s , 9h ) , 2.983.13 ( m , 2h ) , 3.303.37 ( m , 1h ) , 4.23 ( dd , j = 3.2 , 9.1 hz , 1h ) , 4.53 ( dd , j = 3.9 , 9.1 hz , 1h ) , 6.85 ( d , j = 8.9 hz , 2h ) , 7.277.33 ( m , 3h ) , 7.407.51 ( m , 4h ) . c nmr ( 75 mhz , cdcl3 , 297 k ) : 29.7 , 31.5 , 34.2 , 40.8 , 66.6 , 114.2 , 126.4 , 126.6 , 128.7 , 129.2 , 132.0 , 144.6 , 155.8 , 175.6 , 176.8 . hr - esims : m / z 338.1755 ( calcd for c21h24no3 , 338.1751 ) .6 d was also obtained as a clear oil ( 50.3 mg , 46 % ) . h nmr ( 300 mhz , cdcl3 , 296 k ) : 1.32 ( s , 9h ) , 3.513.56 ( m , 1h ) , 4.10 ( dd , j = 4.3 , 11.4 hz , 1h ) , 4.23 ( d , j = 7.3 hz , 1h ) , 4.66 ( dd , j = 3.3 , 11.5 hz , 1h ) , 6.87 ( d , j = 8.1 hz , 1h ) , 7.247.29 ( m , 2h ) , 7.337.48 ( m , 4h ) . c nmr ( 75 mhz , cdcl3 , 297 k ) : 31.5 , 34.4 , 40.0 , 42.3 , 64.1 , 116.4 , 117.3 , 126.3 , 127.0 , 128.7 , 129.1 , 131.8 , 134.2 , 145.7 , 153.0 , 175.2 , 175.7 . hr - esims : m / z 336.1598 ( calcd for c21h22no3 , 336.1600 ) .4 - ( trifluoromethyl ) phenoxyacetic acid ( 143 mg , 0.65 mmol ) , n - methylmaleimide ( 145 mg , 1.3 mmol ) , and tio2 ( 75 mg , 0.98 mmol ) were reacted in accordance with the general procedure . following irradiation for 16 h , the reaction mixture was purified by two rounds of column chromatography on silica gel ( eluent : 20 % etoac in petroleum ether 4060 and subsequently 10 % etoac in ch2cl2 ) to yield 7e as a clear oil ( 54.7 mg , 29 % ) . h nmr ( 400 mhz , cdcl3 , 300 k ) : 2.822.96 ( m , 2h ) , 3.05 ( s , 3h ) , 3.203.26 ( m , 1h ) , 4.22 ( dd , j = 3.4 , 9.2 hz , 1h ) , 4.46 ( dd , j = 4.3 , 9.2 hz , 1h ) , 6.94 ( d , j = 8.5 hz , 2h ) , 7.54 ( d , j = 8.5 hz , 2h ) . c nmr ( 75 mhz , cdcl3 , 300 k ) : 25.1 , 31.6 , 40.5 , 66.1 , 114.6 , 123.9 ( q , jc f = 32.9 hz , 1c ) , 124.4 ( q , jc f = 271.2 hz , 2c ) , 127.0 ( q , jcf nmr ( 376 mhz , cdcl3 , 300 k ) : 62.1 . hr - esims : m / z 288.0838 ( calcd for c13h13no3f3 , 288.0842 ) .6 e was also obtained as a clear oil ( 60.1 mg , 32 % ) . h nmr ( 400 mhz , cdcl3 , 298 k ) : 3.01 ( s , 3h ) , 3.403.44 ( m , 1h ) , 4.044.10 ( m , 2h ) , 4.64 ( dd , j = 3.2 , 11.5 hz , 1h ) , 6.98 ( d , j = 8.6 hz , 1h ) , 7.46 ( d , j = 8.5 hz , 1h ) , 7.87 ( s , 1h ) . c nmr ( 75 mhz , cdcl3 , 298 k ) : 25.5 , 39.4 , 41.8 , 64.0 , 117.9 , 118.4 , 123.9 ( q , jc f = 271.7 hz , 1c ) , 125.1 ( q , jc f = 33.1 hz , 1c ) , 127.2 ( q , jcf = 3.5 hz , 1c ) , 127.6 ( q , jc f = 3.8 hz , 1c ) , 157.7 , 175.3 , 176.1 . f nmr ( 376 mhz , cdcl3 , 298 k ) : 62.3 . hr - esims : m / z 286.0687 ( calcd for c13h11no3f3 , 286.0686 ) .4 - ( trifluoromethyl ) phenoxyacetic acid ( 143 mg , 0.65 mmol ) , n - phenylmaleimide ( 230 mg , 1.3 mmol ) , and tio2 ( 75 mg , 0.98 mmol ) were reacted in accordance with the general procedure . following irradiation for 16 h , the reaction mixture was purified by column chromatography on silica gel ( eluent : 25 % etoac in petroleum ether 4060 ) to yield 7f as a colorless solid ( 52.9 mg , 40 % ) . h nmr ( 400 mhz , cdcl3 , 297 k ) : 2.983.13 ( m , 2h ) , 3.353.40 ( m , 1h ) ,4.28 ( dd , j = 3.1 , 9.1 hz , 1h ) , 4.57 ( dd , j = 4.0 , 9.1 hz , 1h ) , 6.97 ( d , j = 8.5 hz , 2h ) , 7.29 ( d , j = 7.2 hz , 2h ) , 7.41 ( t , j = 7.3 hz , 1h ) , 7.49 ( t , j = 7.2 hz , 2h ) , 7.56 ( d , j = 8.6 hz , 2h ) . c nmr ( 75 mhz , cdcl3 , 297 k ) : 31.9 , 40.6 , 66.6 , 114.7 , 124.0 ( q , jcf = 32.8 hz , 1c ) , 124.3 ( q , jc f = 271.1 hz , 1c ) , 126.5 , 127.1 ( q , jcf = 3.7 hz , 2c ) , 128.8 , 129.3 , 131.9 , 160.4 , 175.2 , 176.3 . f nmr ( 376 mhz , cdcl3 , 297 k ) : 62.1 . hr - esims : m / z 367.1269 ( calcd for c18h18n2o3f3 , 367.1275 ) . h nmr ( 400 mhz , cdcl3 , 297 k ) : 3.573.61 ( m , 1h ) , 4.15 ( dd , j = 4.2 , 11.4 hz , 1h ) , 4.25 ( d , j = 9.3 hz , 1h ) , 4.71 ( dd , j = 3.4 , 11.4 hz , 1h ) , 7.04 ( d , j = 8.5 hz , 1h ) , 7.247.27 ( m , 2h ) , 7.367.51 ( m , 4h ) , 7.93 ( s , 1h ) . c nmr ( 75 mhz , cdcl3 , 297 k ) : 39.5 , 41.7 , 64.1 , 117.7 , 118.5 , 123.9 ( q , jc f = 271.8 hz , 1c ) , 125.2 ( q , jc f = 33.0 hz , 1c ) , 126.2 , 126.4 ( q , jcf = 3.5 hz , 1c ) , 127.7 ( q , jc f = 3.7 hz , 1c ) , 128.9 , 129.2 , 131.5 , 157.8 , 174.3 , 175.0 . f nmr ( 376 mhz , cdcl3 , 297 k ) : 62.3 . hr - esims : m / z 365.1114 ( calcd for c18h16n2o3f3 , 365.1108 ) . a thf ( 60 ml ) solution of methyl bromoacetate ( 0.62 ml , 6.54 mmol , 1.0 equiv ) and triphenylphosphine ( 1.715 g , 6.54 mmol , 1.0 equiv ) was heated at reflux for 4 h until a white precipitate formed . the suspension was allowed to cool to room temperature before filtration ; the precipitate was washed with et2o ( 350 ml ) , and the precipitate was then redissolved in ch2cl2 ( 30 ml ) and h2o ( 20 ml ) . then2 m naoh ( 10 ml ) was added , and the biphasic mixture was stirred overnight . the reaction mixture was extracted with ch2cl2 ( 3100 ml ) , and the combined organic layers were washed with brine , dried ( mgso4 ) , and concentrated under reduced pressure to yield the phosphorane as a colorless powder ( 1.923 g , 88 % ) . h nmr ( 400 mhz , cdcl3 , 295 k ) : 2.90 and 3.51 ( br , 3h ) , 7.437.48 ( m , 6h ) , 7.527.57 ( m , 3h ) , 7.627.70 ( m , 6h ) . c nmr ( 100 mhz , cdcl3 , 298 k ) : 49.9 , 128.5 ( d , j = 12.0 hz ) , 128.8 ( d , j = 12.2 hz ) , 131.9 ( d , j = 2.7 hz ) , 132.1 ( d , j = 9.8 hz ) , 132.9 , 133.0 ( d , j = 10.2 hz ) . hr - esims : m / z 335.1200 ( calcd for c21h20o2p , 335.1195 ) . a chcl3 ( 200 ml ) solution of phosphorane ( 1.893 g , 5.66 mmol , 1.1 equiv ) and 2 - formylphenoxyacetic acid ( 0.927 g , 5.15 mmol , 1.0 equiv ) was heated at reflux for 18 h. the solvent was removed under reduced pressure , and the crude residue was purified by column chromatography ( eluent : gradient of petroleum ether to 1:1 etoac / petroleum ether ) to yield 8a as a colorless powder ( 1.037 g , 85 % ) . h nmr ( 300 mhz , cdcl3 , 295 k ) : 3.80 ( s , 3h ) , 4.77 ( s , 2h ) , 6.61 ( d , j = 16.2 hz , 1h ) , 6.81 ( d , j = 8.3 hz , 1h ) , 7.03 ( t , j = 7.6 hz , 1h ) , 7.33 ( td , j = 1.7 , 7.5 hz , 1h ) , 7.54 ( dd , j = 1.6 , 7.7 hz , 1h ) , 8.04 ( d , j = 16.2 hz , 1h ) , 8.899.30 ( br , 1h ) . c nmr ( 75 mhz , cdcl3 , 298 k ) : 52.2 , 65.4 , 112.5 , 119.5 , 122.5 , 124.4 , 129.8 , 131.8 , 140.4 , 156.7 , 168.6 , 173.8 . hr - esims : m / z 235.0610 ( calcd for c12h11o5 , 235.0612 ) . prepared in the same manner as 8a . bromoacetonitrile ( 0.88 ml , 12.5 mmol ) and pph3 ( 3.28 g , 12.5 ml ) were reacted to give the salt ( 4.580 g , 96 % ) . the phosphorane was prepared as before to give a colorless powder ( 3.422 g , 91 % ) . h nmr ( 300 mhz , cdcl3 , 297 k ) : 7.457.70 ( m , 15h ) . c nmr ( 121 mhz , cdcl3 , 297 k ) : 128.9 ( d , j = 12.1 hz ) , 129.5 ( d , j = 12.4 hz ) , 132.3 ( d , j = 2.6 hz ) , 132.5 ( d , j = 9.9 hz ) , 133.0 ( d , j = 2.1 hz ) , 133.2 ( d , j = 10.1 hz ) .8 b was prepared from the phosphorane ( 3.346 g , 11.11 mmol ) and 2 - formylphenoxyacetic acid ( 1.819 g , 10.10 mmol ) to give a colorless powder ( 1.477 g , 72 % ) . mp : 118 c. h nmr ( 400 mhz , cdcl3 , 297 k ) : 4.67 ( s , 3h ) , 6.31 ( d , j = 16.8 hz , 1h ) , 6.83 ( d , j = 1.1 hz , 1h ) , 7.01 ( t , j = 7.6 hz , 1h ) , 7.337.39 ( m , 2h ) , 7.62 ( d , j = 16.8 hz , 1h ) . c nmr ( 100 mhz , cdcl3 , 297 k ) : 65.1 , 98.0 , 112.2 , 119.1 , 121.9 , 123.0 , 129.8 , 132.2 , 146.5 , 156.5 , 170.5 . hr - esims : m / z 202.0511 ( calcd for c11h8o3n1 , 202.0510 ) . prepared in the same manner as 8a .1 - bromo -2-butanone ( 1.0 g , 6.62 mmol ) and pph3 ( 1.737 g , 6.62 mmol ) were reacted to give the salt ( 2.613 g , 96 % ) . h nmr ( 500 mhz , cdcl3 , 295 k ) : 1.18 ( t , j = 7.6 hz , 3h ) , 2.33 ( qd , j = 1.3 , 7.6 hz , 2h ) , 7.437.47 ( m , 6h ) , 7.527.56 ( m , 3h ) , 7.627.67 ( m , 6h ) .8 c was prepared from the phosphorane ( 1.712 g , 5.15 mmol ) and 2 - formylphenoxyacetic acid ( 0.843 g , 4.70 mmol ) to give a colorless powder ( 0.829 g , 75 % ) . h nmr ( 400 mhz , cdcl3 , 295 k ) : 1.17 ( t , j = 7.3 hz , 3h ) , 2.73 ( q , j = 7.3 hz , 2h ) , 4.78 ( s , 2h ) , 6.82 ( d , j = 6.82 hz , 1h ) , 6.90 ( d , j = 16.4 hz , 1h ) , 7.04 ( t , j = 7.1 hz , 1h ) , 7.35 ( td , j = 1.7 , 7.4 hz , 1h ) , 7.58 ( dd , j = 1.7 , 7.7 hz , 1h ) , 7.96 ( d , j = 16.4 hz , 1h ) . c nmr ( 100 mhz , cdcl3 , 298 k ) : 8.3 , 33.5 , 65.4 , 112.2 , 121.8 , 124.0 , 127.2 , 128.9 , 131.5 , 137.8 , 156.7 , 170.6 , 202.5 . hr - esims : m / z 233.0820 ( calcd for c13h13o4 , 233.0819 ) .2 - bromophenol ( 6.4 ml , 60.5 mmol ) , tert - butyldimethylsilyl chloride ( 10.0 g , 66.5 mmol ) , and imidazole ( 8.23 g , 121.0 mmol ) were dissolved in the minimum volume of dmf , and the mixture was allowed to stir at room temperature overnight . the dmf was removed under reduced pressure , and the resultant residue was taken up in etoac and washed with 1 m hcl , sat . the solvent was then removed under reduced pressure to yield ( 2 - bromophenoxy ) ( tert - butyl ) dimethylsilane ( 17.29 g , 99 % ) . h nmr ( 400 mhz , cdcl3 , 296 k ) : 0.25 ( s , 6h ) , 1.05 ( s , 9h ) , 6.806.84 ( m , 1h ) , 6.87 ( dd , j = 1.5 , 8.1 hz , 1h ) , 7.147.19 ( m , 1h ) , 7.51 ( dd , j = 1.7 , 7.9 hz , 1h ) . c nmr ( 100 mhz , cdcl3 , 297 k ) : 4.2 , 18.4 , 25.8 , 115.4 , 120.3 , 122.4 , 128.2 , 133.4 , 152.6 . hr - esims : m / z 287.0461 ( calcd for c12h20obrsi , 287.0461 ) . the aforementioned silane ( 0.54 g , 1.9 mmol ) was coupled with phenylboronic acid ( 0.27 g , 2.2 mmol ) by refluxing overnight in toluene ( 20 ml ) and ethanol ( 5 ml ) with pd [ p ( ph ) 3 ] 4 ( 0.2 g , 0.2 mmol ) and k2co3 ( 0.9 g , 6.5 mmol ) . the solvent was then removed under reduced pressure , and the reaction mixture was taken up in h2o before being extracted with etoac . the resultant mixture was subjected to column chromatography on silica gel ( eluent : 25 % ch2cl2 in petroleum ether 4060 ) to yield [ 1,1 - biphenyl ] -2-yloxy ) ( tert - butyl ) dimethylsilane ( 0.39 g , 73 % ) . h nmr ( 400 mhz , cdcl3 , 296 k ) : 0.05 ( s , 6h ) , 0.83 ( s , 9h ) , 6.92 ( dd , j = 1.2 , 8.0 hz , 1h ) , 7.04 ( td , j = 1.2 , 7.5 hz , 1h ) , 7.217.24 ( m , 1h ) , 7.307.33 ( m , 2h ) , 7.367.40 ( m , 2h ) , 7.50 ( dd , j = 1.5 , 8.5 hz , 1h ) . c nmr ( 100 mhz , cdcl3 , 297 k ) : 4.6 , 18.1 , 25.6 , 120.4 , 121.6 , 126.7 , 127.8 , 128.3 , 129.8 , 130.9 , 133.6 , 139.2 , 152.6 . the aforementioned biphenylsilane ( 0.36 g , 1.3 mmol ) was treated overnight with acetyl chloride ( 0.3 ml , 0.4 mmol ) in methanol ( 15 ml ) . following removal of the solvent under reduced pressure , the reaction mixture was subjected to column chromatography on silica gel ( eluent : ch2cl2 ) to yield [ 1,1 - biphenyl ] -2-ol ( 0.19 g , 86 % ) . h nmr ( 400 mhz , cdcl3 , 296 k ) : 5.13 ( bs , 1h ) , 6.886.92 ( m , 2h ) , 7.147.19 ( m , 2h ) , 7.287.32 ( m , 1h ) , 7.367.42 ( m , 4h ) . the aforementioned biphenyl alcohol ( 0.19 g , 1.11 mmol ) , methyl bromoacetate ( 0.16 ml , 0.26 mmol ) , and k2co3 ( 0.76 g , 5.5 mmol ) were refluxed overnight in thf ( 20 ml ) . the solvent was then removed under reduced pressure , and the resultant residue was taken up in ch2cl2 before being washed with h2o and dried over mgso4 . the solvent was removed under reduced pressure , and the resultant mixture was subjected to column chromatography on silica gel ( eluent : 25 % ch2cl2 in petroleum ether 4060 ) to afford methyl 2 - ( [ 1,1 - biphenyl ] -2-yloxy ) acetate ( 0.25 g , 94 % ) . h nmr ( 300 mhz , cdcl3 , 294 k ) : 3.82 ( s , 3h ) , 4.66 ( s , 2h ) , 6.94 ( d , j = 8.3 hz , 1h ) , 7.15 ( td , j = 1.0 , 7.5 hz , 1h ) , 7.337.51 ( m , 5h ) , 7.69 ( dd , j = 1.4 , 8.4 hz , 1h ) . c nmr ( 75 mhz , cdcl3 , 295 k ) : 52.2 , 65.8 , 112.8 , 122.2 , 127.1 , 128.1 , 128.6 , 129.7 , 131.3 , 131.4 , 138.1 , 154.8 , 169.6 . hr - esims : m / z 243.1020 ( calcd for c15h15o3 , 243.1016 ) . the aforementioned ester ( 0.19 g , 0.8 mmol ) was hydrolyzed with lioh ( 0.13 g , 3.2 mmol ) in a 3:1 mixture of meoh and h2o . following overnight stirring at room temperature , the reaction mixture was concentrated to ca . the combined extracts were dried over mgso4 and concentrated under reduced pressure , and the resultant residue was chromatographed on silica gel ( eluent : ch2cl2 ) to yield 11a ( 0.13 g , 73 % ) . h nmr ( 300 mhz , cdcl3 , 294 k ) : 4.63 ( s , 2h ) , 6.92 ( dd , j = 1.1 , 8.2 hz , 1h ) , 7.13 ( td , j = 1.1 , 7.5 hz , 1h ) , 7.297.46 ( m , 5h ) , 7.57 ( dd , j = 1.5 , 8.4 hz , 2h ) , 8.8010.10 ( br , 1h ) . c nmr ( 75 mhz , cdcl3 , 295 k ) : 65.9 , 113.4 , 123.1 , 127.7 , 128.7 , 129.1 , 129.9 , 131.8 , 131.9 , 138.3 , 154.6 , 173.7 . hr - esims : m / z 227.0707 ( calcd for c14h11o3 , 227.0714 ) . prepared in the same manner as 11a . ( 2 - bromophenoxy ) ( tert - butyl ) dimethylsilane ( 0.95 g , 3.3 mmol ) , 4 - ( trifluoromethyl ) phenylboronic acid ( 0.75 g , 4.0 mmol ) , pd [ p ( ph ) 3 ] 4 ( 0.38 g , 0.33 mmol ) , and k2co3 ( 1.2 g , 9.9 mmol ) were reacted and then columned on silica gel ( eluent : 25 % ch2cl2 in petroleum ether 4060 ) to afford 3 - ( trifluoromethyl ) - [ 1,1 - biphenyl ] -2-ol ( 0.13 g , 14 % ) . h nmr ( 400 mhz , cdcl3 , 296 k ) : 4.985.10 ( br , 1h ) , 6.96 ( d , j = 8.5 hz , 1h ) , 7.03 ( td , j = 1.1 , 7.5 hz , 1h ) , 7.267.31 ( m , 2h ) , 7.577.65 ( m , 2h ) , 7.71 ( d , j = 7.5 hz , 1h ) , 7.78 ( s , 1h ) . c nmr ( 100 mhz , cdcl3 , 297 k ) : 116.2 , 121.3 , 126.9 , 129.3 , 129.7 , 130.5 , 132.5 , 138.3 , 152.4 . hr - esims : m / z 237.0526 ( calcd for c13h8of3 , 237.0533 ) . the aforementioned biphenyl alcohol ( 0.13 g , 0.55 mmol ) was alkylated as before with methyl bromoacetate ( 0.1 ml , 1.1 mmol ) and k2co3 ( 0.38 g , 2.7 mmol ) and columned on silica gel ( eluent : 50 % ch2cl2 in petroleum ether 4060 ) to afford methyl 2 - ( ( 3 - ( trifluoromethyl ) - [ 1,1 - biphenyl ] -2-yl ) oxy ) acetate ( 0.14 g , 84 % ) . h nmr ( 400 mhz , cdcl3 , 296 k ) : 3.79 ( s , 3h ) , 4.65 ( s , 2h ) , 6.89 ( d , j = 7.7 hz , 1h ) , 7.12 ( td , j = 1.0 , 7.5 hz ) , 7.327.39 ( m , 2h ) , 7.54 ( t , j = 7.7 hz , 1h ) , 7.60 ( d , j = 7.8 hz , 1h ) , 7.81 ( d , j = 7.6 hz , 1h ) , 7.92 ( s , 1h ) . f nmr ( 376 mhz , cdcl3 , 296 k ) : 62.9 . c nmr ( 100 mhz , cdcl3 , 297 k ) : 52.3 , 65.5 , 112.3 , 122.3 , 123.8 ( q , jcf = 3.7 hz ) , 124.4 ( q , jcf = 272.2 hz ) , 126.5 ( q , jcf = 3.7 hz ) , 128.5 , 129.4 , 129.7 , 130.4 ( q , jcf = 32.1 hz ) , 131.2 , 133.0 , 138.8 , 154.6 , 169.2 . hr - esims : m / z 328.1162 ( calcd for c16h17no3f3 , 328.1155 ) . the aforementioned ester ( 0.14 g , 0.5 mmol ) was hydrolyzed with lioh ( 0.08 g , 1.8 mmol ) to afford 11b ( 0.13 g , 95 % ) . h nmr ( 400 mhz , cdcl3 , 296 k ) : 4.68 ( s , 2h ) , 6.91 ( d , j = 8.2 hz , 1h ) , 7.14 ( td , j = 1.0 , 7.5 hz , 1h ) , 7.347.39 ( m , 2h ) , 7.54 ( t , j = 7.7 hz , 1h ) , 7.60 ( d , j = 7.8 hz , 1h ) , 7.76 ( d , j = 7.6 hz , 1h ) , 7.87 ( s , 1h ) . c nmr ( 100 mhz , cdcl3 , 297 k ) : 65.0 , 112.4 , 122.6 , 123.9 ( q , jcf = 3.3 hz ) , 124.2 ( q , jcf = 272.4 hz ) , 126.4 ( q , jcf = 3.6 hz ) , 128.5 , 129.4 , 129.7 , 130.6 ( q , jcf = 32.5 hz ) , 131.2 , 132.8 , 138.6 , 154.1 , 173.0 . hr - esims : m / z 314.1001 ( calcd for c15h15no3f3 , 314.0999 ) . prepared in the same manner as 11a . ( 2 - bromophenoxy ) ( tert - butyl ) dimethylsilane ( 0.63 g , 2.2 mmol ) , 4 - ( trifluoromethyl ) phenylboronic acid ( 0.5 g , 2.6 mmol ) , pd [ p ( ph ) 3 ] 4 ( 0.22 g , 0.22 mmol ) , and k2co3 ( 0.9 g , 6.5 mmol ) were reacted and then columned on silica gel ( eluent : 25 % ch2cl2 in petroleum ether 4060 ) to afford 4 - ( trifluoromethyl ) - [ 1,1 - biphenyl ] -2-ol ( 0.43 g , 82 % ) . h nmr ( 400 mhz , cdcl3 , 296 k ) : 4.99 ( s , 1h ) , 6.97 ( dd , j = 0.5 , 8.1 hz , 1h ) , 7.04 ( td , j = 1.1 , 7.5 hz , 1h ) , 7.267.32 ( m , 2h ) , 7.64 ( d , j = 8.6 hz , 2h ) , 7.74 ( d , j = 8.6 hz , 2h ) . f nmr ( 376 mhz , cdcl3 , 296 k ) : 63.05 . c nmr ( 100 mhz , cdcl3 , 297 k ) : 116.2 , 121.3 , 124.1 ( q , jcf = 272.0 hz ) , 125.9 ( q , jcf = 3.7 hz ) , 126.9 , 129.4 ( q , jcf = 32.4 hz ) , 129.6 , 129.8 , 130.4 , 141.1 , 152.3 . hr - esims : m / z 237.0539 ( calcd for c13h8of3 , 237.0533 ) . the aforementioned biphenyl alcohol ( 0.4 g , 1.66 mmol ) was alkylated as before with methyl bromoacetate ( 0.24 ml , 2.5 mmol ) and k2co3 ( 1.15 g , 8.3 mmol ) and columned on silica gel ( eluent : 25 % ch2cl2 in petroleum ether 4060 ) to afford methyl 2 - ( ( 4 - ( trifluoromethyl ) - [ 1,1 - biphenyl ] -2-yl ) oxy ) acetate ( 0.529 g , 99 % ) . h nmr ( 400 mhz , cdcl3 , 296 k ) : 3.78 ( s , 3h ) , 4.64 ( s , 2h ) , 6.88 ( d , j = 8.2 hz , 1h ) , 7.10 ( td , j = 1.0 , 7.5 hz , 1h ) , 7.327.36 ( m , 2h ) , 7.67 ( d , j = 8.1 hz , 2h ) , 7.73 ( d , j = 8.1 hz , 2h ) . f nmr ( 376 mhz , cdcl3 , 296 k ) : 62.9 . c nmr ( 100 mhz , cdcl3 , 297 k ) : 52.2 , 65.5 , 112.3 , 122.2 , 124.4 ( q , jcf = 271.6 hz ) , 124.9 ( q , jcf = 3.7 hz ) , 129.1 ( q , jcf = 32.4 hz ) , 129.4 , 129.8 , 129.9 , 131.2 , 141.7 , 154.6 , 169.2 . hr - esims : m / z 328.1158 ( calcd for c16h17no3f3 , 328.1155 ) . the aforementioned ester ( 0.49 g , 1.6 mmol ) was hydrolyzed with lioh ( 0.26 g , 6.3 mmol ) to afford 11c ( 0.44 g , 95 % ) . h nmr ( 400 mhz , cdcl3 , 296 k ) : 4.68 ( s , 2h ) , 6.91 ( dd , j = 1.1 , 8.9 hz , 1h ) , 7.13 ( td , j = 1.0 , 7.6 hz , 1h ) , 7.337.39 ( m , 2h ) , 7.667.72 ( m , 4h ) . c nmr ( 100 mhz , cdcl3 , 297 k ) : 65.5 , 112.9 , 123.0 , 125.0 ( q , jcf = 273.5 hz ) , 125.4 ( q , jcf = 3.9 hz ) , 129.7 ( q , jcf = 31.2 hz ) , 129.9 , 130.3 ( 2 ) , 131.7 , 142.0 , 154.6 , 173.2 . hr - esims : m / z 295.0592 ( calcd for c15h10o3f3 , 295.0588 ) . a suspension of 2 - formylphenoxyacetic acid ( 0.515 g , 2.86 mmol , 1.0 equiv ) , methoxylamine hydrochloride ( 0.478 g , 5.72 mmol , 2.0 equiv ) , and sodium acetate ( 0.469 g , 5.72 mmol , 2.0 equiv ) in ethanol ( 30 ml ) was heated at reflux for 18 h. the solvent was removed under reduced pressure , and the crude residue was redissolved in h2o ( 100 ml ) and extracted into ch2cl2 ( 3100 ml ) . the combined organic layers were dried ( mgso4 ) , concentrated under reduced pressure , and purified by column chromatography ( 5 % etoac / ch2cl2 ) to yield 13a as a colorless solid ( 0.390 g , 65 % ) . h nmr ( 300 mhz , cdcl3 , 294 k ) : 4.01 ( s , 3h ) , 4.72 ( s , 2h ) , 6.91 ( d , j = 8.2 hz , 1h ) , 7.12 ( m , 1h ) , 7.34 ( d , j = 7.6 hz , 1h ) , 7.40 ( m , 1h ) , 8.15 ( s , 1h ) . c nmr ( 75 mhz , cdcl3 , 295 k ) : 61.9 , 66.6 , 114.2 , 120.6 , 123.0 , 131.7 , 132.4 , 148.8 , 155.4 , 169.5 . hr - esims : m / z 208.0614 ( calcd for c10h10no4 , 208.0615 ) . a suspension of 2 - formylphenoxyacetic acid ( 1.00 g , 5.55 mmol , 1.0 equiv ) , benzoxylamine hydrochloride ( 1.773 g , 11.11 mmol , 2.0 equiv ) , and sodium acetate ( 0.911 g , 11.11 mmol , 2.0 equiv ) in ethanol ( 60 ml ) was heated at reflux for 18 h. the solvent was removed under reduced pressure , and the crude residue was redissolved in h2o ( 100 ml ) and extracted into ch2cl2 ( 3100 ml ) . the combined organic layers were dried ( mgso4 ) , concentrated under reduced pressure , and purified by column chromatography ( 5 % etoac / ch2cl2 ) to yield 13b as a colorless solid ( 0.422 g , 26 % ) . h nmr ( 300 mhz , cdcl3 , 294 k ) : 4.70 ( s , 2h ) , 5.25 ( s , 2h ) , 6.90 ( d , j = 8.2 hz , 1h ) , 7.11 ( t , j = 6.6 hz , 1h ) , 7.327.44 ( m , 7h ) , 8.26 ( s , 1h ) . c nmr ( 75 mhz , cdcl3 , 295 k ) : 66.5 , 76.2 , 114.0 , 120.6 , 122.9 , 128.2 , 128.5 , 128.5 , 131.7 , 132.2 , 136.6 , 149.3 , 155.3 , 169.5 . hr - esims : m / z 284.0923 ( calcd for c16h14no4 , 284.0928 ) . phenoxyacetic acid ( 304 mg , 2.0 mmol ) and socl2 ( 0.74 ml , 10.0 mmol ) were refluxed in chcl3 for 72 h. the volatiles were removed under reduced pressure to yield phenoxyacetyl chloride . h nmr ( 400 mhz , cdcl3 , 296 k ) : 4.95 ( s , 2h ) , 6.93 ( m , 2h ) , 7.09 ( m , 1h ) , 7.35 ( m , 2h ) . c nmr ( 75 mhz , cdcl3 , 297 k ) : 64.9 , 77.2 , 114.8 , 122.3 , 129.9 , 157.5 , 174.2 . this compound was immediately treated with d2o ( 0.9 ml , 5.0 mmol ) in anhydrous ch3cn ( 10 ml ) , and the mixture was allowed to stir overnight under an argon atmosphere . the solvent was removed under reduced pressure , and the resultant residue was recrystallized from anhydrous et2o to yield 5ad as a white crystalline solid ( 141 mg , 46 % ) . h nmr ( 500 mhz , cdcl3 , 295 k ) : 4.70 ( s , 2h ) , 6.93 ( m , 2h ) , 7.03 ( m , 1h ) , 7.32 ( m , 2h ) . h nmr ( 76 mhz , chcl3 , 315 k ) : 10.13 ( bs , 1d ) . c nmr ( 75 mhz , cdcl3 , 297 k ) : 64.9 , 114.8 , 122.4 , 129.9 , 157.4 , 172.8 . hr - esims : m / z 153.0543 ( calcd for c8h8o3d , 153.0513 ) . phenoxyacetic acid ( 100 mg , 0.66 mmol ) and acrylamide ( 93.9 mg , 1.32 mmol ) in mecn ( 45 ml ) were reacted in accordance with the general procedure in a tio2 sol gel - coated tube . following irradiation for 24 h , the reaction mixture was purified by dry flash chromatography on silica gel ( eluent : gradient of 210 % meoh in ch2cl2 ) to yield 19h as an off - white solid ( 79.8 mg , 68 % ) . h nmr ( 300 mhz , cdcl3 , 294 k ) : 2.13 ( m , 2h ) , 2.45 ( t , j = 7.2 hz , 2h ) , 4.02 ( t , j = 6.0 hz , 2h ) , 5.63 ( bs , 1h ) , 5.82 ( bs , 1h ) , 6.90 ( d , j = 8.8 hz , 2h ) , 6.95 ( t , j = 7.4 hz , 1h ) , 7.29 ( t , j = 7.4 hz , 2h ) . c nmr ( 75 mhz , cdcl3 , 295 k ) : 25.4 , 32.6 , 67.1 , 114.9 , 121.2 , 129.9 , 159.2 , 175.4 .4 - ( tert - butyl ) phenoxyacetic acid ( 137.5 mg , 0.66 mmol ) and acrylamide ( 93.9 mg , 1.32 mmol ) in mecn ( 45 ml ) were reacted in accordance with the general procedure in a tio2 sol gel - coated tube . following irradiation for 30 h , the reaction mixture was purified by dry flash chromatography on silica gel ( eluent : gradient of 27.5 % meoh in ch2cl2 ) to yield the title compound as an off - white solid ( 105.4 mg , 68 % ) containing 5 % 4 - ( tert - butyl ) phenol . h nmr ( 400 mhz , cd3od , 297 k ) : 1.30 ( s , 9h ) , 2.042.11 ( m , 2h ) , 2.43 ( t , j = 7.3 hz , 2h ) , 4.00 ( t , j = 6.3 hz , 2h ) , 6.85 ( d , j = 8.9 hz , 2h ) , 7.30 ( dd , j = 3.2 , 11.5 hz , 1h ) . c nmr ( 75 mhz , cdcl3 , 297 k ) : 27.0 , 32.4 , 33.4 , 35.3 , 68.5 , 115.5 , 127.6 , 144.8 , 158.5 , 179.0 . hr - esims : m / z 236.1647 ( calcd for c14h22no2 , 236.1645 ) .4 - ( trifluoromethyl ) phenoxyacetic acid ( 145.3 mg , 0.66 mmol ) and acrylamide ( 93.9 mg , 1.32 mmol ) in mecn ( 45 ml ) were reacted in accordance with the general procedure in a tio2 sol gel - coated tube . following irradiation for 24 h , the reaction mixture was purified by dry flash chromatography on silica gel ( eluent : 5 % meoh in ch2cl2 ) to yield the title compound as an off - white solid ( 108.4 mg , 66 % ) . h nmr ( 500 mhz , d6 - acetone , 295 k ) : 2.062.11 ( m , 2h ) , 2.41 ( t , j = 7.2 hz , 2h ) , 4.14 ( t , j = 5.9 hz , 2h ) , 6.30 ( bs , 1h ) , 6.86 ( bs , 1h ) , 7.14 ( d , j = 8.7 hz , 2h ) , 7.63 ( d , j = 8.7 hz , 2h ) . c nmr ( 75 mhz , d6 - acetone , 297 k ) : 29.9 , 36.3 , 72.7 , 120.0 , 127.2 ( q , jc f = 33.1 hz , 1c ) , 130.0 ( q , jcf nmr ( 470 mhz , d6 - acetone , 295 k ) : 61.8 . hr - esims : m / z 248.0896 ( calcd for c11h13no2f3 , 248.0896 ) . a suspension of 8c ( 0.050 g , 0.21 mmol , 1.0 equiv ) and tio2 ( p25 , 0.025 g , 0.32 mmol , 1.5 equiv ) in mecn ( 20 ml ) was reacted in accordance with the general procedure for 9 h. following removal of the solvent under reduced pressure , the mixture was subjected to analysis by h nmr and gc ms . gc ms indicated four major components , and one of these ( tr = 10.7 min ) had the correct mass and fragmentation pattern for the cyclized product 10c : m / z ( % ) : 190 ( 40 ) , 161 ( 36 ) , 146 ( 18 ) , 133 ( 23 ) , 119 ( 38 ) , 118 ( 100 ) , 91 ( 41 ) . h nmr ( 400 mhz , cd3cn , 298 k ) : 0.98 ( t , j = 7.3 hz , 3h ) , 2.47 ( q , j = 7.3 hz , 2h ) , 3.263.29 ( m , 1h ) , 4.37 ( dd , j = 2.3 , 8.4 hz , 1h ) , 4.94 ( dd , j = 5.2 , 9.4 hz , 1h ) , 7.037.17 ( m , 2h , ) , 7.507.54 ( m , 2h ) . attempts to isolate and thoroughly characterize 10c were not successful . photoisomerization of 8c to its z isomer was observed during the course of this experiment . h nmr ( 400 mhz , cd3cn , 298 k ) : 7.38 ( d , j = 7.3 hz , 1h ) , 7.30 ( t , j = 7.3 hz , 1h ) , 7.02 ( d , j = 12.0 hz , 1h ) , 6.95 ( t , j = 7.6 hz , 1h ) , 6.88 ( d , j = 8.3 hz , 1h ) , 6.28 ( d , j = 12.5 hz , 1h ) , 4.69 ( s , 2h ) , 2.47 ( q , j = 7.3 hz , 2h ) , 0.97 ( t , j = 7.3 hz , 3h ) . a suspension of 11a ( 0.052 g , 0.23 mmol , 1.0 equiv ) and tio2 ( p25 , 0.027 g ,0.34 mmol , 1.5 equiv ) in mecn ( 20 ml ) was reacted in accordance with the general procedure for 18 h. following removal of the solvent under reduced pressure , h nmr analysis of the reaction mixture showed mainly unreacted 11a together with a small amount of the cyclized product 12a ( 0.01 mmol , 5 % wrt ch2br2 ) . h nmr ( 400 mhz , cdcl3 , 296 k ) : 5.05 ( s , 2h ) , 6.906.95 ( m , 2h ) , 7.007.10 ( m , obscured by sm ) , 7.607.70 ( m , 3h ) . attempts to isolate and thoroughly characterize 12a were unsuccessful . a suspension of 8a ( 0.050 g , 0.21 mmol , 1.0 equiv ) and tio2 ( p25 ,0.025 g , 0.32 mmol , 1.5 equiv ) in mecn ( 20 ml ) was reacted according to the general procedure for 9 h to yield 10a as a colorless powder ( 20 % by nmr ) . h nmr ( 400 mhz , cdcl3 , 294 k ) : 2.52 ( dd , j = 9.5 , 16.5 hz , 1h ) , 2.73 ( dd , j = 5.3 , 16.5 hz , 1h ) , 3.72 ( s , 3h ) , 3.843.91 ( m , 1h ) , 4.18 ( dd , j = 6.3 , 9.2 hz , 1h ) , 4.68 ( t , j = 9.0 hz , 1h ) , 6.80 ( d , j = 7.7 hz , 1h ) , 6.86 ( t , j = 8.3 hz , 1h ) , 7.087.17 ( m , 2h ) . c nmr ( 75 mhz , cdcl3 , 295 k ) : 38.7 , 39.7 , 52.3 , 110.2 , 114.1 , 121.0 , 124.6 , 129.1 , 129.5 , 160.2 , 172.7 . hr - esims : m / z 215.0674 ( calcd for c11h12o3na , 215.0679 ) . photoisomerization of 8a to its z isomer was observed during the course of this experiment . h nmr ( 400 mhz , cd3cn , 298 k ) : 7.48 ( dd , j = 7.6 , 1.8 hz , 1h ) , 7.31 ( t , j = 7.8 hz , 1h ) , 7.19 ( d , j = 12.5 hz , 1h ) , 6.97 ( t , j = 7.6 hz , 1h ) , 6.88 ( d , j = 8.3 hz , 1h ) , 6.01 ( d , j = 12.3 hz , 1h ) , 4.69 ( s , 2h ) , 3.63 ( s , 3h ) . a solution of 8b ( 0.050 g , 0.246 mmol ) in mecn ( 15 ml ) in a tio2 sol gel - coated tubethe solvent was removed under reduced pressure , and the crude residue was purified by column chromatography ( ch2cl2 ) to yield 10b as a colorless powder ( 0.007 g , 28 % ) . h nmr ( 400 mhz , cdcl3 , 296 k ) : 2.582.71 ( m , 2h ) , 3.743.82 ( m , 1h ) , 4.34 ( dd , j = 4.8 , 9.6 hz , 1h ) , 4.69 ( dd , j = 8.7 , 9.6 hz , 1h ) . 6.84 ( d , j = 8.1 hz , 1h ) , 6.93 ( td , j = 1.0 , 7.5 hz , 1h ) , 7.22 ( m , 1h ) , 7.32 ( d , j = 7.5 hz , 1h ) . c nmr ( 75 mhz , cdcl3 , 295 k ) : 22.8 , 38.8 , 75.4 , 110.3 , 117.7 , 121.2 , 124.4 , 127.1 , 129.7 , 159.7 . hr - esims : m / z 159.0676 ( calcd for c10h9no , 159.0679 ) . photoisomerization of 8b to its z isomer was observed during the course of this experiment . h nmr ( 400 mhz , cd3cn , 298 k ) : 8.01 ( dd , j = 7.6 , 1.6 hz , 1h ) , 7.66 ( d , j = 12.5 hz , 1h ) , 7.44 ( t , j = 8.0 hz , 1h ) , 7.11 ( t , j = 7.5 hz , 1h ) , 6.97 ( d , j = 8.3 hz , 1h ) , 5.64 ( d , j = 12.3 hz , 1h ) , 4.74 ( s , 2h ) . a suspension of 11c ( 59 mg , 0.20 mmol , 1.0 equiv ) and tio2 ( p25 , 0.024 g , 0.30 mmol , 1.5 equiv ) in mecn ( 20 ml ) was reacted in accordance with the general procedure for 18 h. following removal of the solvent under reduced pressure , h nmr analysis of the reaction mixture showed mainly unreacted acid ( 79 % ) together with a small amount of the cyclized product 12c ( 0.01 mmol , 5 % wrt ch2br2 ) . h nmr ( 400 mhz , cdcl3 , 296 k ) : 5.07 ( s , 2h ) , 6.936.96 ( m , 2h ) , 6.987.04 ( m ; obscured by sm ) , 7.727.65 ( m , 3h ) . gc ms analysis of the reaction mixture showed 12c as the main product : tr = 11.76 min ; m / z ( % ) 250 ( 58 ) , 249 ( 100 ) , 231 ( 6 ) , 201 ( 10 ) , 181 ( 10 ) , 152 ( 16 ) . also observed was a trace of what was probably the direct reduction product 2 - methoxy - 4 - ( trifluoromethyl ) -1,1-biphenyl : tr = 11.84 min ; m / z ( % ) 252 ( 82 ) , 251 ( 48 ) , 250 ( 61 ) , 249 ( 100 ) , 237 ( 20 ) , 201 ( 16 ) , 183 ( 26 ) , 152 ( 32 ) . attempts to isolate and thoroughly characterize 12c were unsuccessful . a suspension of 13a ( 51 mg ,0.24 mmol , 1.0 equiv ) and tio2 ( p25 , 0.029 g , 0.36 mmol , 1.5 equiv ) in mecn ( 29 ml ) was reacted in accordance with the general procedure for 24 h. following removal of the solvent under reduced pressure , h nmr analysis of the reaction mixture showed that 13a had been entirely consumed and that a complex mixture of products had been formed . ms analysis of the mixture revealed that 14a had been formed : tr = 8.15 min ; m / z ( % ) 165 ( 29 ) , 133 ( 12 ) , 119 ( 100 ) , 91 ( 77 ) 77 ( 26 ) . also observed were benzofuran - 3 ( 2h ) - one o - methyl oxime [ tr = 7.93 min ; m / z ( % ) 163 ( 100 ) , 118 ( 91 ) , 91 ( 52 ) ] , 2,3 - dihydrobenzofuran [ tr = 7.87 min ; m / z ( % ) 120 ( 27 ) , 119 ( 100 ) , 91 ( 57 ) ] , 2,3 - dihydrobenzofuran -3-amine [ tr = 5.06 min ; m / z ( % ) 135 ( 7 ) , 134 ( 74 ) , 119 ( 100 ) , 117 ( 11 ) ] , and benzofuran [ tr = 3.43 min ; m / z ( % ) 118 ( 100 ) , 90 ( 22 ) , 84 ( 30 ) ] . attempts to isolate and thoroughly characterize 14a , or any other products , were unsuccessful . a suspension of 13b ( 62 mg ,0.22 mmol , 1.0 equiv ) and tio2 ( p25 , 0.026 g , 0.33 mmol , 1.5 equiv ) in mecn ( 26 ml ) was reacted in accordance with the general procedure for 24 h. following removal of solvent under reduced pressure , h nmr analysis of the reaction mixture showed that 13b had been entirely consumed and that a complex mixture of products had been formed . gc ms analysis of the mixture revealed that 14b had been formed : tr = 15.53 min ; m / z ( % ) 241 ( 9 ) , 210 ( 9 ) , 133 ( 6 ) , 91 ( 100 ) , 77 ( 14 ) . also observed were benzofuran - 3 ( 2h ) - one o - benzyl oxime [ tr = 15.37 min ; m / z ( % ) 239 ( 37 ) , 222 ( 4 ) , 148 ( 3 ) , 119 ( 7 ) , 91 ( 100 ) , 77 ( 12 ) ] , 2,3 - dihydrobenzofuran -3-amine [ tr = 5.04 min ; m / z ( % ) 135 ( 7 ) , 134 ( 74 ) , 119 ( 100 ) , 117 ( 11 ) ] , benzyl alcohol [ tr = 3.77 min ; m / z ( % ) 108 ( 100 ) , 107 ( 73 ) , 79 ( 76 ) ] , benzofuran [ tr = 3.41 min ; m / z ( % ) 118 ( 100 ) , 90 ( 22 ) , 84 ( 30 ) ] , and benzaldehyde [ tr = 2.90 min ; m / z ( % ) 106 ( 87 ) , 105 ( 100 ) , 77 ( 66 ) ] . tio2 ( 12 mg , 0.15 mmol ) was dried overnight at 150 c under a continuous vacuum in an oven - dried schlenk tube . phenoxyacetic acid ( 15.2 mg , 0.1 mmol ) and acrylamide ( 14.2 mg , 0.2 mmol ) in mecn ( 12 ml ) were added via syringe , and the resultant mixture was irradiated for 18 h. h nmr analysis of the resultant mixture revealed 19h ( 39 % by nmr ) . phenoxyacetic acid ( 15.2 mg , 0.1 mmol ) , acrylamide ( 14.2 mg , 0.2 mmol ) , and tio2 ( 12 mg , 0.15 mmol ) in d3 - mecn ( 12 ml ) were irradiated for 18 h. h nmr analysis of the resultant mixture revealed 19h ( 55 % by nmr ) . d1 - phenoxyacetic acid ( 15.3 mg , 0.1 mmol ) , acrylamide ( 14.2 mg , 0.2 mmol ) , and tio2 ( 12 mg , 0.15 mmol ) in mecn ( 12 ml ) were irradiated for 19 h. h nmr analysis ( wrt ch2br2 standard ) of the resultant mixture revealed 19h ( 49 % by nmr ) . an oven - dried schlenk tube , complete with magnetic stirrer , was connected to a vacuum line , evacuated , and then back - filled with argon while still hot from the oven . in a glovebox , tio2 ( p25 , 0.15 mmol , 12 mg ) was added , and the tube was then heated at 150 c for 3 h under vacuum . in a separate oven - dried vessel , 10 ml of d2o ( freshly opened ) was degassed by three freeze pump thaw cycles before being transferred by cannula to the tube containing the tio2 once it had cooled to ambient temperature . the resultant mixture was allowed to stir overnight before the d2o was removed under reduced pressure . at this pointthe tio2 was again dried for 3 h at 150 c under vacuum . in a separate oven - dried vessel , phenoxyacetic acid ( 0.1 mmol , 15.2 mg ) and acrylamide ( 0.2 mmol , 14.2 mg ) were dissolved in mecn ( 12 ml ) that had been freshly collected after distillation over calcium hydride . the resultant mixture was degassed for 15 min by bubbling with argon and then transferred via cannula to the tube containing the tio2 once it had cooled to ambient temperature . the resultant mixture was then irradiated in accordance with the general procedure for 19 h. h nmr analysis of the resultant mixture revealed 19h ( 58 % by nmr ) . this reaction was performed as above using d1 - phenoxyacetic acid ( 15.3 mg , 0.1 mmol ) for 19 h. h nmr analysis of the resultant mixture revealed no clear signals indicating the formation of 19h or 19d .\noutput:\n" }, { "from": "agent", "value": "photochemical reactions employing tio2 and carboxylic acids under dry anaerobic conditions led to several types of c c bond - forming processes with electron - deficient alkenes . the efficiency of alkylation varied appreciably with substituents in the carboxylic acids . the reactions of aryloxyacetic acids with maleimides resulted in a cascade process in which a pyrrolochromene derivative accompanied the alkylated succinimide . the selectivity for one or other of these products could be tuned to some extent by employing the photoredox catalyst under different conditions . aryloxyacetic acids adapted for intramolecular ring closures by inclusion of 2 - alkenyl , 2 - aryl , or 2 - oximinyl functionality reacted rather poorly . profiles of reactant consumption and product formation for these systems were obtained by an in situ nmr monitoring technique . an array of different catalyst forms were tested for efficiency and ease of use . the proposed mechanism , involving hole capture at the tio2 surface by the carboxylates followed by co2 loss , was supported by epr spectroscopic evidence of the intermediates . deuterium labeling indicated that the titania likely donates protons from surface hydroxyl groups as well as supplying electrons and holes , thus acting as both a catalyst and a reaction partner ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: a 14 - year - old girl was referred to our clinic because of her growth retardation and scoliosis . she had been born via caesarian section at 38 weeks with a birth weight of 1,500 grams , and she had been observed in the neonatal intensive care unit for three days . her laboratory values obtained at the second day of birth were as follows : serum alkaline phosphatase 8 iu ( reference range 430 - 1,140 iu ) , serum calcium 2.30 mmol / l and serum phosphate 1.82 mmol / l . the patient had been diagnosed as having hypophosphatasia and so she had been followed up by the pediatric endocrinology department . the patient had been lost to follow - up by her own choice and had not received any treatment for 12 years . her family history was insignificant except for the congenital hip dysplasia of her mother and the growth retardation of her 13 year old brother , and her 12 year old sister was healthy . the physical examination revealed marked growth retardation ( weight 36 kg [ 5 percentile ] , height 126 cm [ 5 percentile ] ) . her right femur displayed bowing and an external rotation deformity with limitation of internal rotation . the laboratory values were as follows : serum calcium : 9.7 mg / dl , alkaline phosphatase 12 iu and phosphorus 6 mg / dl . radiological examination showed bowing of the ribs , lucent streaks in the metaphysis representing nests of unossified physeal cartilage , and bowing and widening of the femur . the bowdler spurs in both fibulae and in the right hip joint femoral head were directed anteriorly and superiorly ( fig . the femoral necks were short and wide , and there was an increase of the collodiaphyseal angle with anterosuperior displacement of the femoral heads ( fig . there was irregularity at the articular surface of both femoral heads and the acetabulums with narrowing of the joint spaces . hypophosphatasia is a rare inheritable inborn error of metabolism that was first described by rathbun ( 3 ) . this disorder is characterized by defective bone mineralization and a deficiency of serum and liver / bone / kidney tissue alkaline phosphatase activities ( 1 ) . deficiency of alkaline phosphatase results in the accumulation of inorganic pyrophosphates , and this results in undermineralized bone with incomplete ossification of the cartilage and the metaphyseal regions ( 2 ) . large amounts of unmineralized osteoid are present in all bones , and this is especially seen in the metaphyseal regions ( 2 ) . hypophosphatasia causes defective skeletal mineralization that manifests clinically as rickets in infants and children , and it manifests as osteomalacia in adults . six clinical forms are currently recognized : perinatal , infantile , childhood , adult , odontohypophosphatasia and a benign prenatal form that was decently described by pauli et al . ( 4 ) . when hypophosphatasia presents clinically in a severe form either before or during the newborn period , perinatal death occurs . by contrast , the infantile type presents during the first six months of life with growth failure and rachitic like skeletal deformities that result in recurrent respiratory infections and increased intracranial pressure ( 5 ) . our patient had bowdler spurs at birth , but she did not have any serious disease till she reached 14 years old . a wide spectrum of the radiographic and clinical abnormalities seen in perinatal hypophosphatasia was presented by kozlowski and colleagues ( 6 ) . ossification is generally compromised in the entire skeleton and a complete lack of ossification ensues in some individual bones . significant radiological changes are known to ensue with hypophosphatasia , and they include very thin and wavy fractures of the ribs , lucent defects and irregularities , \" metaphyseal cupping \" , \" chrosomal like \" or \" campomelic like \" changes of the femur and humerus , various decreases of ossification in the radius , ulna , tibia and fibula , and the characteristic \" spurs \" of the ulna and fibula ( at the midshaft ) that protrude towards the skin ( 6 ) . in the literature , the bowdler spurs that have been reported on up to now are generally in the perinatal age group . we have presented here a rare adolescent case of hypophosphatasia with bowdler spurs ; thus , we advocate that the diagnosis of hypophosphatasia also be considered for those adolescent patients having radiological evidence of bowdler spurs .\noutput:\n" }, { "from": "agent", "value": "hypophosphatasia is a clinically heterogeneous inheritable disorder characterized by defective bone mineralization and the deficiency of serum and tissue liver / bone / kidney alkaline phosphatase activities . due to the mineralization defect of the bones , various skeletal findings can be radiologically observed in hypophosphatasia . bowing and bowdler spurs of long bones are the characteristic findings . the bowdler spurs reported on in the previous pertinent literature were observed in the perinatal aged patients and these lesions have rarely involved adolescents . we herein report on a 14 - year - old girl with fibular bowdler spurs ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: from september 2008 to september 2011 , we collected blood samples from 136 kiso horses , which represent 91 % of all the horses registered with the kiso horse conservation association . the horses were bred in the mountainous region of central japan : mainly in nagano , gifu and aichi prefectures . within the surveyed horses , 17 were males , 102 were females , and 17 were geldings . after the sample was transferred to an edta blood collection tube , it was promptly taken to the laboratory , and the dna was extracted using the wizard dna extraction kit ( promega kk , tokyo , japan ) . the 411 - bp reference sequence of the mtdna d - loop region between positions 15,437 and 15,847 from each horse was sequenced using the following primers ; forward : 5 ctagctccaccatcaacacc - 3 , reverse : 5 - atggccctgaagaaagaacc - 3 . using the geneamp kit ( applied biosystems , lifetechnologies co. , carlsbad , ca , u.s.a . ) , a total of 15 l of the reagent containing 20 ng of a dna template , 15 pmol primer set , 2.5 mm mgcl2 , 0.33 mm dntps , 1.5 l of 10 buffer and 1.5 u amplitaq gold was subjected to initial denaturation for 10 min at 95c , followed by 30 cycles of pcr ( 30 sec at 94c , 1 min at 60c and 30 sec at 72c ) and final extension for 10 min at 72c . the pcr products were incubated with exonuclease i and shrimp alkaline phosphatase and used as template dna . then , direct sequencing was performed using the big dye terminator v3 .1 cycle sequencing kit ( applied biosystems ) . the sequence products were analyzed using an automatic dna sequencer ( abi prism3130xl , applied biosystems ) , and the resulting sequences were processed using sequencing analysis software ( applied biosystems ) . the accuracy of sequencing was determined using sequencing scanner v1 .0 ( applied biosystems ) . variation of each haplotype was confirmed using multiple alignments by clustal x . to estimate the demographic history of the kiso horse , we used the basic local alignment search tool ( blast ) of national center for biotechnology information ( ncbi ) and searched for homology between the obtained sequences and known sequences . using arlequin , we also performed mismatch analysis to estimate the mutation processes . we then used molecular evolutionary genetics analysis ( mega ) software to build a phylogenetic tree , which shows the relationship of the mtdna haplotypes for 24 horse breeds around the world , including przewalskii ( table 1table 1 . the accession numbers of the haplotypes in 24 horse breeds analyzed for phylogenetic relationship with the haplotypes in the kiso horsepopulationno . of haplotypesaccession numberabbreviationgeographical regionakhal - teke8dq327950 , dq327953 , dq327956 - 60 , dq327962at1 - 8west asiaarabian15af064628 - 9 , ef437553 - 62 , ef437564 - 6are1 - 15west asiabelgian3af064630 - 2bel1 - 3europebreton2ab329597 , ab329617brt1 - 2europecheju7af014405 - 8 , af014410 - 12cj1 - 7east asiahokkaido3ab329589 , ab329596 , ab329620hkd1 - 3japanhucul12jf951834 - 7 , jf951840 - 7hcl1 - 12europeicelandic14hq153701 , hq153711 - 2 , hq153715 , hq153719 , hq153722 - 6 , hq153728 , hq153753 - 4 , hq153757icl1 - 14europeirish draught30dq327892 , dq327898 - 900 , dq327902 , dq327904 - 6 , dq327909 - 10 , dq327912 , dq327915 - 6 , dq327918 - 21 , dq327923 , dq327925 - 28 , dq327933 - 36 , dq327938 , dq327944 - 5 , dq327948id1 - 30europekiso * 3ab329600 , ab329626 - 7ks1 - 3japanmisaki1ab329624mskjapanmongolian19af014413 - 5 , af056071 , dq327986 - 7 , dq327989 - 92 , ab329587 , ab329592 , ab329604 , ab329606 , ab329618 , ab329622 - 3 , ab329625 , ab329628mng1 - 19east asianoma2ab329591 , ab329609nm1 - 2japanorlov trotter9dq328002 - 5 , dq328007 , dq328012 - 3 , dq328015 , dq328018ot1 - 9north asiapercheron2ab329603 , ab329619pcr1 - 2europepottoka10ay519958 - 67pot1 - 10europeprzewalskii2ap012267 , ap012269prw1 - 2taishu2ab329588 , ab329614 , af169009 - 10ts1 - 4japanthoroughbred18ab329590 , ab329593 - 5 , ab329599 , ab329601 - 2 , ab329605 , ab329607 - 8 , ab329610 - 3 , ab329615 , ab329621 , d14991 , d23665trb1 - 18europetibetan3ef597512 - 4tb1 - 3east asiatokara1ab329598tkrjapanvyatka10dq328020 - 4 , dq328026 , dq328028 , dq328034 - 5 , dq328037vyt1 - 10north asiayakutian13dq328038 - 40 , dq328042 - 5 , dq328050 , dq328052 - 4 , dq328056 - 7yk1 - 13north asiayunnan1af014416yneast asia * from kakoi , h. et al . ) . the statistical reliability of each node within this phylogenetic tree was confirmed by 1,000 random bootstrap replicates . * from kakoi , h. et al . to assess the diversity of current maternal lineage in the kiso horse , we classified the resulting sequences and calculated the haplotype diversity ( h ) and nucleotide diversity ( ) using arlequin . the relationship among haplotypes was visualized by a median - joining network using network 4.6.0.0 ( http://www.fluxus-engineering.com . suffolk , u.k . ) . to predict future change of the diversity of maternal lineage in kiso horseaccording to the results of analysis of the d - loop region ( 411 bp of 136 kiso horses ) , we confirmed that the kiso horse has 7 haplotypes ( k1k7 ) , namely haplotypes k1 , k2 , k3 , k4 , k5 , k6 and k7 . forty horses ( 29.4 % ) had k1 , 33 horses ( 24.3 % ) had k2 , 28 horses ( 20.6 % ) had k3 , 19 horses ( 14.0 % ) had k4 , 9 horses ( 6.6 % ) had k5 , 6 horses ( 4.4 % ) had k6 , and 1 horse ( 0.7 % ) had k7 . when we compared these results with the reference standard x79547 , there were 25 polymorphic sites in the corresponding genomic region of the kiso horse ( table 2 table 2 . the mitochondrial dna d - loop region of haplotypes k1 - k7 in the kiso horse compared with the reference sequence x79547 ) . these 25 mutations were all point mutations between identical types of bases showing significant deviation that occurs between transversion and transition in the course of evolution of mtdna in mammals , and the analyzed region was a / t rich ( a : 30.3 % , t : 27.7 % , c : 28.5 % and g : 13.5 % ) ; this finding correlates with the findings of previous report on equine species . according to the blast results , the 6 haplotypes , k1 , k2 , k4 , k5 , k6 and k7 , correlated with ab329626 ( kiso horse - derived h46 ) , ab329627 ( kiso horse - derived h47 ) , ab329588 ( taishu horse - derived h2 ) , ab329600 ( kiso horse - derived h14 ) , ab329589 ( hokkaido horse - derived h3 ) and ab329604 ( mongolian native horse - derived h18 ) , respectively . there were no sequences , however , that matched k3 , suggesting that k3 is a new sequence in terms of evolution . in the mismatch analysis , sequence differences ranged from 1 to 14 bp , showing a bimodal distribution with a major peak at 0 mutational differences and a secondary one at 12 mutational differences ( fig . the number of pairs with nucleotide site differences is labeled on the top of each bar . the number of pairs with nucleotide site differences is labeled on the top of each bar . the h in the kiso horse was 0.790.01 ( mean sd ) , while was 0.0170.009 . the number of nucleotide mutations among the haplotypes ranged from 1 ( between k1 and k2 and between k4 and k6 ) to 14 ( between k3 and k5 ) , and the distance between bases ranged from 0.002 to 0.036 . according to the median - joining network , which visualizes this information , k1 and k2 as well as k4 and k6 form a group ( each pair ) ; this result shows that the mtdna d - loop haplotypes of the kiso horse were divided into 4 clusters ( fig . the relationship between the kiso horse haplotypes and the haplotypes of horse breeds worldwide was elucidated in the neighbor - joining tree ( fig . 3fig .3 . neighbor - joining phylogenetic relationships between 7 haplotypes of the kiso horse and the haplotypes of other 24 breeds . the branched numbers represent bootstrap probability ( 1,000 replicates ) , and the letters athe 7 haplotypes of the kiso horse k1 , k2 , k3 , k4 , k5 , k6 and k7 were distributed in clusters f , f , c , e , b , e and c , respectively . neighbor - joining phylogenetic relationships between 7 haplotypes of the kiso horse and the haplotypes of other 24 breeds . the branched numbers represent bootstrap probability ( 1,000 replicates ) , and the letters awith regard to the regional distribution of each haplotype , the distribution of the haplotype was different in each prefecture . in nagano prefecture , main breeding region of kiso horse , there were k1 ( 28 horses ) , k3 ( 24 horses ) , k2 ( 15 horses ) , k4 ( 7 horses ) , k5 ( 4 horses ) , k6 ( 3 horses ) and k7 ( 1 horse ) in decreasing order . then , the distribution in gifu prefecture in decreasing order was k2 ( 11 horses ) , k4 ( 7 horses ) , k1 ( 5 horses ) , k6 ( 3 horses ) , k3 ( 2 horses ) and k5 ( 1 horse ) . the distribution in aichi prefecture in decreasing order was k1 ( 6 horses ) , k5 ( 3 horses ) and k4 ( 2 horses ) ( fig . the figures within the graph represent the number of horses for each haplotype . ) . in this study , we attempted to elucidate the genetic characteristics of the kiso horse by looking at the genetic diversity of the maternal lineage . our research provided compelling suggestions about the demographic history , the current maternal lineage diversity and prediction about its future changes . this is because approximately 6,000 years ago , many horses that inhabited eurasia were caught and domesticated , and the descendants of those horses rapidly spread throughout the world . the fact that k1k7 are categorized into various clusters shows that the kiso horse also has various ancestors . in addition , although k3 and k5 are haplotypes confirmed only in the kiso horse , we were able to confirm that haplotype k1 is present in arabian horse ; haplotype k2 is present in the mongolian native horse ; k4 is present in the taishu horse ( japanese native ) , misaki horse ( japanese native ) and mongolian native horse ; k6 is present in the hokkaido horse ( japanese native ) ; and k7 is present in the asian and european breeds of horses . furthermore , mismatch analysis showed bimodal distribution , which suggests reconvergence of the populations . these results may support the information on the demographic history of the kiso horse obtained from various studies of proteins and nuclear dna and from archeological researches , that is , a ) horses with various roots entered the japanese archipelago from areas , such as the mongolian grasslands , and then stayed in kiso , and these horses became the ancestors of the kiso horse , and b ) in the various eras , mares were brought in kiso area from other regions of japan , and the kiso horse breed was improved in accordance with the region and / or the era . second , we would like to discuss the current diversity of the maternal lineage in the kiso horse . the kiso horse has 7 haplotypes that were divided into 4 clusters . in this study , because we were able to collect samples from 91 % of the entire population of this breed , we were able to identify more haplotypes including a new one than those identified in previous report . unfortunately , the 28 - year - old mare with the k7 haplotype died immediately after the survey ; therefore , haplotype k7 has disappeared from the kiso horse population . however , the number of haplotypes in the remaining kiso horses is smaller than those in the lusitano ( 27 haplotypes ) , lipizzan ( 37 haplotypes ) and arabian horses ( 27 haplotypes ) , but greater than those in the iberian , south american and north american horses ( 26 haplotypes ; mean 3.8 ) . furthermore , if we keep in mind the sorraia horse , which is also endangered with a similar size of the population as the kiso horse has only 2 haplotypes , the number of haplotypes in the kiso horse is by no means small . in addition , h in the kiso horse is 0.790.01 , which is slightly lower than that in the thoroughbred and breton horses ( 0.89 and 0.88 , respectively ) . also , in the kiso horse is 0.0170.009 , which is similar to that in the mongolian native ( 0.021 ) , thoroughbred and breton ( 0.020 ) and percheron ( 0.014 ) horses . given that ranges from 0.000 to 0.104 in different breeds , with a mean of 0.0104 , in the kiso horse is considered an average level . these data show that although the kiso horse has only a small population , the genetic diversity of the maternal lineage is comparatively preserved . third , we would like to predict future changes of the maternal lineage in the kiso horse . interestingly , although we did not find regional differences in microsatellite dna distribution in the previous study , the mtdna d - loop region haplotype exhibited different distribution in each prefecture . the kiso horse , which experienced a bottleneck in 1970s , was almost exclusively bred within nagano prefecture until the 1980s , and later , kiso horse enthusiasts in various regions began breeding this horse until the present day . therefore , it is thought that there was a founder for the maternal lineage in each region , and colonies were formed in each region mainly with that founder . in addition to this regional isolation and artificial factors , there has been a decline in the number of private owners , because of aging , together with the increasing number of zoological parks and equestrian clubs keeping the kiso horses in herds of several animals . this trend , bringing a biased - breeding for a specific use of the horse and / or the preference of a limited number of breeders keeping horses in herds , is suggested to accelerate the deviation of haplotypes of each region and the decline in the diversity of the maternal lineage . in this study , we attempted to understand the kiso horse population on the basis of the diversity of the maternal lineage . the results clearly show that the genetic diversity of the maternal lineage in the kiso horse has been maintained reasonably well . nevertheless , the population is still small , and thus , the kiso horse may be in the extinction vortex : when the population becomes small , and that such decline could accelerate loss of their genetic diversity , while inbreeding will progress further . moreover , various genes of the kiso horse have been fixed because of the past population bottleneck , and those genes are considered to include the genes that bring about inbreeding depression . furthermore , as suggested in this study , it is possible that diversity of maternal lineage of kiso horse which was preserved by traditional manner of breeding will be decreasing . consequently , to preserve the kiso horse for our next generation , the following key vital measures should be taken , that is , i ) clarify the genetic characteristics of the kiso horse from various perspectives , ii ) use reproductive technologies to preserve sperm and zygotes , iii ) search for new ways to utilize the horses , thereby inspiring demand to breed the kiso horse and iv ) take action aimed at gathering national support for conserving our unique genetic resource and living cultural asset of the region .\noutput:\n" }, { "from": "agent", "value": "abstractto determine genetic characteristics of the maternal lineage of the kiso horse based on polymorphisms of the mitochondrial dna d - loop region , we collected blood samples from 136 kiso horses , 91 % of the entire population , and sequenced 411 bp from 15,437 to 15,847 in the region . first of all , we estimated the demographic history ; by searching homology between the obtained and known sequences using basic local alignment search tool , by mismatch analysis to evaluate the mutation processes using arlequin , and by building a phylogenetic tree showing the relationship of the mtdna haplotypes for 24 horse breeds around the world using molecular evolutionary genetics analysis softwear . the results suggested that various horses that came to japan stayed at kiso region and became ancestors of kiso horse and also genetically supported the theory that the kiso horse was historically improved by other japanese native horse breeds . next , we analyzed the diversity of current maternal lineage by classifying the resulting sequences , and by calculating the haplotype diversity and nucleotide diversity using arlequin . then , we visualized the relationship among haplotypes by a median - joining network using network 4.6.0.0 . the results suggested the diversity of maternal lineage in the kiso horse was reasonably maintained . lastly , we predicted future change of the diversity of maternal lineage in kiso horse by assessing the regional distribution of the acquired haplotypes . the distribution suggested that diversity of maternal lineage would possibly be reducing ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the analysis of dna sequence is increasingly being used to guide the discovery of natural product biosynthetic gene clusters capable of encoding for novel metabolites . when studying cultured bacteria , it is possible to fully sequence a bacterial genome and therefore carry out detailed analyses of complete biosynthetic gene clusters to identify those likely to encode for novel metabolites . similar full gene cluster analyses are not usually possible when exploring complex environmental microbiomes because the immense size of most metagenomes precludes full sequencing and assembly of complete gene clusters . to circumvent this limitation , we and others have explored the use of the detailed phylogenetic analysis of individual , highly conserved natural product biosynthetic genes as markers for guiding the discovery of functionally novel natural product biosynthetic gene clusters from complex metagenomes . in this approach , individual biosynthetic genes are pcr - amplified from environmental dna ( edna ) and sequenced in bulk . the resulting amplicon sequences ( i.e. , natural product sequence tags ) are then aligned with reference sequences from functionally characterized gene clusters . in previous studies , we have shown that sequence tags that are only distantly related to any known sequence ( e.g. , sequence tag a in figure 1 ) can guide the identification of gene clusters that encode structurally novel bioactive natural products . we have also shown that sequence tags that are very closely related ( e.g. , sequence tag b in figure 1 ) to known genes can guide the discovery of gene clusters that encode congeners of known molecules . while the utility of sequence tags that reside at the phylogenetic boundaries is now clear , many sequence tags fall at a more ambiguous intermediate distance from known sequences ( e.g. , sequence tag c in figure 1 ) . sequence tags , especially those that fall between clades containing sequences known to encode for structurally distinct subclasses of natural products , might be useful for guiding the discovery of gene clusters that both encode novel bioactive metabolites and provide insights into the evolution of natural products structural diversity . here , we explore these concepts through the comparison of the genotypes ( i.e. , gene content ) and chemotypes ( i.e. , molecules encoded by ) of edna - derived aromatic polyketide ( pk ) pentangular polyphenols ( pps ) . aromatic pks are a large group of secondary metabolites generated by iterative ( i.e. , type ii ) pks biosynthetic systems . the initial step in aromatic pk biosynthesis involves the action of a minimal polyketide synthase ( min - pks ) . the min - pks is composed of the three proteins ks , ks and acp , which together catalyze the iterative condensation of malonyl - coa into polyketides ranging from 16 to 30 carbons in length . pps are constructed from the largest nonreduced pk precursors known ( 2430 carbons in length ) and are , therefore , potentially the most structurally diverse subclass of metabolites in this family . ( a ) phylogeny - guided strategy for the discovery of new natural products . ( b ) az , ab and tx denote amplicon sequences derived from arizona , california and texas desert soil edna libraries , respectively . a number of edna - derived pp ks sequence tags fall between clades associated with pps derived from polyketide precursors of different lengths ( c24 and c26 ) . the specific group of intermediate edna sequence tags used in this study are highlighted in orange . the highly conserved ks and ks genes from the min - pks have proved particularly useful as sequence tags for guiding the discovery of new aromatic polyketides from metagenomes . while edna ks and ks sequencing studies suggested the presence of large numbers of unique pp clusters in the environment , the biosynthetic landscape of pps from culture - based studies remained quite limited . in this studypp gene clusters associated with edna - derived ks and ks sequence tags that fall between well - defined clades containing genes from the biosynthesis of pradimicin and xantholipin type pp metabolites were recovered from archived soil edna libraries . the molecules encoded by these pp gene clusters were accessed through heterologous expression in streptomyces albus and found to encode new bioactive pentangular polyphenols with potent antiproliferative and antibacterial activities . by comparing the gene cluster genotypes and chemotypes across this expanded pentangular polyphenol biosynthetic landscape , we gain specific insights into pentangular polyphenol biosynthesis and general insights into potential limitations of the evolution of natural product structural diversity . to identify novel gene clusters encoding pp pks , archived soil edna libraries were screened with degenerate primers targeting either the ks or ks genes of the min - pks . ks and ks phylogenetic trees were constructed with the resulting edna amplicon sequences and sequences from previously characterized type ii pks gene clusters deposited in genbank . in this phylogenetic analysiswe identified two sequence tags of interest ( ks tag ab1692 and ks tag ab1414 ) from our anza borrego desert ( ab ) edna library . both sequence tags fall between well - defined clades containing ks genes from gene clusters that encode structurally distinct pp subfamilies , pradimicins and xantholipin ( figure 1b ) . sequence tags ab1692 and ab1414 were used to guide the recovery of edna cosmid clones containing pp biosynthetic gene clusters associated with these ks sequences . the recovered cosmids were pgm ( personal genome machine ) - sequenced and this sequence data was subsequently used to guide the recovery of additional cosmid clones overlapping each end of the two min - pks containing cosmids . sequencing and bioinformatics annotation ( tables s3 and s4 , supporting information ) of each set of three overlapping cosmid clones revealed a biosynthetic gene cluster flanked by collections of genes predicted to encode primary metabolic enzymes , suggesting that both gene clusters were recovered in their entirety on three overlapping cosmids . to access the metabolites encoded by the ab1692 and ab1414 pp gene clusters , each set of three overlapping edna cosmid clones ( ab1692 , ab916 and ab170 ; ab1442 , ab1414 and ab561 ) was assembled into bacterial artificial chromosomes ( bac - ab1692 / 916/170 and bac - ab1442 / 1414/561 ) using pathway specific ptara ( e. coli : yeast : streptomyces ) shuttle capture vectors and transformation - associated recombination ( tar ) in yeast ( figure 2 ) . these approximately 90 kb bac constructs were pgm - sequenced to ensure correct assembly and transferred into streptomyces albus by intergenic conjugation and integrated into the s. albus genome using the c31 integrase . for heterologous expression purposes , the resulting strains , s. albus bac - ab1692 / 916/170 and s. albus bac - ab1442 / 1414/561 , were grown at 30 c in r5a liquid media for 9 days . lc ms analysis of etoac extracts derived from these cultures showed the presence of one and two major clone - specific peaks , respectively ( figure 2 ) . the three clone - specific metabolites were purified from the extracts of 1 l cultures using , in each case , two rounds of c18 reversed - phase hplc . this gave calixanthomycin a ( 1 ) ( 12 mg / l ) from s. albus bac - ab1692 / 916/170 , and arenimycins c ( 2 ) ( 4.6 mg / l ) and d ( 3 ) ( 2.5 mg / l ) from s. albus bac - ab1442 / 1414/561 . heterologous expression and the structures of calixanthomycin a ( 1 ) , and arenimycins c ( 2 ) and d ( 3 ) . two pp gene clusters were recovered from california desert soil edna library on three overlapping edna cosmid clones ( ab1692 / 916/170 and ab1442 / 1414/561 ) . they were each reconstructed into bac clones using tar . the heterologous expression of these two pp gene clusters by s. albus led to the production of three clone - specific metabolites , compound 1 from the strain s. albus bac - ab1692 / 916/170 , and compounds 2 and 3 from the strain s. albus bac - ab1442 / 1414/561 . detailed hplc trace analysis can be found in the supporting information ( figure s2 ) . key 2d nmr correlations used for determining the structures of calixanthomycin a ( 1 ) and arenimycin c ( 2 ) . the structures of compounds 13 were determined by spectroscopic methods , including hresims , and 1d and 2d nmr ( figure 3 , see supporting information discussions s1 and s2 for structure elucidation details ) . the structure of calixanthomycin a ( 1 ) features a xanthone - containing pp core structure . the polycyclic xanthone core is tailored by oxidation , o - methylation and glycosylation . rare structural features include the f ring lactone , which is more commonly seen as a lactam in xanthone - containing pps , and the ortho - dimethoxy functionality on the a ring . calixanthomycin a ( 1 ) is most closely related to ib - 00208 from an unsequenced marine actinomadura sp . they differ by the position of methoxy groups around the a ring , the presence or absence of the double bond in the d ring and the oxidation state of the c ring . the structures of arenimycins c ( 2 ) and d ( 3 ) produced by s. albus bac - ab1442 / 1414/561 feature a highly oxidized benzo [ a ] naphthacene quinone core ( rings a through e ) . this core structure is appended with a disaccharide ( ome - l - rhamnose - ome - l - olivose ) in 2 and a monosaccharide ( l - rhamnose ) in 3 via a rare n - glycosidic linkage . these structures share an aglycone with the sf2446s from a soil actinomycete streptomyces sp . sf2446 , and the recently reported arenimycins a and b from a marine actinomycete salinispora sp . calixanthomycin a ( 1 ) is extremely toxic to hct - 116 cancer cells ( ic500 .43 nm ) ; however , it shows no antibacterial activity against mrsa ( methicillin - resistant s. aureus ) and vre ( vancomycin - resistant enterococcus faecium ) at the highest concentrations tested ( 50 g / ml ) , and weak activity against b. subillis ( mic = 3.1 g / ml ) . this is quite interesting as most reported xanthone - containing pps display a broad spectrum of activity with both potent human cell cytotoxicity and antibacterial activities . arenimycin c ( 2 ) shows potent gram - positive antibacterial activity ( mic = 98 ng / ml against mrsa ; 1.5 ng / ml against b. subtilis ) and moderate cytotoxicity against hct - 116 cells ( ic50 = 0.17 m ) . the biosynthesis of compounds 13 can be rationalized based on the predicted functions of the biosynthetic genes found on each producing bac construct ( figure 4 ) . bac - ab1692 / 916/170 is predicted to harbor the 50 kb clx ( calixanthomycin ) gene cluster ( genbank km881706 ) containing 47 genes involved in the biosynthesis , regulation and resistance of calixanthomycin a ( 1 ) . in our biosynthetic proposal , the predicted min - pks ( clx911 ) , cyclases ( clx8 , 30 and 31 ) and a ketoreductase ( clx1 ) are responsible for generating a benzo [ a ] naphthacene quinone intermediate using an acetate starter unit and 12 malonyl coa extension steps . the quinone could then be transformed to a xanthone via an oxidative rearrangement catalyzed by the predicted bayer - villiger oxidase ( bvo ) clx27 ( 51 % identity to pnxo4 from the fd - 594 gene cluster ) . the final tailoring steps in our proposed calixanthomycin a ( 1 ) biosynthesis scheme involve formation of the ortho - dimethoxy functionality in the a ring and glycosylation in the e ring . formation of the rare ortho - dimethoxy functionality would require reduction at c - 13 and hydroxylation at c - 12 followed by two o - methylations . the mechanism of c - 13 reduction is not clear at this point , but the hydroxylation at c - 12 is predicted to be catalyzed by the cytochrome - p450 hydroxylase clx28 due to its sequence similarity to pnxo5 ( 61 % sequence identity ) from the fd - 594 gene cluster . methylation of the ortho - hydroxyl groups could then occur by the action of the predicted o - methyltransferases clx2 and clx43 . in our proposed biosynthesis , the resulting hexacyclic xanthone aglycone is appended with a d - quinovose sugar moiety by the predicted glycosyltransferase clx40 . proposed biosynthesis of calixanthomycin a ( 1 ) , and arenimycins c ( 2 ) and d ( 3 ) ( in boxes ) based on the predicted gene function and pfam domain analysis . the presence of arenimycin b in the culture extract was confirmed by lc ms . detailed gene annotation tables for the clx and arn gene clusters appear in tables s3 and s4 . bac - ab1442 / 1414/561 harbors the 40 kb arn ( arenimycin ) gene cluster ( genbank kj440489 ) containing genes predicted to be involved in the biosynthesis , regulation and resistance of arenimycins c ( 2 ) and d ( 3 ) . in our proposed biosynthetic schemethe benzo [ a ] naphthacene core is synthesized via a min - pks ( arn31 , 32 and 36 ) , an aromatase ( arn21 ) , two cyclases ( arn19 and 20 ) and a ketoreductase ( arn33 ) ( figure 4 ) . on the basis of their high sequence identityto pdmh from the pradimicin gene cluster , arn 22 and 37 are predicted to oxidize c - 6 and c - 10 to form the two 1,4 - benzoquinone moieties ( a and c rings ) seen in 2 and 3 . arn 17 , which shows 54 and 43 % sequence identity to grho8 from the griseorhodin gene cluster and xano5 from the xantholipin gene cluster , respectively , is likely to be involved in hydroxylations at the two angular positions ( c - 5 and c - 18 ) . finally , this aglycone is predicted to be glycosylated by two glycosyltransferases arn11 and arn14 , completing the biosynthesis of 2 and 3 . the mechanism of n - glycosidic bond formation is not clear at this point . different pp chemistries are organized according to the phylogenetic analysis of ks gene sequences ( figure 1 ) . we have designated these scaffolds pp - a , pp - b , pp - c and pp - d . each different pp scaffold andthe arn gene cluster harbors all genes predicted to be required for the biosynthesis of the sugar moieties ( rhamnose and olivose ) found in 2 and 3 ( figure 4 ) . interestingly , it also contains three additional predicted sugar biosynthesis genes , whose functions could not be assigned to a specific transformation in the biosynthesis of the sugar moieties found on 2 or 3 . these include genes predicted to encode for an n , n - dimethyltransferase ( arn6 ) , an aminotransferase ( arn7 ) and a 3,4 - dehydratase ( arn8 ) . these observations along with the recently reported structure of arenimycin b , which contains the dimethylated amino deoxysugar forosamine in place of the ome - l - olivose seen in 2 , led us to re - examine culture broth extracts obtained from bac - ab1442 / 1414/561 by lcthe selective ion chromatogram for m / z = 809 revealed the presence of a minor clone specific compound with a mass corresponding to that of arenimycin b ( figure s9 ) . it appears that the edna - derived arn gene cluster has the potential to encode a number of different glycosylated compounds , with arenimycin c ( 2 ) being the major product . the annotated genome of salinispora arenicola cnb527 , the arenimycin b producer , was recently made publicly available ( genbank : nz_azxi01000002 ) . a comparison of the arenimycin b and the arn gene clusters reveals that these two gene clusters are very closely related , showing 90 to 95 % sequence identity between most biosynthetic genes . in total ,12 pp biosynthetic gene clusters have now been sequenced and functionally characterized , including eight clusters from culture - based studies and four from culture - independent studies . in addition to the edna - derived clx and arn clusters described here , we previously reported edna gene clusters that encode for fasamycin and arixanthomycin type pps . ks and ks sequence tags associated with these four edna clusters were selected by us for detailed analyses because they all fall between well characterized ks clades ( i.e. , intermediate sequence tags ) . in the following analyses , we explore this closely related collection of biosynthetic gene clusters to gain insights into the evolution of natural product structural diversity . the individual proteins that makeup min - pks ( ks , ks , and acp ) are highly conserved across type ii pks gene clusters . ks and ks phylogenetic trees show very similar topologies , both of which correlate closely with differences in the core polyketide structure ( e.g. , chain length and cyclization pattern ) encoded by the gene cluster from which the min - pks arises . ks and , to a lesser extent , ks genes have thus proved to be useful phylogenetic markers for predicting differences in polyketide core structures encoded by type ii pks gene clusters . while pps have so far been considered a single class of type ii polyketides , based on both ks phylogeny and natural product structure , it appears that they arise from four distinct min - pks lineages . these lineages differ in starter unit selectivity ( acetate or hexanoate ) and the number of malonyl coa chain extension steps they carry out ( 11 or 12 ) . pp polyketide precursors range from 24 to 30 carbons in length and generate four unique pp scaffolds that we have designated pp - a ( c24acetate and 11 extensions ) , pp - b ( c26acetate and 12 extensions ) , pp - c ( c28hexanoate and 11 extensions ) and pp - d ( c30hexanoate and 12 extensions ) ( figure 5 ) . the 30 - carbon d scaffold is the largest polyketide chain observed in aromatic polyketide biosynthesis . withmore than 30 predicted b scaffold - based natural products reported in the literature , this 26 - carbon scaffold , which arises from an acetate starter unit and 12 malonyl coa extension steps is responsible for most of the structural diversity seen in known pps ( figure 5 ) . the only reported gene clusters predicted to encode the a , c , and d scaffolds are the pradimicins ( pp - a ) , arenimycins ( pp - a ) , benastatins ( pp - c ) , fd - 594s ( pp - c ) and fredericamycins ( pp - d ) . although both ks and ks gene phylogenies indicate that the four pp scaffolds ( a c ) have evolved independently from a common ancestor , similar tailoring modifications are observed across scaffolds from different lineages . this is especially interesting in light of the fact that some of modifications seen in multiple different pp lineages ( e.g. , the xanthone core and the gem - dimethyl functionality ) are in fact quite rare outside of pp biosynthesis . this suggests that functionally successful horizontal transfer of the tailoring genes responsible for these modifications has not occurred globally throughout bacterial secondary metabolism but instead locally within the limited universe of pp biosynthesis . to evaluate evolutionary relationships between the genes responsible for the common modifications found across different pp scaffolds , we carried out detailed phylogenetic analyses of the four common tailoring genes seen in pp gene clusters including baeyer villiger oxidase , geminal bis - methyltransferase , asn - synthetase homologue and glycosyltransferase ( figure 6 ) . the most notable tailoring modification observed in pp biosynthesis is an oxidative rearrangement of the pp scaffold to generate either a xanthone or a spiroketal . these oxidative rearrangements involve the action of fad - dependent baeyer villiger oxidase ( bvo ) . bvos are also found in some angucycline gene clusters ( giloi , jadh and urdm ) and in the mithramycin gene cluster ( mtmoiv ) . to determine the phylogenetic relationship between these genes , a maximum likelihood phylogenetic tree was generated using full - length bvo gene sequences ( figure 6 ) . in this analysis , the pp bvo genes form a monophyletic clade that is distinct from other bvo genes , suggesting that the pp bvo gene was acquired once in pp biosynthesis and diverged to enable the production of distinct xanthone and spiroketal functionalities . interestingly , the bvo genes clx27 and pnxo4 from the calixanthomycin a and fd - 594 gene clusters , respectively , show the highest sequence identity even though their ks genes belong to distinct pp lineages ( figure 6 ) . this suggests that once the bvo gene successfully entered the pp biosynthetic universe it was not only passed down vertically through the pp - b lineage , but also horizontally transferred between pp lineages . curiously , while it appears that this bvo gene was capable of horizontal transfer between pp lineages with related core structures , similar , more global transfer to numerous other sequenced type ii pks gene cluster families is not observed , as the bvo genes found in other type ii pks gene clusters appear to be of distinct phylogenetic lineages . geminal bis - methylation is another rare tailoring reaction that is seen in pp biosynthesis . the introduction of this functional group is known to occur through the action of a single , sam - dependent methyltransferase ( geminal bis - methyltransferase , gbm ) via two rounds of c - methylation . known aromatic polyketides with this functionality include two pps , the fasamycins and the benastatins , a pentacyclic polyketide resistomycin , and the tetracyclic quinone tetarimycin . in resistomycin biosynthesis , two methyl transferasesare predicted to be required to introduce the dimethyl functionality , neither of which is closely related to the pp gbms . the three tetracyclic structures upon which the pp - like gbms act ( fasamycins , benastatins and tetarimycins ) are closely related ( figure 6 ) , once again suggesting that horizontal transfer of these tailoring genes has been limited to interchange between gene clusters that encode closely related core structures . ( a ) phylogenetic relationships between ks , ks , baeyer villiger oxidase , asn synthase homologue , geminal bis - methyltransferase and glycosyltransferase genes from pp biosynthetic gene clusters are reconstructed from the maximum likelihood phylogenetic trees to highlight the relationships between genes from clusters of different pp lineages . ( b ) the parent maximum likelihood phylogenetic trees for bvo genes , gbm genes and asn synthase homologue genes are shown . for both bvo and gbm tailoring genes , it appears that functionally successful horizontal gene transfer has been limited to gene clusters that encode metabolites with closely related core chemical structures . this would explain their presence in different pp lineages and few other gene clusters outside of pp biosynthesis and suggest that for many tailoring enzymes the challenge of changing substrate specificity ( or limited substrate promiscuity ) may have restricted their more extensive spread throughout natural product biosynthesis by horizontal gene transfer mechanisms . the terminal carboxylate in pp structures undergoes a variety of reactions including o - methylation , esterification / cyclization , alanine addition , serine addition / cyclization and amidation / cyclization . among these , amidation in general and , more specifically , transamination carried out by asn synthetase homologues is the most commonly seen transformation . in the phylogenetic analysis of ppasn transaminase genes , we once again see what appears to be horizontal transfer between different pp lineages . we also see what appears to be horizontal transfer between different polyketide classes as the closest relatives of the llpa and xana genes from the lysolipin and xantholipin gene clusters , respectively , are found in tetracycline - type gene clusters . one of the most common tailoring steps found in aromatic polyketide biosynthesis is glycosylation . to investigate relationships between pp glycosyltransferases , a phylogenetic tree was constructed using 40 glycosyltransferase genes found in sequenced pp gene clusters and additional glycosyltransferase genes found in gene clusters that encode a diverse collection of non - pp aromatic polyketides ( figure s1 ) . this maximum likelihood phylogenetic tree shows that clades do not correlate strongly with aromatic polyketide aglycone substrate structures or donor sugar types . among pp glycosyltransferse genes , clx40 , arx9 , arx3 , llpu and xanpdo form a monophyletic clade , suggesting that they have been vertically transferred through pp scaffold b gene cluster evolution . other pp glycosyltransferases , including arn11 , arn14 , pnxgt1 , pnxgt2 , pdms and pdmq , do not clade based on their respective pp min - pks lineages , suggesting that they have likely entered the pp biosynthetic gene clusters in distinct horizontal gene transfer events . for tailoring genes that to date are exclusively found in secondary metabolism ( e.g. , bvo and gbm ) , we see limited introduction of these genes into pp biosynthesis . within the examined set of gene clusters , both bvo and gbm genes appear to have entered pp biosynthesis only once . however , for tailoring gene families that are common across the global metagenome ( e.g. , asn - synthetase homologue and glycosyltransferase genes ) , we see many more introduction events resulting in their more varied use in pp structural diversification . the more frequent introduction of asn - synthetase homologue and glycosyltansferase genes into pp biosynthesis is likely due to both their more frequent appearance in the environment and their more relaxed substrate specificity . soil metagenomes represent the products of nature s ongoing combinatorial biosynthetic efforts . here , we show that sequence tag - based metagenomic screening methods provide an opportunity to identify collections of related natural product gene clusters that not only encode novel metabolites , but can also provide insights into the natural combinatorial biosynthetic process . more specifically , we show that the functional characterization of gene clusters whose sequence tags fall between clades associated with two related but distinct chemotypes ( intermediate sequence tags ) can be used to increase the chemical and the biosynthetic diversity associated with a targeted class of natural products . on the basis of the differences in min - pks gene phylogeny and the pp chemical structuresour phylogenetic analysis of pp tailoring genes indicates that the horizontal transfer of at least a subset of pp tailoring genes has likely been restricted to gene clusters that encode closely related chemical structures . if true , this would suggest that nature has sampled only a fraction of the natural product - like chemical space that can theoretically be encoded by secondary metabolite tailoring genes . these observations provide a more detailed picture of the nature s combinatorial biosynthetic process , which can help guide future laboratory - based combinatorial biosynthetic efforts and help ensure the construction of a set of molecules that is orthogonal to those produced naturally . in particular , our study suggests that combinatorial biosynthetic experiments focused on widely distributed enzymes ( e.g. , glyocsyl - or amino - transferases ) are likely to yield metabolites already sampled by evolution . on the other hand , experiments focused on increasing the substrate promiscuity of tailoring genes that are unique to secondary metabolism ( e.g. , bvo or gbm ) would be much more likely to yield metabolites not yet encoded by natural biosynthetic pathways . all recovered cosmids and tar constructs were sequenced using iontorrent personal genome machine ( pgm ) . optical rotations of isolated compounds were measured on a jasco p - 1020 polarimeter and ir spectra were recorded on a bruker tensor27 ir spectrometer . all nmr data used for structural characterization were obtained on a bruker avance dmx 600 mhz nmr spectrometer equipped with a cryoprobe . h and c nmr chemical shifts were referenced to the dmso - d6 solvent signals ( h 2.50 and c 39.51 , respectively ) . hresims data was acquired on the lct premier time - of - flight mass spectrometer . our ab ( california ) , az ( arizona ) and tx ( texas ) desert soil edna libraries were used for screening with ks and ks degenerate primers . each library contains 10 clones , which is predicted to approach saturation of the genetic diversity present in soil microbiomes . these libraries are arrayed as 5000 membered subpools to facilitate screening and gene cluster recovery studies . dna aliquots from the 5000 membered subpools found in each arrayed library were screened using degenerate primers designed to amplify partial ks and full - length ks genes . each 25 l pcr reaction contained 50 ng of cosmid dna , 2.5 m of each primer , 2 mm dntps , 1x thermopol reaction buffer ( new england biolabs ) , 0.5 units taq dna polymerase and 5 % dmso . pcr was conducted using the following touchdown protocol : denaturation ( 95 c , 2 min ) , 8 touchdown cycles [ 95 c , 45 s ; 65 c ( 1 c per cycle ) , 1 min ; 72 c , 1 min ] , 35 standard cycles ( 95 c , 45 s ; 58 c , 1 min ; 72 c , 1 min ) and a final extension step ( 72 c , 2 min ) . approximately 500 bp of ks or 600bp of ks gene ( corresponding to nucleotides 5621061 of bena or 25621 of benb ) fragments from each amplicon were aligned using clustalw . the edna clones from which the ab1692 and ab1414 amplicon sequences were amplified were recovered from the ab1692 and ab1414 subpools using serial dilution method . briefly , overnight cultures of the subpools were inoculated into 96 - well microtiter plates at a dilution of 50 cells / well . after overnight shaking at 37 c , the diluted cultures were screened by whole - cell pcr using specific primers designed to recognize the ab1692 and ab1414 amplicon sequences . pcr - positive wells from the second round were plated onto lb agar media to give distinct colonies that were screened individually using colony pcr to identify the clones ab1692 and ab1414 . the ab library was screened for overlapping edna clones using clone - specific primers designed to recognize the sequence at each end of the edna clones ab1692 and ab1414 . hits were identified in subpools ab916 for the ab1692 clone , and ab1442 and ab561 for the ab1414 clone . the overlapping edna clones were recovered from these subpools using the serial dilution method outlined above . all three cosmids were pgm - sequenced and annotated using metagenemark , in combination with blast search and pfam domain analysis . annotation results indicated that the biosynthetic gene cluster associated with the ab1414 ks sequence was completely captured in three overlapping clones , ab1442 , ab1414 and ab561 , but the gene cluster associated with ab1692 ks sequence was not complete in the ab916 , therefore the additional overlapping clone was recovered using the same method described above . sequencing of the additional overlapping clone ab170 suggested the complete recovery of the ab1692 ks sequence - associated pp gene cluster over three overlapping edna clones , ab1692 , ab916 and ab170 . the three overlapping edna cosmid clones ( ab1692 , ab916 and ab170 ; ab1442 , ab1414 and ab561 ) that are predicted to contain the ab1692 and ab1414 amplicons - associated pentangular polyphenol gene clusters were assembled into bac clones in yeast using tar . the ab1692 and ab1414 pentangular polyphenol pathway - specific tar capture vectors were constructed using infusion cloning methodology ( clontech ) . five hundred bp upstream ( ups ) and downstream ( dws ) homology arms were amplified from the ab1692 and ab170 cosmids , and the ab1442 and ab561 cosmids , respectively , using the primers listed in the supplementary protocol 1 . gel - purified amplicons ( qiagen ) and bmti / sphi linearized ptara vector were added into a standard infusion cloning reaction ( clontech ) to yield the pathway - specific capture vectors . for tar assembly , 200 ng of each drai - cut cosmid ( ab1692 , ab916 and ab170 ; ab1442 , ab1414 and ab561 ) were mixed with 100 ng of the hpai - digested pathway - specific capture vector and then transformed into 200 l of saccharomyces cerevisiae cry12 spheroplasts prepared according to published protocols . transformed spheroplasts were mixed with synthetic complete ( sc ) top agar ( 1 m sorbitol , 1.92 g / l synthetic complete uracil dropout supplement , 6.7 g / l yeast nitrogen base , 2 % glucose and 2.5 % agar ) and overlaid onto sc dropout plates without uracil . plates were incubated at 30 c for approximately 72 h , until colonies appeared . twelve yeast colonies were picked and cultured overnight in sc dropout liquid media without uracil . dna was isolated using a zymolyase lysis protocol ( zymo research ) and screened by pcr with primers designed to recognize sequences from each cosmid . a bacterial artificial chromosome ( bac ) clones that amplified with all the primer sets were electroporated into e. coli epi300 ( epicenter ) . dna isolated from the resulting e. coli epi300 was pgm - sequenced to confirm the correct reassembly of the three overlapping cosmids into approximately 90 kb insert bac clones ( bac - 1692 / 916/170 and bac - ab1442 / 1414/561 ) . bac - ab1692 / 916/170 and bac - ab1442 / 1414/561 were transformed into e. coli s17 .1 and transferred into s. albus via intergenic conjugation to generate the strains s. albus bac - ab1692 / 916/170 and s. albus bac - ab1442 / 1414/561 ( apramycin selection ) . calixanthomycin a ( 1 ) , and arenimycins c ( 2 ) and d ( 3 ) were isolated from 1l cultures ( 200 rpm at 30 c ) of s. albus bac - ab1692 / 916/170 and s. albus bac - ab1442 / 1414/561 , respectively , in 125 ml baffled flasks , each containing 50 ml of r5a media . the cultures were harvested after 9 days , extracted with ethyl acetate [ 1:3 ( v : v ) , ethyl acetate to the culture ] and dried in vacuo . calixanthomycin a ( 1 ) , and arenimycins c ( 2 ) and d ( 3 ) were isolated from the resulting ethyl acetate extracts using two rounds of reversed - phase hplc ( c18 column , 10 mm 250 mm , 3.5 ml / min ) . the first round of hplc ( isocratic , 60 % acetonitrile for 1 ; 40 % acetonitrile for 2 and 3 ) yielded crude samples , from which 13 were purified . the second rounds of hplc used 60 % aqueous methanol for calixanthomycin a ( 1 , 6.0 mg / l ) , and 70 and 60 % aqueous methanol with 0.1 % trifluoroacetic acid for arenimycins c ( 2 , 4.6 mg / l ) and d ( 3 , 2.5 mg / l ) , respectively . yellow brownish powder ; d 68 ; uv ( meoh ) max 226 , 295 , 329 nm ; ir ( neat ) max 3393 , 2927 , 2736 , 1679 , 1604 , 1557 cm ; h and c nmr , cosy , and hmbc data , see table s1 ; hresims m / z 695.2327 [ m + h ] ( calcd for c36h39o14 , 695.2340 ) . dark reddish powder ; d 77 ; uv ( meoh ) max 216 , 256 , 421 , 477 nm ; ir ( neat ) max 3384 , 3070 , 2929 , 2856 , 1682 , 1620 , 1511 cm ; h and c nmr , cosy , and hmbc data , see table s2 ; hresims m / z 812.2770 [ m + h ] ( calcd for c40h46 no17 , 812.2766 ) . dark reddish powder ; d 133 ; uv ( meoh ) max 215 , 254 , 416 , 474 nm ; ir ( neat ) max 3392 , 3072 , 3050 , 2931 , 2858 , 2738 , 1686 , 1641 , 1619 cm ; h and c nmr data , see table s2 ; hresims m / z 654.1826 [ m + h ] ( calcd for c32h32no14 , 654.1823 ) . minimal inhibitory concentrations ( mic ) for calixanthomycin a ( 1 ) , and arenimycins c ( 2 ) and d ( 3 ) against staphylococcus aureus usa - 300 ( mrsa ) , bacillus subtilis rm125 , enterococcus faecalis ( vre ) and escherichia coli drc39 were determined by liquid dilution methods . each bacterial strain was grown overnight in either brain heart infusion ( mrsa and vre ) or lb ( b. subtilis rm125 and e. coli drc39 ) liquid media . overnight cultures were diluted 1000-fold and transferred to 96 - well microtiter plates ( 75 l / well ) . compounds were dissolved in dmso , added to the media in the first well of row to give a concentration of 50 g / ml and serially diluted 2-fold / well across the plate . these solutions ( 75 l ) were then added to the corresponding well in an assay plate and incubated at 30 c overnight without shaking . bacterial growth was visually inspected and the last well with no bacterial growth was reported as the mic . the antiproliferative activity of calixanthomycin a ( 1 ) , and arenimycins c ( 2 ) and d ( 3 ) was evaluated in duplicate using the colon carcinoma cell line hct - 116 ( atcc ; ccl - 247 ) . hct - 116 cells were grown in mccoy s 5a modified medium ( gibco ) supplemented with 10 % ( v / v ) fbs . trypsinized cells were seeded into 96 - well plates ( 1000 cells / well ) and incubated overnight at 37 c in the presence of 5 % co2 . compounds 13 ( in dmso ) were sequentially diluted in culture media ( 2 or 3-fold dilutions starting at 50 g / ml ) across a 96 - well plate and 100 l was transferred to the appropriate well in an assay plate . the plates were incubated at 37 c for 3 days and then evaluated for viability using a crystal violet - based colorimetric assay . cell viability was recorded based on the a590 of stain present in each well relative to no drug dmso control wells .\noutput:\n" }, { "from": "agent", "value": "sequence - guided mining of metagenomic libraries provides a means of recovering specific natural product gene clusters of interest from the environment . in this study , we use ketosynthase gene ( ks ) pcr amplicon sequences ( sequence tags ) to explore the structural and biosynthetic diversities of pentangular polyphenols ( pp ) . in phylogenetic analyses , edna - derived sequence tags often fall between closely related clades that are associated with gene clusters known to encode distinct chemotypes . we show that these common intermediate sequence tags are useful for guiding the discovery of not only novel bioactive metabolites but also collections of closely related gene clusters that can provide new insights into the evolution of natural product structural diversity . gene clusters corresponding to two edna - derived ks sequence tags that reside between well - defined ks clades associated with the biosynthesis of ( c24 ) - pradimicin and ( c26 ) - xantholipin type metabolites were recovered from archived soil edna libraries . heterologous expression of these gene clusters in streptomyces albus led to the isolation of three new pps ( compounds 13 ) . calixanthomycin a ( 1 ) shows potent antiproliferative activity against hct - 116 cells , whereas arenimycins c ( 2 ) and d ( 3 ) display potent antibacterial activity . by comparing genotypes and chemotypes across all known pp gene clusters , we define four pp subfamilies , and also observe that the horizontal transfer of pp tailoring genes has likely been restricted to gene clusters that encode closely related chemical structures , suggesting that only a fraction of the natural product - like chemical space that can theoretically be encoded by these secondary metabolite tailoring genes has likely been sampled naturally ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: cardiovascular disease is responsible for a large and increasing proportion of death and disability worldwide . there is evidence that cardiovascular mortality decrease observed in industrialised countries in the second half of the 20th century has occurred concomitantly with an improved control of hypertension ( 13 ) . however , 70 % of hypertensive patients have their blood pressure ( bp ) uncontrolled what may result a significant increase in cardiovascular risk ( 4,5 ) . even small elevations above optimal bp values increase the likelihood of developing hypertension and incurring target organ damage ( 6,7 ) . therefore , bp lowering is critical to help reduce the risk of cardiovascular disease and prevent major coronary events . nevertheless , although the control of bp is important , clinical practice guidelines agree that the aim of treatment in hypertensive patients should be not only to control bp , but also protect the target organs affected by hypertension and reduce associated morbidity and mortality ( 8,9 ) . the latest european guidelinesalso emphasises that the global assessment of cardiovascular risk in the hypertensive patient includes the identification of lesions caused by hypertension in the target organs . according to the clinical guidelines , the cardiovascular risk is defined by the presence of cardiovascular risk factors , target organ damage and associated clinical conditions ( 9 ) . calcium channel blockers ( ccb ) clearly have a place within the therapeutic tools aimed to reduce cardiovascular risk . while earlier research were focused on increasing potency and selectivity , the most recent developments have brought dihydropyridinic ccb with a particularly slow onset and long duration of action which may result a better tolerability ( 10 ) . among them , lercanidipine is a third - generation vasoselective dihydropyridine ( dhp ) acting through the blockade of the l - type calcium channels in cell membranes ( 1113 ) . this drug has a high lipophilicity , which enables a slower and smooth onset and longer duration of action than other dhp ( 14 ) . in some studies , lercanidipine appears to be a well - tolerated drug with a low adverse events rate because of its long - lasting and vascular - selective calcium entry - blocking activity , while sympathetic activation and reflex tachycardia is not induced ( 11,12 ) . the overall side effects rate is lower than observed with other dhp ( 15,16 ) . the efficacy of lercanidipine has been evaluated in non - comparative ( 17,18 ) and in comparative studies with other ccb and different antihypertensive drugs ( 1923 ) showing a comparable effect with all of the cases . the effect of lercanidipine has also been successfully evaluated in severe or resistant hypertension , elderly subjects and diabetics ( 23,24 ) . from a clinical point of view , it should be of interest to know whether a bp - lowering drug is effective and well tolerated along the different cardiovascular risk profiles . thus , the laura study was aimed to assess whether the effectiveness and tolerability of lercanidipine may be different according to the cardiovascular risk level in a wide sample of a hypertensive population . the laura study ( estudio del comportamiento de lercanidipino segun niveles de riesgo cardiovascular ) was a multicentre , prospective , observational , non - comparative , open - label study , designed to determine the effectiveness and safety of antihypertensive treatment with lercanidipine in patients drawn from the general population , with different cardiovascular risk profiles . the purpose of the study was to evaluate the drug in conditions of daily clinical practice , to determine whether its effect was independent of the cardiovascular risk level in a hypertensive population . a total of 500 family physicians were invited to recruit patients with mild - to - moderate essential hypertension ( eight patients each ) who according to their criteria were candidates to be treated with lercanidipine . eligible patients were male and female aged 18 years with newly diagnosed hypertension , defined as systolic blood pressure ( sbp ) 140 ( 130 in diabetics ) and 180 mmhg , and diastolic blood pressure ( dbp ) 90 ( 80 in diabetics ) and 110 mmhg , or previously treated hypertensives in whom the physician had decided to switch the current therapy as a result of side effects or lack of control were eligible . the exclusion criteria were severe hypertension ( sbp 180 mmhg or dbp 110 mmhg ) , known hypersensitivity or history of severe adverse events to any dhp , evidence of unstable angina or decompensated congestive heart failure , myocardial infarction within the previous 30 days , left ventricular outflow obstruction , liver dysfunction ( serum aminotransferases 2-fold increase or serum bilirubin 1.5-fold increase above upper limit of normal ) , and renal insufficiency [ serum creatinine concentration 1.5 mg / dl ( 133 mol / l ) in men and 1.4 mg / dl ( 124 mol / l ) in women ] , as well as any contraindication for prescribing lercanidipine as stated in the technical form of the product . pregnant women , nursing mothers , or women of childbearing potential not using adequate methods of contraception were also excluded . blood pressure readings were taken with a mercury sphygmomanometer with the patient in a seated position and the back supported , and after resting 5 min . the patients were advised to avoid smoking or drinking coffee within 30 min before bp assessment . the visit bp was the average of two separate measurements taken by the examining physician ( a third measure was obtained when there was a difference 5 mmhg between the two readings ) . adequate bp control was defined as sbp 140 mmhg and dbp 90 mmhg ( 130 and 80 mmhg for diabetics ) ( 9 ) . all patients underwent a complete physical examination and investigation of other cardiovascular risk factors . with the available information about bp levels , associated cardiovascular risk factors , target organ damage and associated clinical conditions the patients were classified according to the esh / esc guidelines 2003 in the different added cardiovascular risk groups : low , medium , high or very high . according to the esh / esc guidelines 2003 ( 9 ) , the following data were recorded : ( a ) cardiovascular risk factors : levels of sbp and dbp , age ( men 55 years , women 65 years ) , smoking , dyslipidaemia [ total cholesterol 250 mg / dl ( 6.5 mmol / l ) or ldl - cholesterol 155 mg / dl ( 4.0 mmol / l ) or hdl - cholesterol 40 mg / dl ( 1.0 mmol / l ) in men and 48 mg / dl ( 1.2 mmol / l ) in women ] , family history of premature cardiovascular disease ( at age 55 years in men and 65 years in women ) , abdominal obesity ( abdominal circumference 102 cm in men and 88 cm in women ) and c - reactive protein 1 mg / dl ; ( b ) target organ damage : left ventricular hypertertrophy ( electrocardiogram : sokolowlyons 38 mm ; cornell 2440 mm ms ; echocardiogram : left ventricular mass index 125 in men and 110 g / m in women ) , ultrasound evidence of arterial wall thickening ( carotid imt 0.9 mm ) or atherosclerotic plaque , slight increase in serum creatinine [ 1.31.5 mg / dl ( 115133 mol / l ) in men and 1.21.4 mg / dl ( 107124mol / l ) in women ] , microalbuminuria [ 30300 mg / 24 h ; albumin creatinine ratio 22 mg / g ( 2.5 mg / mmol ) in men and 31 mg / g ( 3.5 mg / mmol ) in women ] ; ( c ) diabetes mellitus ( fasting plasma glucose 126 mg / dl ( 7.0 mmol / l ) or postprandial plasma glucose 198 mg / dl ( 11.0 mmol / l ) ] ; ( d ) associated clinical conditions : cerebrovascular disease ( ischaemic stroke , cerebral haemorrhage or transient ischaemic attack ) , heart disease ( myocardial infarction , angina , coronary revascularisation or congestive heart failure ) , renal disease [ diabetic nephropaty , serum creatinine 1.5 mg / dl ( 133 mol / l ) in men and 1.4 mg / dl ( 124 mol / l ) in women or proteinuria ( 300 mg / 24 h ) ] , peripheral vascular disease , advanced retinopathy ( haemorrhages or exudates , papilloedema ) . the daily dose was one tablet of lercanidipine 10 mg , taken in the morning , immediately after wake up . in previously treated hypertensive patients , a washout period of 710 dayspatients were followed at 4 , 12 , and 24 weeks after beginning of treatment with lercanidipine . at each visit , bp and heart rate were measured , treatment compliance was checked , and patients were interviewed for the occurrence of adverse events . lercanidipine could be uptitrated to 20 mg / day if bp control was not attained at any visit . if bp was still uncontrolled after 20 mg other antihypertensive medication could be added . the recommendation of a reduced calorie diet and the prescription of hypocholesterolemic and hypoglycemic agents was left at the discretion of the physician . all adverse events were designated by the investigator as either drug or not drug - related . at the study end , effectiveness and tolerability of treatment with lercanidipineflow chart of the study protocol sbp , systolic blood pressure ; dbp , diastolic blood pressure . categorical data are expressed as numbers and percentages and continuous data as mean and standard deviation ( sd ) . the student 's t - test for paired and unpaired data was used to assess treatment effects on continuous variables . categorical variables were analysed with the chi - square ( ) test . to study differences in the quantitative variables over time as well as progression , or between group differences , the analysis of covariance ( ancova ) was used to assess the effect of lercanidipine in subsets of the study population divided according to low , medium , high and very high cardiovascular risk groups . the spss statistical software package for windows ( version 9.1 ) was used to analyse the data . categorical data are expressed as numbers and percentages and continuous data as mean and standard deviation ( sd ) . the student 's t - test for paired and unpaired data was used to assess treatment effects on continuous variables . categorical variables were analysed with the chi - square ( ) test . to study differences in the quantitative variables over time as well as progression , or between group differences , the analysis of covariance ( ancova ) was used to assess the effect of lercanidipine in subsets of the study population divided according to low , medium , high and very high cardiovascular risk groups . the spss statistical software package for windows ( version 9.1 ) was used to analyse the data . a total of 3175 patients with a mean age of 6310 years were included in the study . remarkably , grade i hypertension was diagnosed in 43 % of patients and grade ii in 57 % and baseline bp levels were sbp 159.511.7 mmhg and dbp 95.27.4 mmhg . with regard to the cardiovascular risk factors , the most frequent , after hypertension , was hypercholesterolemia ( 32 % of patients ) . the most prevalent target organ damage was left ventricular hypertrophy ( 18 % of patients ) . finally , the most prevalent associated clinical conditions was ischaemic heart disease ( 10 % of patients ) . the patients were stratified as follows : 237 patients ( 7.5 % ) at low cardiovascular risk , 1396 ( 44 % ) medium , 722 ( 22.7 % ) high , and 820 ( 25.8 % ) at very high risk . characteristics of the study population at baseline m , male ; f , female ; bmi , body mass index ; sbp , systolic blood pressure ; dpb , diastolic blood pressure . table 3 shows the previous drugs and reasons for the use of lercanidipine . treatment with lercanidipine was indicated by the investigators because of poorly controlled hypertension with previous agents in 46 % of patients , as first therapy in nave hypertensives in 38 % , and resulting from adverse events related to antihypertensive drugs in 13 % . previous antihypertensive medication and reasons for the use of lercanidipine changes in sbp and dbp during the study period in the overall population as well as in the different cardiovascular risk groups are shown in table 4 . at baseline , after 6 months of treatment , mean sbp was 136.09.7 and dbp 79.76.8 mmhg . the decrease in sbp and dbp at each follow - up visit compared with baseline was statistically significant both in the intergroup and intragroup comparisons ( p 0.001 , one - way anova ) . mean decreases in sbp and dbp were 18.53.3 and 13.82.3 mmhg in the low risk group , 233.9 and 15.22.7 mmhg in the medium risk group , 24.44.0 and 16.13.1 mmhg in the high risk group , and 27.44.2 and 17.43.2 mmhg in the very high risk group . decreases in sbp and dbp in each cardiovascular risk group at the follow - up compared with baseline are shown in figures 1 and 2 . bp was controlled in 55 % of patients treated with 10 mg / day of lercanidipine , while systolic bp was controlled in 60.7 % of patients , and diastolic bp in 71.0 % . in consequence , after having uptitrated to 20 mg / day of lercanidipine , bp was controlled in 82 % of patients , while systolic bp was controlled in 85.4 % of patients , and diastolic bp in 89.1 % . . changes of sbp and dbp during the study period sd , standard deviation ; sbp , systolic blood pressure ; dbp , diastolic blood pressure . mean 1 sd decreases in systolic blood pressure ( sbp ) in the four risk groups for cardiovascular disease during the study period when compared with baseline mean 1 sd decreases in diastolic blood pressure ( dbp ) in the four risk groups for cardiovascular disease during the study period when compared with baseline ninety - four per cent of patients completed the 6 - month treatment period with lercanidipine . the incidence of adverse events is shown in table 5 . as much as 11.5 % of patients presented adverse events , being the most frequent the oedema ( 5.1 % , more frequent with the 20 mg dose ) . no significant differences in the percent of patients suffering from adverse events according to stratification in the different risk groups were observed . as much as 91 % of physicians and 84 % of patients considered that tolerability of antihypertensive treatment with lercanidipine wasthe present results obtained in a cohort of patients with mild - to - moderate essential hypertension recruited in actual conditions of daily clinical practice confirm the effectiveness and favourable tolerability profile of lercanidipine . these findings are consistent with data previously reported in randomised trials ( 10,24 ) and in surveillance studies such as the elypse study ( 17 ) . previous studies have shown that the majority of hypertensive patients daily attended in primary care setting in spain belong to the medium or high coronary risk groups ( 25,26 ) . this point is relevant , because these patients are normally polymedicated and they have an increased risk of presenting side effects . the efficacy of an antihypertensive drugs does not only depend on bp control , but in its tolerability too . the presence of adverse events may be one of the main causes for the poor patient compliance of the prescribed therapy . thus , the use of well tolerated drugs may result in a better patient adherence and probably in a better bp control ( 2729 ) . on the other hand , in usual care the different antihypertensive drugsvery rarely achieve bp control in 3040 % when used in monotherapy , and these figures are much lower when considering bp control in high coronary risk groups ( 25,26 ) . our results indicates that lercanidipine has a good antihypertensive effectiveness among the different degrees of cardiovascular risk . in fact , lercanidipine showed to be more effective in patients with higher cardiovascular risk levels , most likely to be in relation to higher sbp and dbp values at baseline . mean decreases of sbp and dpb were 18.5 / 13.8 mmhg in the low risk group compared with 27.4 / 17.4 mmhg in the very high risk group . moreover , the majority of patients were controlled only with lercanidipine ( 18 % of patients needed to add another antihypertensive drug to achieve a good bp control ) including high risk group . in this large study , the efficacy of this drug has therefore proven to be similar to the previously published papers ( 1723 ) . on the other hand , although the bp lowering effect of lercanidipine was greater in patients with higher cardiovascular risk levels , tolerability of the drug was independent of the cardiovascular risk profile . therefore , lercanidipine was found to be an effective and well - tolerated antihypertensive drug for any hypertensive patient in daily clinical practice , regardless the cardiovascular risk profile . this represents an added value at the time of prescribing this antihypertensive medication in all kind of hypertensive patients , from low to high coronary risk . this good tolerability profile implies a low withdrawal rate , indicating a satisfactory patient compliance . lercanidipine appears to be associated with a better tolerability profile and less risk of vasodilation - related adverse reactions compared with other dhps in the clinical practice setting ( 15,16,1921 ) . however , the percentage of patients with oedema was superior in our patients compared with others treated with lercanidipine , probably because our study was performed in the summer time . as it is known , the presence of oedema is more frequent during this season because of a bigger trend to the vasodilatation . in conclusion , despite the limitations that this kind of observational intervention studies which are open and non - comparative , the laura study demonstrates that lercanidipine is an a effective and well - tolerated antihypertensive agent in daily clinical practice , regardless the cardiovascular risk profile . these results confirm the previous findings from randomised controlled trials , and support that this drug is a fair option to be considered in the antihypertensive armamentarium . dr a. navarro is the medical director of recodarti spain , the pharmaceutical industry proprietary of the study drug lercanidipine .\noutput:\n" }, { "from": "agent", "value": "to determine whether the antihypertensive effectiveness of lercanidipine was independent of the different cardiovascular risk levels.patients with treated or untreated mild - to - moderate essential hypertension were included in a multicentre , prospective , non - comparative , open - label study . patients received lercanidipine ( 10 mg / day , uptitrated to 20 mg / day ) during 6 months.a total of 3175 patients , age 63 10 years , 51 % women , were included . the cardiovascular risk was low in 237 patients , medium in 1396 , high in 722 , and very high in 820 . at baseline , blood pressure ( bp ) was 159.5 11.7 / 95.2 7.4 mmhg . bp was progressively higher according to increase in cardiovascular risk . after 6 months of treatment , bp was 136.0 9.7 / 79.7 6.8 mmhg . the decrease in systolic bp and diastolic bp at each follow - up visit compared with baseline was statistically significant both in the intergroup and intragroup comparisons ( p < 0.001 ) . mean decreases of systolic blood pressure ( sbp ) and diastolic blood pressure ( dbp ) were 18.5 / 13.8 mmhg in the low risk group , 23/15 .2 mmhg in the medium risk group , 24.4 / 16.1 mmhg in the high risk group , and 27.4 / 17.4 mmhg in the very high risk group . most frequent side effects were oedema ( 5.1 % ) , headache ( 3.3 % ) , flushes ( 2.5 % ) , and asthenia ( 1 % ) . only 1.7 % of patients discontinued antihypertensive medication because of adverse events . tolerability of lercanidipine was independent of the cardiovascular risk group.lercanidipine was effective and well - tolerated in patients with mild - to - moderate hypertension in the daily practice . the effectiveness and safety of the drug were independent of the degree of cardiovascular risk ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: many species of helminths are parasitic multicellular organisms of medical and economic importance as they infect humans and animals and sometimes provoke fatal diseases such as schistosomiasis . they can also be responsible for economic losses due to decreased milk or meat production and the cost of anthelminthic treatments of parasitized individuals . . they can be classified into 3 taxonomic groups , that is , nematodes , trematodes , and cestodes , often with very different parasitic cycles . for example , ( i ) they may be transmitted orally ( strongyles , fasciola sp . , etc . ) by transcutaneous route ( ankylostoma sp . , strongylodes sp . , schistosoma sp . , etc . ) by an arthropod vector ( onchocerca volvulus , dirofilaria immitis , etc . ) ; ( ii ) their definitive and intermediate hosts range from mammals , birds , reptiles to fish , molluscs and arthropods , and so forth ; ( iii ) they may be localized in organ lumen or in tissues such as gut , liver ( parenchyma and bile ducts ) , lung , lymphatic vessels , and so forth ; ( iv ) the successive developmental stages of parasitic species may infect different tissues and cells of different organs . despite this great complexity , helminths usually cause asymptomatic or subclinical chronic infection , although some parasitized individuals can suffer from severe disease which may be fatal . indeed , worms tend to be aggregated in their distribution , with a large number of hosts harboring few parasites and few heavily infected hosts . this remarkable equilibrium between most hosts and parasites is the product of long - term coevolution of the two partners and particularly of the immune defence of the host and the immune evasion of the parasite . the immune responses of the hosts to helminth infection are generally characterized by a skewed th2 - like response . these immunomodulatory abilities enable the worm to persist in the host and can lead to interactions with inflammatory and immune mechanisms involved in other infections or to vaccines or in allergic and autoimmune diseases . the focus in this review is on pathogenic helminths of veterinary importance , especially in ruminants medicine , and includes fasciola spp . and gastrointestinal nematodes . helminth infections are typically associated with hypereosinophilia , considerable ige production , mucous mastocytosis , and goblet cells hyperplasia . these immune parameters are involved in different effector mechanisms highly depending on where the helminth is localized . these parasites are mainly larval stages , for example , of trematodes ( schistosoma spp . , fasciola spp . ) or nematodes , which migrate through tissue . antibody dependent cellular cytotoxicity ( adcc ) is dependent on eosinophils , neutrophils , macrophages , or platelets as effector cells and ige , igg , or iga as antibodies . the parasitic structures covered by antibodies are destroyed by cells carrying receptors to the fc fragment ( rfc ) ( figure 1 ) . when these cells are activated by fixation of the antibodies to the rfc , they release products that are toxic to the worm ( major basic protein , eosinophil cationic protein , eosinophil - derived neurotoxin , reactive nitrogen intermediates , ) . adccs are also able to immobilize nematode larval stages as they migrate through the gut mucosa . a granuloma can occur around the parasite in the tissue which stops the worm migration and development . the granuloma is composed of eosinophils , macrophages , and lymphocytes with an increasingly fibrotic extracellular matrix , which surrounds and segregates the eggs from the hepatic tissue . in the long term , fibrosis may develop as the eggs die and the granuloma is resolved . finally , nitric oxide ( no ) , toxic to the worm , is released by the macrophages classically activated by ifn and tnf ( figure 1 ) . , fasciola sp . ) during acute infection , before egg production in schistosoma mansoni . tissue - dwelling parasites have developed several mechanisms to escape to the effector response of the host ( figure 2 ) . escapes from the immune responses by different means as follows : fasciola gigantica produces superoxide dismutase which neutralizes superoxide radicals toxic for juveniles . f. hepatica releases cathepsin l - protease which cleaves ige and igg involved in the adcc . while eosinophils do not express fc receptor , igm deposition on fluke tegument could inhibit eosinophil adhesion . igg2 produced during fasciolosis in susceptible sheep has been also suspected to be a blocking immunoglobulin of the adcc . excretory - secretory products of f. hepatica ( espfh ) can depress the sheep and rat lymphocytes stimulation and induce eosinophil apoptosis . milbourne and howell ( 1990 , 1993 ) have shown that there is anil5 - like substance in the excretory - secretory products ( esps ) probably responsible in part of the local and systemic eosinophilia observed during fasciolosis . cathepsin l - proteases induce a decrease of lymphoproliferation in sheep and of the cd4 expression on human and ovine t cells . gst from f. hepatica induces a significant inhibition of nitrite production by rat peritoneal macrophages . intestinal anaphylaxis , with ige - induced mast cells degranulation , is responsible for changes in the intestine physiology as well as architecture and chemistry of the gut epithelium , including stimulation of fluid , electrolyte and mucus secretion , smooth muscle contractility , increased vascular and epithelial permeability , and recruitment of immune cells such as eosinophil or mast cells ( figure 3 ) . this can lead to rapid elimination of the gastrointestinal larvae , before they reach their tissue niche , and to expulsion of the adult . furthermore , iga on the surface of the gut mucosa helps to neutralize the metabolic enzymes released by digestive strongyles and interfere with the worm 's ability to feed . as for tissue - dwelling parasites , parasites localized in the lumen of ducts are able to produce immunomodulatory substances to escape to the host immune responses . for example , necator americanus secretes a metalloprotease which cleaves eotaxin , a chemotactic factor for eosinophils . gastrointestinal nematodes produce also superoxide dismutase and glutathione s - transferase which neutralize toxic oxide radicals . a cystatin produced by h. contortus and n. brasiliensis modulates the antigen presentation to t cells by inhibiting cysteine proteases of antigen presenting cells , involved in the processing of the antigen . all these mechanisms , except the classically activated macrophages , are regulated by th2 - like cytokines and immunomodulatory cell types ( figure 1 ) . interleukin - 4 is involved in the ige isotype - switched b - cell responses , il - 5 is involved in the production of eosinophils , and il - 13 has similar functions to il - 4 and is involved mainly in the effector phase of inflammation and the development of fibrosis . t regulatory cells produce the suppressive cytokines il - 10 and tgf - which have antiinflammatory effects and could be involved in the skewed th2 - like responses . immune deviation may also be promoted by the development of a th2 - driving dendritic cell population induced by excretory - secretory antigens from n. brasiliensis or soluble egg antigen from schistosome . finally , il - 4 and il - 13 are able to alternatively activate macrophages ( aamps ) which have strong antiinflammatory properties , enhance th2 cell differentiation , contribute to fibrosis , and repair at the site of injury . thus , an environment , with downregulated proinflammatory responsiveness , activated damage repair mechanisms , and a controlled development of th2 - like anti - parasite effector responses is created during infection with helminths . several proteins produced by helminths were involved in the regulation of cytokine production . schistosome soluble egg antigen contains molecules as alpha - 1 or omega - 1 that initiate a th2 - like response . es - 62 , a leucine aminopeptidase secreted by acanthocheilonema vitae , reduces cd4 + cell il - 4 and ifn production but promotes il - 10 production by peritoneal b1 cells . it also inhibits the antigen - presenting cells ability to produce il12p70 and drives th2 - like differentiation in vitro . helminths could also secrete cytokine homologues as macrophage migration inhibitory factor ( mif ) which induces , with il - 4 , the development of alternatively activated macrophage . despite the th2 - like response induced against helminths , these parasites are often able to persist in the host for a long time , resulting in chronic infection . however2 types of immunity evaluated from the partial elimination of settled parasites and from host resistance to reinfection have been described , namely , premune immunity and partial immunity . premunition or concomitant immunity has been defined by macdonald et al . as a statewherein the host is protected from further infection with a given species by ongoing persistent infection with the same organism . thus immune mechanisms existing concomitantly with parasites ( adults and encysted larval stages ) in animals infected by gastrointestinal nematodes prevent the establishment of new larvae . in contrast , the elimination of adult worms by the phenomenon of self - cure ( spontaneous expulsion of adults by massive larval invasion during a short period of exposure ) or by anthelminthic treatment results in the installation of new larvae until an equilibrium state is obtained . premune immunity can also be expressed as a reduction in adult worm size and in female worm fertility . in contrast , the primary immune response against fasciola hepatica in bovine limits the number of metacercariae which develops in adults and reduces the fertility of the females . however it is unable to prevent the establishment of new parasites , which is a great difference with the premune immunity . effector mechanisms regulated by th2 - like responses play a major role in immune protection to strongyles . comparison of the immune responses of different breeds of sheep to haemonchus contortus revealed a greater production of th2 - like cytokines ( il - 4 , il - 5 , il - 13 ) in resistant breeds . similarly , balb / c mice , which develop a th2 - like response against trichuris muris , were soon able to eliminate the parasite , in contrast to akr mice which express th1 - like responses and chronic infection with the same parasite . the protective role of th1 - and th2 - like responses during fluke infection is less clear : th1 - like responses might act on larvae migrating through the liver parenchyma whereas the chronic phase with f. hepatica might be due to th2 - like responses against which the fluke has developed several escape mechanisms . as described during infection with schistosoma mansoni , th2 - like responses are predominant during infection by f. hepatica but early th1 - like responses seem to be involved in protection against this parasite . indeed , sheep susceptible to f. hepatica develop a mixed th1 - and th2 - like response with ifn and il - 10 production during the first 6 weeks of infection , whereas the immune response of sheep resistant to f. gigantica is th1 like , with production of ifn only . similarly , vaccinal trials with cathepsin l - protease from f. hepatica proved that protection induced by this antigen is mediated by a th1 - like response . although the host immune reaction against helminths may control the infection , it can also be responsible for tissue lesions and symptoms which are often the primary cause of disease during worm infection . immunopathologic phenomena have been thoroughly investigated in infections with schistosoma spp . as described above for f. hepatica infection , acute schistosomosisthe th2 - like responses , induced as a result of egg antigens secretion , downregulate the production and effector functions of th1 - like mediators . when th2 - like responses against the eggs were blocked experimentally , an exacerbated granuloma driven by th1 and th17 cells resulted in hepatic damage and death . whereas tissue fibrosis stimulated by th2 - like cytokine ( il - 13 ) promotes tissue healing , excessive fibrosis may become pathogenic with loss of hepatic functions and portal hypertension . it seems that during trematode infections th1 - like responses are more protective than th2 - like responses against which these parasites have developed many escape mechanisms . although th1 - like responses are closely associated with immunopathogenesis , th2 - like responses may also contribute to inflammatory damage . treg cells seem to regulate this detrimental immune response by suppressing the th1 - like response and by downregulating any excessive th2 - like response during granuloma formation . a recent study has shown that experimental downregulation of the th2 - like response to nippostrongylus brasiliensis suppresses resistance to gastrointestinal nematode infection , pulmonary granulomatous inflammation , and fibrosis . these clinical signs could result from smooth muscle contractility , increased mucus production , loss of specialized cells in the abomasal epitheliums induced by ige - mediated immediate hypersensitivity reactions , and degranulation of mast and goblet cells and of proinflammatory mediators . hence , protection against gastrointestinal nematodes and against tissue - dwelling trematodes is controlled by th2 - and th1 - like responses , respectively . the migration step in tissueis considered an immunoevasive strategy due to the predominant th2 - like response during helminth infection whereas protection in tissue is mediated by the th1 - like response . however , the immune mechanisms , particularly those regulated by th1 - like cytokines , are responsible for considerable immunopathological damage and for the clinical signs observed during a helminthic disease . even if the immune responses against most of helminths are orchestrated by th2 - like cytokines , the worms are still able to persist in the host for a long time . indeed , the immune response during the chronic phase of infection was recently reported to be a modified th2 - like response , that is , a th2 - like response associated with treg activity and the production of antiinflammatory cytokines such as il - 10 and tgf . the induction of immunomodulatory th2 / treg responses would allow the survival of both partners , by downregulating the host 's inflammatory response and the immunopathological lesions observed during helminth infection , and also the protective immune mechanisms directed against the parasite . some helminths are able to downregulate the th1 - like response because their high immunomodulator activity allows the induction of th2 / treg - type responses . similarly f. hepatica is also able to change the predictive value of the tuberculosis diagnosis test by modifying the immune response against mycobacterium bovis . helminths can affect the evolution of coinfection by making animals more resistant to pathogens in which protection is mediated by the th2 - like response and more susceptible to pathogens in which protection is mediated by the th1 - like response . for example , the expulsion of t. muris by mice is dependent on the th2 - like response . . demonstrated that mice susceptible to t. muris and coinfected with s. mansoni which induced the th2 - like response were able to eliminate t. muris by producing th2 - like cytokines . in contrast , mice infected with s. mansoni were more susceptible to toxoplama gondii ( protected by the th1 - like response ) by inducing high mortality and weak production of ifn and no , compared to mice solely infected with t. gondii . helminths were also able to inhibit the development of protective immunity regulated by th1 - like cytokines against plasmodium sp . . many analyses of helminth - plasmodium coinfections have provided controversial results as the parasite burden of plasmodium sp . is dependent on the helminth species used , the intensity and duration of worm infection , and the age of the individual under study . helminths influence not only host resistance to another pathogen but also the gravity of the resulting disease . helminth infections are able to decrease the production of these cytokines by secreting il - 10 and tgf and thereby diminish the risk of severe disease . the nematode heligmosomoides polygyrus promotes an immune response regulated by th2 - like cytokines , alternative activated macrophages , and regulatory t cells , and hence , prevents the inflammatory reaction controlled by th1 cytokines and severe immunopathological lesions observed during schistosomosis . in contrast , h. polygyrus promotes intestinal lesions due to bacteria such as citrobacter rodentium by alternative activation of macrophages . for example , miller et al . recently showed that the production of th1 - like cytokines and classic activation of macrophages were little altered when f. hepatica infection preceded or succeeded t. gondii infections , whereas the production of f. hepatica - specific th2 - like cytokines and recruitment of aamp were suppressed by t. gondii infection . similarly , neutrophil - activating protein from helicobacter pylori downmodulated the th2 - like response to trichinella spiralis infection . the effects of helminths on infections with other pathogens are complex and dependent on many factors such as the helminth species , coinfecting pathogen , protective and pathological immune mechanisms , and also the host and the individual . several studies have shown that helminths can influence vaccine efficacy by modulating host immune response , in particular when th1 - like and cellular - dependent responses are required . onchocerca volvulus infections decrease the efficacy of vaccine against tuberculosis or tetanus , and ascaris suum alters the efficacy of vaccine against mycoplasma hyopneumoniae . in mice , h. polygyrus was able to downregulate the strong immunity against plasmodium chabaudi induced by blood stage antigens . effects of helminth infections on vaccine efficacy must be taken into account when using vaccines and also when developing new vaccines , in particular by choosing adapted adjuvants which are able to counterbalance the immunomodulatory activities of the helminth . for several years , epidemiologic observations have shown that the prevalence of helminth infection is decreasing in westernized countries whereas the prevalence of diseases due to immune or inflammatory disorders such as allergic or autoimmune diseases is increasing . humans infected with worms rarely develop allergic reactions and an allergic reaction against ovalbumin was inhibited in mice infected with h. polygyrus or schistosoma sp . . similarly , immunization with toxascaris leonina - derived proteins was able to inhibit allergy - specific th2 - like responses to ovalbumin . these results are paradoxical because allergy is linked to mastocyte degranulation by ige ; the production of which is stimulated by helminths . in fact , worms induce the production of large quantities of antiinflammatory cytokines ( il - 10 , tgf ) by the regulatory t cells which then inhibit allergic inflammation . in the same way , helminths can protect the host against autoimmune disease or at least decrease the gravity of symptoms induced by autoimmune inflammation . for example , s. mansoni infection inhibits the development of type 1 diabetes in nod mice or of experimental autoimmune encephalomyelitis in mice . helminth - specific treg cells and their antiinflammatory cytokines ( il - 10 , tgf ) seem to be largely implicated in the inflammatory disorders associated with allergic diseases . several studies are currently underway to investigate the possibility of treating allergic inflammatory diseases with immunomodulatory molecules from helminths , with special focus on the molecules involved and the ways in which helminths manipulate the host response , particularly how they activate and induce the expansion of treg cells . trichuris suis has been tested recently to treat patients with inflammatory bowel disease and crohn 's disease with success . an excretory - secretory protein of acanthocheilonema vitae , es62 , has been well studied for its antiinflammatory property . es62significantly decreases the severity of collagen - induced arthritis in mice and of cutaneous hypersensitivity dependant on mast cells . however , these immunomodulatory molecules could have side effects by increasing the risk of infections . furthermore , they could be responsible for allergic reactions because they could be allergens or they could cross - react with allergens derived from pollen or another source . in conclusionthis has led to a strict adaptation which enables them to settle and persist in the host . helminths are strong immunomodulators able to interfere with immune and inflammatory mechanisms induced by themselves and by coinfecting pathogens , inflammatory disorders , or vaccine . . effects of helminths on the host immune system are not properly known because data are partial or can not be generalized between species . nevertheless these effects need to be taken in account when controlling helminths and the diseases induced by worms . however , an individual could be infected by several pathogens and it will be necessary to evaluate the overall immune equilibrium resulting from the immune interaction between host and pathogens in different tissues and organs , which is still difficult , for instance .\noutput:\n" }, { "from": "agent", "value": "helminth parasites are of considerable medical and economic importance . studies of the immune response against helminths are of great interest in understanding interactions between the host immune system and parasites . effector immune mechanisms against tissue - dwelling helminths and helminths localized in the lumen of organs , and their regulation , are reviewed . helminth infections are characterized by an association of th2 - like and treg responses . worms are able to persist in the host and are mainly responsible for chronic infection despite a strong immune response developed by the parasitized host . two types of protection against the parasite , namely , premune and partial immunities , have been described . immune responses against helminths can also participate in pathogenesis . th2 / treg - like immunomodulation allows the survival of both host and parasite by controlling immunopathologic disorders and parasite persistence . consequences of the modified th2 - like responses on co - infection , vaccination , and inflammatory diseases are discussed ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: osteosarcoma ( os ) is one of the most common non - hematological primary bone tumors in children and young adults . although neoadjuvant chemotherapy and improved surgical technology have been the most important treatments to increase the survival rate , the existence of intrinsic or acquired chemoresistance has greatly impeded further improvement in survival rate of osteosarcoma patients with localized tumors and metastatic disease at presentation . earlier studies have shown that tumor chemoresistance is a complex , multistep process characterized by numerous abnormal genes , proteins , micrornas ( mirnas ) , and some related signalling pathways . micrornas are a class endogenous small non - coding rnas that regulate diverse target mrnas at the level of mrna degradation or translation in several diseases , including cancers . recently , mir - 184 has been reported to be a candidate tumor suppressor gene in breast cancer , glioma , renal cell carcinoma , and other carcinomas . recently , increased attention has been paid to the role of mirnas in chemoresistance , and their potential role in determining drug sensitivity or resistance has been confirmed . anomalous mirnas expression can influence chemoresistance by modulating gene expression of a number of different target genes , such as mirna - 133b , mir - 31 , mirna - 196a , and mir - 506 . however , few studies have focused on the involvement of mirna - 184 in the development of doxorubicin resistance in osteosarcoma patients . in this study , we demonstrated the function of mir - 184 in a doxorubicin therapy os cell line and found that doxorubicin induced time - dependent expression of mir - 184 in os cell lines u-2 os and mg - 63 . moreover , doxorubicin inhibited bcl2l1 expression , which was reversed by mir - 184 overexpression in os cells . in addition , mir - 184 agomir reduced doxorubicin - induced cell apoptosis , whereas mir - 184 antagomir enhanced apoptosis in the doxorubicin - resistant osteosarcoma cell line , suggesting that up - regulation of mir - 184 contributed to chemoresistance of the os cell line . u-2 os and mg - 63 were purchased from the cell bank of the institute of biochemistry and cell biology , china academy of sciences ( shanghai , china ) and cultured in dmem ( gibco , ca , usa ) supplemented with 10 % fbs ( gibco , ny , usa ) . for transfection , cells were cultured to 80 % confluence and transfected with 50 nm mir - 184 agomir or 100 nm antagomir ( ribobio company , guangzhou , china ) according to the manufacturer s protocol . total rna , including mirna , was extracted from the cell lines and tissue samples using trizol reagent ( invitrogen , usa ) . rna was synthesized into cdna using a reverse transcriptase kit ( takara , dalian , china ) . amplification of cdna was performed according to the manufacturer s protocol using sybrpremix ex taq ( takara , dalian , china ) . pcr was carried out in triplicate and analyzed using the abi 7500 fast realtime pcr system ( applied biosystems , life technologies , usa ) . the relative gene expression level was calculated by the comparative ct method 2 using u6 as an internal reference . the rt and pcr primers for mir - 184 and u6 were purchased from ribobio ( guangzhou , china ) . the wide - type ( wt ) or mutant ( mt ) 3utr of bcl2l1 was cloned into the renilla luciferase gene . a mutant 3utr of bcl2l1 was cloned by use of genechem ( shanghai genechem co. , ltd , shanghai , china ) . the u-2 os cells were cotransfected with the vectors carrying wt 3utr or mt 3utr and mir - 184 agomir or antagomir . cells were collected 48 h after transfection and analyzed using the dual - luciferase reporter assay system ( promega corporation , fitchburg , usa ) . protein quantification was performed according to the bradford method using the bio - rad protein assay kit ( bio - rad laboratories inc . the membranes were blocked overnight in 5 % skim milk in tris - buffered saline . for immunoblotting , the membranes were incubated at 4c overnight with the bcl2l1 antibody ( 1:500 ; proteintech group , chicago , usa ) or gapdh antibody ( 1:5000 ; beyotime biotechnology , haimen , china ) , followed by the incubation with the appropriate irdye 800cw - conjugated secondary antibody ( 1:5000 ; li - cor bioscience , usa ) . the infrared fluorescence image was obtained using the odyssey infrared imaging system ( li - cor bioscience , usa ) . after 48 h of transfection in 6 - well plates , cells were exposed to the freshly prepared medium containing different concentrations of 0.5 nm doxorubicin for 24 h. cells were then harvested and washed with ice - cold phosphate - buffered saline ( pbs ) and then subjected to annexin v apoptosis detection kit ( bd pharmingen , usa ) for staining , which was followed by flow cytometry analysis . statistical evaluation was performed using the student s t - test to differentiate the means of different groupsu - 2 os and mg - 63 were purchased from the cell bank of the institute of biochemistry and cell biology , china academy of sciences ( shanghai , china ) and cultured in dmem ( gibco , ca , usa ) supplemented with 10 % fbs ( gibco , ny , usa ) . for transfection , cells were cultured to 80 % confluence and transfected with 50 nm mir - 184 agomir or 100 nm antagomir ( ribobio company , guangzhou , china ) according to the manufacturer s protocol . total rna , including mirna , was extracted from the cell lines and tissue samples using trizol reagent ( invitrogen , usa ) . rna was synthesized into cdna using a reverse transcriptase kit ( takara , dalian , china ) . amplification of cdna was performed according to the manufacturer s protocol using sybrpremix ex taq ( takara , dalian , china ) . pcr was carried out in triplicate and analyzed using the abi 7500 fast realtime pcr system ( applied biosystems , life technologies , usa ) . the relative gene expression level was calculated by the comparative ct method 2 using u6 as an internal reference . the rt and pcr primers for mir - 184 and u6 were purchased from ribobio ( guangzhou , china ) . the wide - type ( wt ) or mutant ( mt ) 3utr of bcl2l1 was cloned into the renilla luciferase gene . a mutant 3utr of bcl2l1 was cloned by use of genechem ( shanghai genechem co. , ltd , shanghai , china ) . the u-2 os cells were cotransfected with the vectors carrying wt 3utr or mt 3utr and mir - 184 agomir or antagomir . cells were collected 48 h after transfection and analyzed using the dual - luciferase reporter assay system ( promega corporation , fitchburg , usa ) . protein quantification was performed according to the bradford method using the bio - rad protein assay kit ( bio - rad laboratories inc . the membranes were blocked overnight in 5 % skim milk in tris - buffered saline . for immunoblotting , the membranes were incubated at 4c overnight with the bcl2l1 antibody ( 1:500 ; proteintech group , chicago , usa ) or gapdh antibody ( 1:5000 ; beyotime biotechnology , haimen , china ) , followed by the incubation with the appropriate irdye 800cw - conjugated secondary antibody ( 1:5000 ; li - cor bioscience , usa ) . the infrared fluorescence image was obtained using the odyssey infrared imaging system ( li - cor bioscience , usa ) . after 48 h of transfection in 6 - well plates , cells were exposed to the freshly prepared medium containing different concentrations of 0.5 nm doxorubicin for 24 h. cells were then harvested and washed with ice - cold phosphate - buffered saline ( pbs ) and then subjected to annexin v apoptosis detection kit ( bd pharmingen , usa ) for staining , which was followed by flow cytometry analysis . statistical evaluation was performed using the student s t - test to differentiate the means of different groupsas shown in figure 1a , exposing mg - 63 to 0.5 nm or 1.0 nm doxorubicin significantly promoted time - dependent expression of mir - 184 . after being treated with 0.5 nm doxorubicin for 12 h , moreover , 1.0 nm doxorubicin - induced mir - 184 expression mimicked the effect of 0.5 nm doxorubicin . consistently , the effect of doxorubicin on expression of mir - 184 in u-2 os was further confirmed ( figure 1b ) . bcl2l1 was predicted to be target gene of mir - 184 by targetscan . to verify the prediction , we constructed the luciferase reporter vector containing wild - type or mutant 3utr of bcl2l1 . as shown in figure 2a , mir - 184 distinctly induced the luciferase activity of vector carrying wild - type 3utr of bcl2l1 compared to that carrying mutant 3utr of bcl2l1 . as shown in figure 2b , doxorubicin inhibited bcl2l1 expression in a time - dependent manner . to clarify the relation between bcl2l1 and mir - 184 , we further assayed the effect of mir184 on the expression of bcl2l1 in cells treated with or without doxorubicin . we found that up - regulated mir - 184 led to a marked increase in the level of bcl2l1 when u-2 os was treated with doxorubicin , whereas down - regulated mir - 184 suppressed bcl2l1 expression ( figure 2c ) . as shown in figure 3a , up - regulated mir - 184 significantly inhibited the cell apoptosis induced by doxorubicin , whereas down - regulated mir - 184 facilitated doxorubicin - induced cell apoptosis in u-2 os . as shown in figure 1a , exposing mg - 63 to 0.5 nm or 1.0 nm doxorubicin significantly promoted time - dependent expression of mir - 184 . after being treated with 0.5 nm doxorubicin for 12 h , moreover , 1.0 nm doxorubicin - induced mir - 184 expression mimicked the effect of 0.5 nm doxorubicin . consistently , the effect of doxorubicin on expression of mir - 184 in u-2 os was further confirmed ( figure 1b ) . bcl2l1 was predicted to be target gene of mir - 184 by targetscan . to verify the prediction , we constructed the luciferase reporter vector containing wild - type or mutant 3utr of bcl2l1 . as shown in figure 2a , mir - 184 distinctly induced the luciferase activity of vector carrying wild - type 3utr of bcl2l1 compared to that carrying mutant 3utr of bcl2l1 . as shown in figure 2b , doxorubicin inhibited bcl2l1 expression in a time - dependent manner . to clarify the relation between bcl2l1 and mir - 184 , we further assayed the effect of mir184 on the expression of bcl2l1 in cells treated with or without doxorubicin . we found that up - regulated mir - 184 led to a marked increase in the level of bcl2l1 when u-2 os was treated with doxorubicin , whereas down - regulated mir - 184 suppressed bcl2l1 expression ( figure 2c ) . as shown in figure 3a , up - regulated mir - 184 significantly inhibited the cell apoptosis induced by doxorubicin , whereas down - regulated mir - 184 facilitated doxorubicin - induced cell apoptosis in u-2 os . the combination of local radiotherapy / chemotherapy and surgery is currently the main anti - tumor therapy , but treatment fails in many patients , in part due to resistance to chemotherapeutic agents . accumulating studies have recently demonstrated that micrornas play a key role in cancer chemotherapeutic resistance . microrna - 184 functions as a tumor suppressor in carcinomas such as malignant gliomas and non - small cell lung cancers and all these antitumor functions are involved in cell proliferation and metastasis . however , little is known about the contribution of mir - 184 to chemoresistance of cancers . in this study , we demonstrated that doxorubicin induced time - dependent expression of mir - 184 in os cells , which suggests that mir - 184 is critical for chemoresistance in os . to determine the role of mir - 184 in chemoresistance of os , the target of mir - 184 was predicted by targetscan and luciferase reporter assaythe results showed that mir - 184 directly targeted the bcl -2-like protein 1 ( bcl2l1 ) in u-2 os cells . recently , changes in survival and apoptotic pathways such as akt , bcl - 2 , and nf - b pathways have been shown to have a major role in determining the effectiveness of chemotherapeutic agents . it is also reported that genomic alterations in bcl2l1 contribute to drug sensitivity in gastric cancer . in addition , the bcl2 family members are dual agents , regulating autophagy and apoptosis in drug resistance . we hypothesized that elevated levels of mir - 184 suppressed bcl2l1 expression , allowing os cells to withstand the toxicity of doxorubicin . we next analyzed the effects of mir - 184 agomir and antagomir on bcl2l1 expression in os cells treated with or without doxorubicin . our data show that doxorubicin reduced bcl2l1 expression , which was reversed by mir - 184 overexpression and was further decreased by mir - 184 inhibition . given these data , it was likely that mir - 184 promotes bcl2l1 expression , which might be related to the doxorubicin - induced up - regulation of mir - 184 . then , it was necessary to confirm whether mir - 184 amplified bcl2l1 expression to protect os cells from doxorubicin - induced apoptosis . thus , we next examined the effects of up - regulated or down - regulated mir - 184 on cell death in the presence or absence of doxorubicin . the data showed that mir - 184 significantly reduced the number of apoptotic cells from doxorubicin - induced cell death , but down - regulated mir - 184 promoted doxorubicin - induced cell apoptosis . these findings suggest that up - regulation of mir - 184 made os cells resistant to doxorubicin . we found that mir - 184 was up - regulated in doxorubicin - treated os and leads to poor response to drug therapy by targeting bcl2l1 . our data suggest that mir - 184 might be a potential biomarker for doxorubicin resistance in os . for other chemotherapy drugs ,\noutput:\n" }, { "from": "agent", "value": "backgroundearly metastasis of osteosarcoma ( os ) is highly lethal and responds poorly to drug and radiation therapies . micrornas ( mirnas ) are a class of small noncoding rnas that modulate gene expression at the post - transcriptional level . however , the detailed functions of specific mirnas are not entirely understood . the aim of the present study was to investigate the role of mir - 184 as a mediator of drug resistance in human osteosarcoma.material / methodsqrt - pcr was used to analyze the expression level of mir - 184 in os cell line u-2 os and mg - 63 treated with doxorubicin . mir - 184 agomir or mir - 184 antagomir was transferred into cells to regulated mir - 184 . the target of mir - 184 was predicted by targetscan and confirmed by luciferase reporter assay . bcl -2-like protein 1 ( bcl2l1 ) expression was detected by western blot . cell apoptosis was determined by annexin v staining and analysis by flow cytometry.resultsdoxorubicin induced time - dependent expression of mir - 184 in os cell line u-2 os and mg - 63 . luciferase reporter assay identified bcl2l1 as the direct target gene of mir - 184 . furthermore , doxorubicin reduced bcl2l1 expression , which was reversed by mir - 184 overexpression and further decreased by mir - 184 inhibition in os cells . in addition , mir - 184 agomir reduced doxorubicin - induced cell apoptosis , whereas mir - 184 antagomir enhanced apoptosis in os cells , suggesting that up - regulation of mir - 184 contributes to chemoresistance of the os cell line.conclusionsour data show that mir - 184 was up - regulated in os patients treated with doxorubicin therapy and leads to poor response to drug therapy by targeting bcl2l1 ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: patients with dme were dilated with tropicamide 1 % and 2.5 % phenylephrine and underwent consecutive oct examination using the stratus oct ( version 3.0 software ; carl zeiss meditec ) and spectral domain oct ( cirrus hd - oct , zeiss meditec ) . a maximum of 3 scans each was performed randomly on each patient by a single experienced operator who is certified for multicentre clinical trials . all the included scans were free of retinal boundary identification errors within the central zone . automated measures were recorded by two independent readers on each device masked to the identity of the patients . time domain oct imaging was performed with the stratus oct ( carl zeiss meditec inc , dublin , ca ) . a fast macular - thickness scan with six 6 mm linear scans oriented 30 apart in a radial spoke like pattern was acquired in a continuous automated sequence . each of the six linear scans is composed of 128 equally spaced transverse axial scans per line , intersecting at the fovea ( total of 768 sampled points ) within a scan time of 1.9 seconds . the map is composed of nine sectorial thickness measurements in three concentric circles with diameters of 1 , 3 , and 6 mm . the area bounded by the outer ( 6 mm ) and middle ( 3 mm ) circles forms the outer ring while the area bounded by the middle ( 3 mm ) and inner circles ( 1 mm ) forms the inner ring . each ringthe central 1 mm circular region represents the foveal area . scanning with the cirrus hd - octwas performed with the 512128 scan pattern where a 66 mm area on the retina is scanned with 128 horizontal lines , each consisting of 512 a - scans per line ( total of 65,536 sampled points ) within a scan time of 2.4 seconds . these were defined as scans with a signal strength 6 that exhibit correct delineation of the retina layers as detected automatically by the intrinsic software segmentation algorithm and are without image artifacts caused by eye movement and pupillary shadowing . in the computational software , retinal thicknesses in both instrumentsare averaged within nine retinal subfields in a 6 mm diameter circle centered on the fovea . each individual scan from both devices was evaluated for automated segmentation error and manually approximated to give the final thickness between the inner limiting membrane and retinal pigment epithelium layers . a minimal sample size of 33 eyes was necessary for detecting a 20 % difference in macular thickness in a paired study design . macular thickness readings for each of the retinal subfields were obtained for each patient on both oct scanners , and bland -- altman plots ( prism , ver .4 ; graph - pad , san diego , ca ) were constructed to compare and assess agreement in macular measurements between the stratus oct and cirrus hd - oct systems . a pearson coefficient test was used for the correlation studies and a paired student test for performed for analysis . the coefficient of variation and intraclass correlation coefficient ( icc ) were calculated for each scanner in a grouped fashion and evaluated with the kruskal -- wallis test . pearson correlation analysis was performed for the mean subfield measurements for each eye ( prism , ver . 4 ; graph - pad ) . the sensitivities and specificities were calculated for cirrus hd - oct and stratus oct in diabetic edema versus published normative datasets . the receiver operating characteristic ( roc ) curves were used to determine the discriminatory capabilities between healthy and retinal edematous eyes in this study and from data from previously published studies . the area under receiver operating characteristic curve ( aroc ) was calculated to assess the ability of each device to differentiate dme from normal eyes . an aroc of 1.0 represents perfect discrimination , whereas aroc of 0.5 represents chance discrimination . time domain oct imaging was performed with the stratus oct ( carl zeiss meditec inc , dublin , ca ) . a fast macular - thickness scan with six 6 mm linear scans oriented 30 apart in a radial spoke like pattern was acquired in a continuous automated sequence . each of the six linear scans is composed of 128 equally spaced transverse axial scans per line , intersecting at the fovea ( total of 768 sampled points ) within a scan time of 1.9 seconds . the map is composed of nine sectorial thickness measurements in three concentric circles with diameters of 1 , 3 , and 6 mm . the area bounded by the outer ( 6 mm ) and middle ( 3 mm ) circles forms the outer ring while the area bounded by the middle ( 3 mm ) and inner circles ( 1 mm ) forms the inner ring . each ring is divided into four quadrants , superior , nasal , inferior , and temporal . scanning with the cirrus hd - oct was performed with the 512128 scan pattern where a 66 mm area on the retina is scanned with 128 horizontal lines , each consisting of 512 a - scans per line ( total of 65,536 sampled points ) within a scan time of 2.4 seconds . these were defined as scans with a signal strength 6 that exhibit correct delineation of the retina layers as detected automatically by the intrinsic software segmentation algorithm and are without image artifacts caused by eye movement and pupillary shadowing . in the computational software , retinal thicknesses in both instrumentsare averaged within nine retinal subfields in a 6 mm diameter circle centered on the fovea . each individual scan from both devices was evaluated for automated segmentation error and manually approximated to give the final thickness between the inner limiting membrane and retinal pigment epithelium layers . a minimal sample size of 33 eyes was necessary for detecting a 20 % difference in macular thickness in a paired study design . macular thickness readings for each of the retinal subfields were obtained for each patient on both oct scanners , and bland -- altman plots ( prism , ver .4 ; graph - pad , san diego , ca ) were constructed to compare and assess agreement in macular measurements between the stratus oct and cirrus hd - oct systems . a pearson coefficient test was used for the correlation studies and a paired student test for performed for analysis . the coefficient of variation and intraclass correlation coefficient ( icc ) were calculated for each scanner in a grouped fashion and evaluated with the kruskal -- wallis test . pearson correlation analysis was performed for the mean subfield measurements for each eye ( prism , ver . 4 ; graph - pad ) . the sensitivities and specificities were calculated for cirrus hd - oct and stratus oct in diabetic edema versus published normative datasets . the receiver operating characteristic ( roc ) curves were used to determine the discriminatory capabilities between healthy and retinal edematous eyes in this study and from data from previously published studies . the area under receiver operating characteristic curve ( aroc ) was calculated to assess the ability of each device to differentiate dme from normal eyes . an aroc of 1.0 represents perfect discrimination , whereas aroc of 0.5 represents chance discrimination . a total of 36 out of 38 eyes from 19 patients that were confirmed to have clinically significant and angiographically confirmed dme were recruited for this study . two eyes were excluded as a scan was not possible due to poor media clarity . only scans with proper delineation of retinal layers on both systems were included . the mean age of patients was 58.8112.92 years with an equal male to female distribution . the signal strength in the cirrus hd - oct and stratus oct was 8.28 and 6.39 respectively . mean measurements of macular thickness in each of the nine subfields as well as the total macular volume , manual measurements with bland altman agreement limits and pearson correlation coefficient with p values are indicated in table 1 . the mean difference in this study between the cirrus hd - oct and stratus oct in the central foveal zone was 49.89 m . there was a significant difference in the central , inner inferior , outer superior , outer temporal , outer inferior regions . intrasessional correlation coefficient of data acquired from consecutive scans using a grouped analysis did not show a significant difference between the two devices , as shown in table 2 . comparison of retinal thickness measurements in the nine zones using stratus optical coherence tomography and cirrus optical coherence tomography grouped analysis of intrasessional repeated measures for macular subfield thicknesses the retinal thickness sensitivity and specificity using the stratus oct in relation to detection macular edema was equivalent to 88.9 % [ 95 % confidence interval ( ci ) , 51.75 to 99.2 ] compared to the cirrus hd - oct that showed 77.8 % [ 95 % ci , 39.99 to 97.19 ] . equivalent data from similar studies comparing the cirrus hd - oct and stratus oct in dme detection that have been published previously were also calculated and demonstrated in table 3 . sensitivity and specificity of the cirrus and stratus oct devices from the current and other published studies measuring increased retinal thickness in diabetic macular edema including 95 % confidence intervals and area under receiver operator curves the cutoff value of the retinal thickness measurements using cirrus hd - oct in this study that best discriminated significantly between normal and dme eyes was 291.5 m and for stratus oct was 248.8 m ( p 0.05 ) . similar cutoff values from other studies using these two machines have been detected with equivalent specificity ( 88.89 % ) . the sensitivity of detection of increased retinal thickness in other studies with these cutoffs using the cirrus hd - oct ranged from 55.6 to 100 % , whilst the stratus oct ranged from 77.8 to 100 % . the area under receiver operating curve ( aroc ) for dme patients calculated in this study showed that the discriminating power of the cirrus hd - oct ( 0.877 ) was similar to stratus oct ( 0.938 ) . similar arocs were noted on further analysis of published data from two other studies ( keirnan et al . and foroorghian et al . ) using these two devices when compared to normal patients . in healthy normal patients , increased retinal thickness was defined as any measurement 250 m with a specificity of 88.89 % in all studies . analysis of arocs comparing data from normal patients using stratus oct showed a small range of discriminating power from 0.642 to 0.8395 . the roc curves of retinal thickness measurements in this and other studies using cirrus hd - oct and stratus oct are shown in figs . 1 - 2 . receiver operating curves comparing sensitivity and specificity of measured retinal thickness in the present and previously published studies using the cirrus hd oct in diabetic macular edema patients referenced to normative database receiver operating curves comparing sensitivity and specificity of measured retinal thickness in the present and previously published studies using the time domain stratus oct in diabetic macular edema patients referenced to normative databasethis study of dme patients demonstrates the differences of automated retinal thickness measurements between the cirrus hd - oct and stratus oct devices . cirrus hd - oct generated significantly higher values in the central , inner temporal , outer superior , outer temporal , and outer inferior macular subfields . this is crucial as the central subfield mean thickness is the preferred oct measurement for the central macula because of its higher reproducibility and correlation with other measurements of the central macula . interestingly , the oct software systems that perform automated delineations of retinal boundaries uses different anatomic landmarks of the inner and outer retinal boundary . the cirrus hd - oct segmentation algorithm identifies the thickness of the retina from the retinal pigment epithelium ( rpe ) to the inner limiting membrane ( ilm ) , while the stratus oct segmentation algorithm identifies the thickness of the retina based on the distance between the ilm and junction of the outer segments ( os ) and inner segments ( is ) of the photoreceptors . as a result , the cirrus hd - oct system would be expected to give macular measurements that are larger than those obtained by the stratus oct in this study ranging from 15.31 to 49.99 m . the difference in thickness measurements between the cirrus hd - oct and stratus oct systems should correspond to the length of photoreceptor outer segments within the macula . the bland atlman 95 % limits of agreement between devices in our study were large , with retinal thickness values particularly in the central zone , up to 160 m indicating poor agreement . this is similar to recent work that has compared the cirrus hd - oct and stratus oct . the reproducibility of the stratus oct in healthy normal eyes and in those with dme has been established previously , although each study used a different method , the results are believed to be comparable . it is expected that the cirrus hd - oct would perform better compared to the stratus oct due to the greater sampling that occurs within the central cube ; however our grouped results show no difference [ table 2 ] . this is the first study looking at the sensitivity and specificity of these two devices in measuring retinal thickness in the dme using data from our own work and from other published data . these findings are similar to other authors [ table 3 ] showing a sensitivity range of 66.7 to 100 % with the cirrus hd - oct ( cutoff 290 m ) compared to 77.8 to 100 % with the stratus oct ( cutoff 250 m ) in detection of dme . we can reliably infer from this study that a 43 m difference has to be allowed if using stratus oct and cirrus hd - oct machines interchangeably for the accurate diagnosis of increased retinal thickening in dme using oct , although the recommended preference is to use the same machine for each patient per visit . the stratus oct has showed the lowest thicknesses compared with those with the cirrus hd - oct and spectralis hra + oct in healthy normal eyes as these devices include the rpe layer in the retinal segmentation . recent work from data received for clinical trial research at a reading center has shown that among experienced operators , given the same operator , machine , and eye at the same sitting , stratus oct retinal thickness maps appear to have a correlation that is likely to be less than the clinically important difference . the stratus oct has similar discriminating power to cirrus hd - oct in the detection of dme . this study shows that stratus oct show a moderately high sensitivity and specificity for detection of dme . the cirrus oct sensitivity and specificity results and roc curves obtained in the current study are quite comparable with those of stratus oct . we conclude that cirrus oct better delineates morphological characteristics compared to stratus oct with good signal strength and remains a valuable device in discriminating dme . larger studies comparing stratus oct and fourier domain octs are necessary for confirmation in diseased eyes where segmentation errors remain a concern in patients with structurally complex retinal disease .\noutput:\n" }, { "from": "agent", "value": "purpose : the purpose was to evaluate the sensitivity and specificity of measurements of central macular thickness ( cmt ) in diabetic macular edema using stratus time - domain and cirrus spectral - domain optical coherence tomography ( oct ; carl zeiss meditec , dublin , ca ) . materials and methods : a total of 36 eyes from 19 patients with clinically significant diabetic macular edema ( dme ) were included . all participants underwent automated scanning patterns using cirrus hd - oct and stratus oct examinations on the same day . the sensitivity / specificity of retinal thickness measurements was calculated from published normative data . agreement was calculated using bland -- altman method . the receiver operating characteristic curves ( roc ) and areas under the roc were plotted.results : the mean difference between the cirrus hd - oct and stratus oct in the central foveal zone was 49.89 m . bland -- altman analysis confirmed that the retinal thickness measurements had poor agreement in patients with dme . the areas under the roc for retinal thickness measurements were 0.88 using cirrus hd - oct and 0.94 with stratus.conclusions : in patients with dme , the cirrus hd - oct gives a higher reading than stratus oct with poor agreement between the devices in most regions within the nine subfield zones . the sensitivity and specificity of the stratus oct was comparable to the cirrus ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: hundred married females from an urban area of pune city were taken for this study by random sampling . after due consent , each participant was subjected to psychosocial performa designed for this study ( pretested and validated ) , personal attribute questionnaire ( a 24 - paired - item scale , each pair describing contradictory characteristics in which scoring brings out the masculinity and the femininity response of each individual ) , general health questionnaire 12 ( ghq , a self - administered standardized 12 - item screening test sensitive for the presence of psychiatric disorders in individuals that is not designed to detect symptoms that occur with specific psychiatric diagnosis ) , beck 's depressive inventory ( bdi , a self - administered standardized 21 - item instrument to assess the presence and severity of depression with a reliability of 0.730.92 in nonpsychiatric samples ) , beck 's anxiety inventory ( bai , a self - administered standardized 21 - item instrument to assess the presence and severity of anxiety ) , and perceived stress scale ( pss , a most widely used 10 - item psychological instrument to measure the degree to which situations in an individual 's life are appraised as stressful , which measures the perceived stress over last 1 - month duration ) . the participants were subsequently analyzed on the basis of their presence of masculinity and femininity scores and compared and correlated with various sociodemographic and outcome variables . table 3 shows the mean and median scores of the population on ghq , bdi , bai , and pss . psychopathology was found in 30 % , while proportions of anxious , depressed , and stressful were 25 , 23 , and 36 % , respectively [ table 4 ] . there was no statistically significant association between age , income , occupation of the spouse , and education of the participants with scores on psychopathology ( ghq ) , depression ( bdi ) , anxiety ( bai ) , and perceived stress ( pss ) . table 5 shows that the number of years since marriage and masculinity and femininity scores were found to have statistically significant association with all these scores . table 6 shows that masculinity scores of the participants were negatively correlated while femininity scores were positively correlated with the scores on ghq , bdi , bai , and pss all these were statistically significant . furthermore , a multivariate analysis ( logistic regression ) was done to assess the impact of independent variables ( masculinity and femininity ) and others such as education of the wives , family structure , and occupation of the spouse that are likely to confound the results [ table 7 ] . the analysis revealed that after controlling for all the variables , masculinity had a protective effect on scores of ghq ( psychopathology ) , bdi ( depression ) , bai ( anxiety ) , and pss ( perceived stress ) whereas raised femininity scores corresponded with increased scores on general psychopathology and depression . sociodemographic profile of the study participants distribution of various sociodemographic and individual characteristics distribution of various dependent variables distribution of participants regarding dependent variables of psychopathology , depression , anxiety , and stress association of masculinity and femininity scores in family and years of marriage with various dependent variables correlation of masculinity and femininity scores in family to various dependent variables multivariate analysis ( logistic regression ) of the dependent and independent variables graphical representation of the relationship between ghq and masculinity scoresthis study attempts to understand the role of optimal mix of psychological aspect of masculinity and femininity on the psychopathology of the participants , depressive symptoms , anxiety , and stress perceived by the individual . the median masculinity score of 32 ranging from 24 to 42 is more than the median femininity score ranging from 18 to 26 . these suggest , in general , the societal acceptance of psychological androgyny with a stronger emphasis on the masculine pattern in the female population today . the mean score of the participants on the outcome variables was skewed ; however , the median scores on general psychopathology ( ghq ) , depression ( bdi ) , anxiety ( bai ) , and perceived stress ( pss ) were well below the cutoff in all [ table 3 ] . the cutoff - based evaluation of these scales revealed that around one fourth to one third of the sample population was psychologically distressed , which is in accordance with the findings by other researchers in similar population [ table 4 ] . the absence of any significant relationship between age , income , occupation of the spouse , and education of the participants on one side with scores on psychopathology ( ghq ) , depression ( bdi ) , anxiety ( bai ) , and perceived stress ( pss ) on another side lay emphasis on the more stronger role of individual 's intrinsic factor than extrinsic factors . these findings go in favor of the top - down approach in coping as suggested by watson et al . the number of years since marriage was significantly associated with scores of ghq , bdi , bai , and pss , which had statistically significant negative correlation with these . this implied that as the number of years of married life increased , the scores on psychopathology , anxiety , depression , and perceived stress decreased . this reflects increasing pattern of adaptability in people and more specifically female participants over the years in marital life . masculinity scores of the participants were found to be significantly associated with various outcome variables ( i.e. , psychopathology , depression , anxiety , and perceived stress . ) this again emphasizes the role of individual intrinsic factors ( i.e. , top - down model ) in coping with life events . correlation analysis revealed that people with higher masculinity scores tend to have less psychopathology , were less depressed and anxious , and had reduced perception of stress . on the other hand , femininity scores of the participantswere found to be significantly affecting the various outcome variables ( i.e. , psychopathology , depression , anxiety , and perceived stress ) reiterating the role of individual intrinsic factors ( i.e. , top - down model ) in coping with life events . correlation analysis revealed that people with higher femininity scores tend to have more psychopathology , get more depressed and anxious , and have increased perception of stress . these findings lead to a construct where masculinity is positively associated with better mental health and coping and wherein increased amount of femininity in the female made them vulnerable manifesting with stress and psychopathology . the finding of similar nature came out in multivariate analysis wherein masculinity was found to have a psychoprotective effect and that of femininity detrimental . similar findings have been shown by various researchers who advocate greater emphasis on intrinsic factors in increasing psychological resilience in people . our findings do find androgyny with more emphasis toward masculinity having psychoprotective attributes in our female participants . to conclude , our study revealed that a strong component of psychological masculinity in feminine individuals increase their resilience and coping and makes them less vulnerable to psychopathology in general , depression , anxiety , or the perception of stress . the role of intrinsic individual factors can not be ignored and fostering the same may lead to better mental health . however , the replication and validation of these findings is a continuous process and should move parallel with simultaneous constructive intervention . our findings establish the point that targeting the individual 's own intrinsic factor during psychotherapeutic sessions might improve therapeutic outcome and empowerment - oriented approach would be more valuable in effective preventive and remediation strategies rather than mere stress reduction or environmental manipulation . this study does not attempt to underplay the role of stress reduction or environmental manipulation but wants to make a conscious effort to understand individual vulnerabilities and empowering them , such as with more psychological masculine attributes in a feminine individual . the study aimed to target only the female gender and to study the protective value of masculine traits in them . whether the prominence of masculine trait is effective or the optimal androgynic trend could have been generalized can not be commented upon , as it did not involve both the genders . there could be a varied number of extrinsic and intrinsic factors that may affect the outcome variable ; the exclusion of the same in a general population is impractical . this study has just attempted a cross - sectional analysis in a normative sample of the female population for the role of gender orientation in psychological distress . this study generates an insight into this direction , and more research , especially longitudinal studies , in this dimension would be further conclusive . our findings establish the point that targeting the individual 's own intrinsic factor during psychotherapeutic sessions might improve therapeutic outcome and empowerment - oriented approach would be more valuable in effective preventive and remediation strategies rather than mere stress reduction or environmental manipulation . this study does not attempt to underplay the role of stress reduction or environmental manipulation but wants to make a conscious effort to understand individual vulnerabilities and empowering them , such as with more psychological masculine attributes in a feminine individual . the study aimed to target only the female gender and to study the protective value of masculine traits in them . the male population was not included . whether the prominence of masculine trait is effective or the optimal androgynic trend could have been generalized can not be commented upon , as it did not involve both the genders . there could be a varied number of extrinsic and intrinsic factors that may affect the outcome variable ; the exclusion of the same in a general population is impractical . this study has just attempted a cross - sectional analysis in a normative sample of the female population for the role of gender orientation in psychological distress . this study generates an insight into this direction , and more research , especially longitudinal studies , in this dimension would be further conclusive .\noutput:\n" }, { "from": "agent", "value": "background : in our society , adherence to feminine traits by the female gender had been culturally promoted and socially desired . a few studies , however , entertained the possibility that healthy men and women have some common attributes in their gender orientation . androgyny and masculinity were found related to positive mental health.materials and methods : a cross - sectional study was conducted to assess the level of masculinity and femininity and its relationship with the perception of stress and various psychopathology including anxiety and depression.results : masculinity scores of the participants negatively correlated while femininity scores positively correlated with the scores on general health questionnaire , beck 's depressive inventory , beck 's anxiety inventory , and perceived stress scale.conclusion : androgyny is psychoprotective . empowerment - oriented psychological approaches aimed to encourage psychological androgyny , and masculinity might be therapeutic ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: hemorrhagic shock ( hs ) and resuscitation is known to result in multiple organ injury and activate inflammatory responses that can lead to death . despite the advances in critical care , hs , trauma , and multiple organ dysfunction remain a challenge in the treatment of trauma patients . the exact mechanism ( s ) however , there are several mechanisms involved in the pathogenesis of multiple organ injury and failure following hemorrhagic shock . hemorrhagic shock and resuscitation activate an inflammatory process that can increase the risk of death after trauma , hs activate the immune system that result in the activation of monocytes and leukocytes . activation of the inflammatory pathways is associated with multiple organ injury , dysfunction , and failure . tumor necrosis factor ( tnf ) is one of the most characteristic inflammatory factors contributing to organ injury following hs . apelin is a novel endogenous ligand for the g - protein - coupled receptor apj . apelin receptors are present in the central nervous system and the peripheral tissues , in the heart , lung , kidney , and endothelial cells and endothelial cells . apelin has been shown to be involved in the regulation of cardiovascular function , angiogenesis , fluid homeostasis , and energy metabolic . it is becoming apparent that apelin may play a pathophysiological role in many of the regulatory systems . progress has been made in recent years in clarifying the significance of apelin , much remains to be discovered . this study investigated the protective effects of apelin administration before resuscitation of hemorrhagic in preventing multiple organ injury . furthermore , we analyze the possible mechanism of protection by analyzing the potential of apelin to lower systemic tnf production following resuscitation . the study was approved by the ethical committee at king abdul - aziz city for science and technology . male sprague - dawley rats were injected intra - peritonealy ( i.p . ) with heparin sodium 2000 iu 15 min prior to anesthesia . the left carotid artery was cannulated using polyethylene tubing size 60 , and was connected to an in - line pressure transducer for continuous blood pressure monitoring . the animals were assigned randomly to 33 experimental groups ( n = 6 per group ) : ( 1 ) normotensive rats ( n ) , ( 2 ) hs rats and ( 3 ) hemorrhagic shock rats treated with apelin - 13 ( hs - ap ) . as previously described , rats were hemorrhaged using a reservoir ( a 10 ml syringe ) that is connected to the arterial ( carotid artery ) three - way stopcocks . blood was continuously withdrawn or re - infused to the animal to maintain a mean arterial pressure of approximately 40 mmhg . the same surgical procedures were performed as for the sham hemorrhage group except rats will not be hemorrhaged . after 60 min hemorrhage period , hearts were resuscitated in vivo , by reinfusion of the shed blood to restore normotension and blood pressure were monitored for 30 min . three experimental groups ( n = 6 ) were assigned for the study : normotensive rats ( n ) - rats will undergo the same surgical preparation and were monitored for continuous blood pressure measurements for the experimental period 120 minhs rats - after 30 min stabilization period , rats were hemorrhaged to 40 mmhg for 60 min . rats were then resuscitated and monitored for 30 mineffect of apelin - 13 during hs ( hs - ap ) - after 30 min stabilization period , rats were hemorrhaged to 40 mmhg for 60 min . - rats will undergo the same surgical preparation and were monitored for continuous blood pressure measurements for the experimental period 120 min hs rats - after 30 min stabilization period , rats were hemorrhaged to 40 mmhg for 60 min . rats were then resuscitated and monitored for 30 min effect of apelin - 13 during hs ( hs - ap ) - after 30 min stabilization period , rats were hemorrhaged to 40 mmhg for 60 min . rats were then resuscitated and monitored for 30 min . to perform a histological examination of multiple organs , rat heart , intestine , kidney , and liver were harvested and stored in 10 % formalin solution ( n = 6 in each group ) . we obtained 2 transverse sections per organ for histological examination and sections were stained with hematoxylin and eosin ( h and e ) stain . the areas affected by hs and resuscitation consisting of inflammatory cells , necrosis , and hemorrhage , were determined in the h and e staining . blood ( 0.5 ml ) was collected from the left carotid artery cannula before hemorrhage , before resuscitation and 30 min after resuscitation and centrifuged at 2500 g for 10 min and plasma was stored at 80c until analysis for tnf - measurement . means were analyzed using duncan 's test and were considered significant when yielding a p 0.05 . the study was approved by the ethical committee at king abdul - aziz city for science and technology . male sprague - dawley rats were injected intra - peritonealy ( i.p . ) with heparin sodium 2000 iu 15 min prior to anesthesia . the left carotid artery was cannulated using polyethylene tubing size 60 , and was connected to an in - line pressure transducer for continuous blood pressure monitoring . the animals were assigned randomly to 33 experimental groups ( n = 6 per group ) : ( 1 ) normotensive rats ( n ) , ( 2 ) hs rats and ( 3 ) hemorrhagic shock rats treated with apelin - 13 ( hs - ap ) . as previously described , rats were hemorrhaged using a reservoir ( a 10 ml syringe ) that is connected to the arterial ( carotid artery ) three - way stopcocks . openingblood was continuously withdrawn or re - infused to the animal to maintain a mean arterial pressure of approximately 40 mmhg . the same surgical procedures were performed as for the sham hemorrhage group except rats will not be hemorrhaged . after 60 min hemorrhage period , hearts were resuscitated in vivo , by reinfusion of the shed blood to restore normotension and blood pressure were monitored for 30 min . three experimental groups ( n = 6 ) were assigned for the study : normotensive rats ( n ) - rats will undergo the same surgical preparation and were monitored for continuous blood pressure measurements for the experimental period 120 minhs rats - after 30 min stabilization period , rats were hemorrhaged to 40 mmhg for 60 min . rats were then resuscitated and monitored for 30 mineffect of apelin - 13 during hs ( hs - ap ) - after 30 min stabilization period , rats were hemorrhaged to 40 mmhg for 60 min . - rats will undergo the same surgical preparation and were monitored for continuous blood pressure measurements for the experimental period 120 min hs rats - after 30 min stabilization period , rats were hemorrhaged to 40 mmhg for 60 min . rats were then resuscitated and monitored for 30 min effect of apelin - 13 during hs ( hs - ap ) - after 30 min stabilization period , rats were hemorrhaged to 40 mmhg for 60 min . to perform a histological examination of multiple organs , rat heart , intestine , kidney , and liver were harvested and stored in 10 % formalin solution ( n = 6 in each group ) . we obtained 2 transverse sections per organ for histological examination and sections were stained with hematoxylin and eosin ( h and e ) stain . the areas affected by hs and resuscitation consisting of inflammatory cells , necrosis , and hemorrhage , were determined in the h and e staining . blood ( 0.5 ml ) was collected from the left carotid artery cannula before hemorrhage , before resuscitation and 30 min after resuscitation and centrifuged at 2500 g for 10 min and plasma was stored at 80c until analysis for tnf - measurement . means were analyzed using duncan 's test and were considered significant when yielding a p 0.05 . the animals were subjected to hs to lower the mean arterial blood pressure to the desired level of hypotension ( 3540 mmhg ) . the total volume of blood withdrawn was 151.1 ml / kg body weight . there was no significant difference in the amount of blood withdrawn among the groups of animals subjected to hs . as observed in figure 1 , hs caused a significant increase in the serum levels of tnf - when compared to normotensive group ( p 0.05 ) . treatment with apelin before resuscitation following hs significantly lowered the levels of tnf - [ figure 1 ] . hemorrhage increased tumor necrosis factor - levels . * p 0.05 versus sham group ( n = 6 per group ) , and p 0.05 versus hemorrhage group ( n = 6 per group ) hs and resuscitation caused multiple organ injury [ figure 2 ] . heart sections in the h and e - stain showed areas of hemorrhage , coagulation necrosis with diffuse edema and neutrophil infiltration [ figure 2a c ] . blood vessels in the heart sections showed swollen endothelium with neutrophil infiltration [ figure 2d and e ] . ( a - c ) heart section showing inflammatory cell infiltration around blood vessels and edema ( h and e , 100 , 400 and 400 ) . ( d and e ) endothelium of blood vessel in the heart , showing swollen endothelium with neutrophil infiltration ( h and e , 400 and 600 ) sections from multiple organs of treated animals before resuscitation of hs showed normal tissue with no evidence of inflammation and tissue injury . figure 3 shows tissues obtained from multiple organs from animals treated with apelin before resuscitation following hs . the inflammatory infiltration and the increase in the number of neutrophils were prevented by treatment with apelin . light micrographs of multiple organs from hemorrhagic shocked rats treated with apelin showing normal tissue . ( b and c ) endothelium ( h and e , 400 and 600 ) . ( d and e ) intestinal section ( h and e , 100 and 400 ) . ( f and g ) liver section ( h and e , 400 and 200 ) . as observed in figure 1 , hs caused a significant increase in the serum levels of tnf - when compared to normotensive group ( p 0.05 ) . treatment with apelin before resuscitation following hs significantly lowered the levels of tnf - [ figure 1 ] . p 0.05 versus sham group ( n = 6 per group ) , and p 0.05 versus hemorrhage group ( n = 6 per group ) heart sections in the h and e - stain showed areas of hemorrhage , coagulation necrosis with diffuse edema and neutrophil infiltration [ figure 2a c ] . blood vessels in the heart sections showed swollen endothelium with neutrophil infiltration [ figure 2d and e ] . ( a - c ) heart section showing inflammatory cell infiltration around blood vessels and edema ( h and e , 100 , 400 and 400 ) . ( d and e ) endothelium of blood vessel in the heart , showing swollen endothelium with neutrophil infiltration ( h and e , 400 and 600 ) sections from multiple organs of treated animals before resuscitation of hs showed normal tissue with no evidence of inflammation and tissue injury . figure 3 shows tissues obtained from multiple organs from animals treated with apelin before resuscitation following hs . the inflammatory infiltration and the increase in the number of neutrophils were prevented by treatment with apelin . light micrographs of multiple organs from hemorrhagic shocked rats treated with apelin showing normal tissue . ( b and c ) endothelium ( h and e , 400 and 600 ) . ( d and e ) intestinal section ( h and e , 100 and 400 ) . ( f and g ) liver section ( h and e , 400 and 200 ) . despite the advances in critical care , resuscitation strategies fail to prevent deleterious inflammatory responses . resuscitation can cause systemic inflammatory responses that can lead to multiple organ injury , dysfunction , and death . this study showed that hs and resuscitation are associated with multiple organ injury and activation of inflammatory responses . the results from the present study are in agreement with previous reports that showed that resuscitation following hs results in multiple organ injury and dysfunction . the present study showed that apelin decreased the inflammatory response to shock and protected against postresuscitation organ injury . however , the protective mechanism of apelin against multiple organ injury is not fully understood . our previous study showed that apelin protect against myocardial dysfunction following in vivo and ex vivo resuscitation following hs . apelin is an endogenous substance that may involve activation of phosphatidalipase c , protein kinase c , and sacrolemmal sodium hydrogen exchange , and sodium - calcium exchange . the mechanisms of the apelin protective effects may be from enhancing the activity of sodium hydrogen exchange with consequent intracellular alkalization . however , the activation of the inflammatory pathways is the key process in organ dysfunction following hs and the production of inflammatory markers such as tnf . the results of the present study and other previous studies on apelin had led to speculation that apelin could be a future target for therapeutic strategies following hs and resuscitation . apelin protect against multiple organ injury following resuscitation of hs by attenuation of the inflammatory response . this work was supported by a grant from the national plan for science , technology and innovation ( 12 - med2525 - 02 ) at king saud university , riyadh , saudi arabia . this work was supported by a grant from the national plan for science , technology and innovation ( 12 - med2525 - 02 ) at king saud university , riyadh , saudi arabia .\noutput:\n" }, { "from": "agent", "value": "introduction : hemorrhagic shock ( hs ) result in multiple organ injury and inflammatory response that lead to death . the exact mechanism is not clear . apelin is an endogenous ligand of orphan g - protein coupled receptor apj . apelin has anti - inflammatory effects on the release of inflammatory mediators.objectives : to examine the protective effects of apelin against multiple organ injury and the possible involvement of inflammatory pathways.methodology : male sprague - dawley rats ( 300350 g ) were subjected to hemorrhage over 60 min to reach a mean arterial blood pressure of 40 mmhg . then , rats were treated or not with 1 ml of 10 nm / l apelin - 13 intraarterially resuscitation was performed in vivo by the reinfusion of the shed blood for 30 min to restore normotension . blood samples were collected for measurement of tumor necrosis factor ( tnf ) using elisa ( r and d systems ) . biopsies were obtained from organs for light microscopic examination.results : hs rats showed significant increase the levels of tnf . apelin significantly lowered the production of tnf - . histological examination of hemorrhagic shocked untreated rats revealed structural damage . less histological damage was observed in the organs of treated rats . apelin - treatment decreased the number of inflammatory cells and mitochondrial swollen in cells.conclusion : treatment with apelin before resuscitation protects against multiple organ injury in hs by attenuation the inflammatory response and might be a therapeutic target for hs ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: micrornas ( mirnas ) are a class of regulatory small rnas that control diverse biological events in plants , animals , and many single - cell eukaryotes ( baulcombe , 2004 ; brodersen and voinnet , 2009 ) . by degrading or blocking the translation of target messenger rnas , mirnas modulate the expression of genes for development , differentiation , metabolism , and defense ( bartel , 2004 ; voinnet , 2005 ; 2009 ) . because of the important roles of mirnas in biological events , extensive researches have been performed to delineate the precise mechanisms of mirna processing ( kim , 2005 ; kurihara et al . , 2006 ; parizotto et al . , 2004 ; ren and yu , 2012 ) . in general , mirnas are processed from long transcripts , called primary mirnas ( pri - mirnas ) , which are generated from their own genes or from introns ( okamura et al . , 2007 ) . a single pri - mirna contains one or more imperfect hairpin - loop structure with mirna sequences ( bielewicz et al . , 2013 ; meng et al . ,2013 ) . in animals , the apical element and stem of a pri - mirnais recognized by digeorge syndrome critical region 8 ( dgcr8 ) through its double - stranded rna domain and rna - binding heme domain , respectively ( landthaler et al . , 2004 ; nguyen et al . , 2015 ) . drosha , a type iii rnase , forms a heterotrimeric complex , known as a microprocessor , with two molecules of dgcr8 in order to process pri - mirna into precursor - mirna ( pre - mrna ) ( gu et al . , 2012 ; kwon et al . , the processed product is subsequently exported to the cytoplasm where it is further cleaved by another rnase type iii enzyme , dicer . dicer recognizes 5 and 3 ends of the pre - mirna and excises the loop to release mature mirna ( denli et al . , 2004 ; saito et al . , 2005 ; zeng et al . , 2005 ) . in plants , the two - step cleavage of pri - mirna is performed by a dicer homolog , dicer - like1 ( dcl1 ) . two dcl1 - binding proteins , hyponastic leaves 1 ( hyl1 ) and serrate ( se ) are essential for the accuracy of pri - mirna processing ( dong et al . , 2008 ; hua enhancer 1 ( hen1 ) adds a methyl group to the 3 end of mirnas prior to their transport out of the nucleus ( park et al . , in addition to these core proteins , more than 20 components are directly or indirectly involved in plant pri - mirna processing ( ben chaabane et al . , 2013 ; zhang et al . , 2013 ; 2014 ) . for instance , tough ( tgh ) is a g - patch domain protein , which directly binds to the dcl1 , se , and hyl1 complex to assist in the recruitment of pri - mirnas ( rogers and chen , 2013 ) . receptor for activated c kinase 1 ( rack1 ) is a scaffold protein required for protein - protein interactions , which interacts with se to modulate pri - mirna processing ( speth et al . , 2013 ) . sickle ( sic ) , a proline - rich protein , is involved in the maturation of mirnas ( zhan et al . ,2012 ) . stabilized 1 ( sta1 ) , a pre - mrna processing factor 6 homolog protein , regulates the splicing of pri - mirnas ( ben chaabane et al . , 2013 ) . the final step in both plants and animals involves mature mirnas being selectively loaded to argonaute 1 ( ago1 ) protein , which is one of the essential catalytic components of the rna - induced silencing complex ( risc ) in the cytoplasm ( rogers and chen , 2013 ) . since the discovery of mirnas and their roles in gene expression , most studies on mirnas have focused on improving understanding of processing and functional mechanisms . in contrast to the post - translational modifications of proteins in many regulatory pathways , such as light signaling , hormone regulation , and stress responses , which have been widely studied in plants , knowledge on post - translational modifications of the mirna processing and silencing machinery is still rudimentary . recently , several pioneering studies on the post - translational regulation of rna silencing machinery have been performed in both animals and plants . this review focuses on published studies on the post - translational regulation of the silencing machinery , focusing on hyl1 , drb4 , and ago1 in plants . the biological impacts of proteolytic regulation will be discussed along with several perspectives on the current findings in this field . ago1 plays key roles in both mirna - and sirna - mediated gene silencing either by destabilization of target mrnas or by translational repression ( valencia - sanchez et al . , 2006 ) . considering the important functions of ago1 in plant growth , development , and defense , it is not surprising that the expression of ago1 is tightly regulated by highly programmed regulatory consoles ( bohmert et al . , 1998 ) . ago1 is negatively regulated by mir168 and by itself , in a process known as ago1 - catalyzed mrna cleavage . in the self - regulation pathway , the transcriptional co - regulation of mir168 and ago1 , and post - transcriptional stabilization of mir168 by ago1 , are important to modulate the efficiency of assembling risc complexes ( vaucheret et al . , 2004 ; 2006 ) . in addition to post - transcriptional regulation , post - translational regulation of ago1 protein has been reported in the context of plant - virus interactions ( alvarado and scholthof , 2011 ) . since the p0 protein of beet western yellows virus ( bwyv ) was shown to suppress the plant s rna silencing defense mechanism . many p0 proteins from members of the genera polerovirus and enamovirus have also been identified as suppressors ( pfeffer et al . , 2002 ) . because of the f - box like central region , the p0 proteins of these viruses are considered to be f - box like proteins . in general , f - box proteins are part of the scf skp1 - cullin - f - box protein ( scf ) e3 ubiquitin ligase complexes , which tether poly - ubiquitin to a target protein and subsequently mediate the modified protein for proteasome - mediated degradation ( callis , 2014 ; cardozo and pagano , 2004 ; von arnim , 2001 ) . in plants , the assembling of multiple f - box proteins into the same scf complex permits the recognition of a broad range of target proteins ( hare et al . , therefore , it was suggested that the viral f - box protein ( p0 ) proteins could snatch the host scf ubiquitin - protein ligase ( e3 ) system by mimicking the host f - box protein and subsequently incapacitating the host defense system . the hijacking ability of p0s has been reported in two poleroviruses , bwyv and cucurbit aphid - borne yellows virus ( cabyv ) , which directly interact with s - phase kinase related protein 2 ( skp2 ) , a component of the scf family of ubiquitin e3 ligases ( pazhouhandeh et al . , 2006 ; pfeffer et al . , 2002 ) . however , this is insufficient to explain the exact mode of action of p0 in impeding the host rna silencing system . in 2007 , using the tobacco transient - expression system , baumberger et al . showed that the p0 of polerovirus targets the paz domain of ago1 and leads to the destabilization of ago1 ( baumberger et al . , 2007 ) . ( 2007 ) also demonstrated that the ectopic expression of p0 in arabidopsis triggers ago1 degradation . those authors further showed that p0 is incapable of promoting the destabilization of pre - loaded ago1 . however , there is no clear evidence of a direct association between p0 and ago1 . this strategy , utilizing viral suppressor proteins to neutralize the ago1 - dependent defense system , is found widely in other viruses . p25 is the silencing suppressor of potato virus x , which directly interacts with ago1 ( chiu et al . , 2010 ) . pea enation mosaic virus - 1 ( pemv - 1 ) is able to inhibit local and systemic rna silencing systems by destabilizing ago1 ( fusaro et al . , 2012 ) . cucumber mosaic virus ( cmv ) - encoded 2b protein directly interacts with ago1 and inhibits the rna silencing system , but is not associated with the destabilization of ago1 ( chiu et al . several studies have further demonstrated the detailed mechanism of ago1 destabilization in both viral - and non - viral contexts . p0 of polerovirus is known to deceive the host scf - type complexes , resulting in the proteasomal degradation of their target proteins . contrary to the relationship between p0 and scf - complexes , the degradation of ago1 by p0 was surprisingly unaffected by inhibition of the 26s proteasome ( derrien et al . , 2012 ) . ago1 was also negatively modulated by a host f - box protein , f - box , and wd - repeat domain - containing protein 2 ( fbw2 ) , which is known to mediate the ubiquitination of interacting targets . in contrast , overexpression of fbw2 significantly decreased the protein level of ago1 , demonstrating the negative function of fbw2 in ago1 stability . however , the reduced level of ago1 in the transgenic plants was not fully restored following mg132 treatment ( earley et al . , 2010 ) . these results indicated that ago1 destabilization by either p0 or fbw2 is not subjected to the ubiquitin - proteasome system ( ups ) pathway . indeed , ago1 degradation was mediated by autophagy , which initiates the orderly degradation and recycling of cellular components . ago1 protein dramatically accumulated in response to treatment with 3 - ma , an autophagy flux inhibitor or e64 , an autophagic protease inhibitor . furthermore , ago1 co - localized with autophagosomal membrane protein atg8 , strongly indicating that ago1 was associated with the autophagosome ( derrien et al . , 2012 ) . although autophagy has been considered to represent a random method of degradation , many recent studies have shown that specific ubiquitin e3 ligases and substrate ubiquitination are tightly linked to the autophagy pathway to remove aggregated proteins ( kraft et al . , 2010 ; myeku and figueiredo - pereira , 2011 ) . in this context , autophagy - dependent degradation of ubiquitinated ago1 in connection with endogenous scf e3 ligase complexes can be understood ( fig . however , this autophagy - dependent pathway may not always occur in other viral suppressors . for instance , when mg132 was infiltrated into n. benthamiana leaves 2 h before co - infiltration with agrobacterium strains to express p25 and ago1 , the accumulation of ago1 increase 10-fold even in the presence of the p25 suppressor , implying the indirect or direct involvement of the ups system in ago1 destabilization ( chiu et al . in fact , two pathways for ago1 destabilization , autophagic and ups pathways , could function independently in plants . for instance , if two viral f - box proteins , p0 and p25 , target different negative regulators of ago1 , assuming that at least two negative regulators of ago1 exist , the different mechanisms could be understood . however , the presence of two independent and pathogen - specific pathways for ago1 degradation should be further demonstrated experimentally using specific pathway inhibitors and mutants ( fig . dcl1 processes pri - mirna into mirnas , dcl2 processes double - stranded rna into 22 - nucleotide small interfering rnas and is redundantly involved in mirna processing . dcl4 is responsible for the production of endogenous rdr6 - dependent trans - acting sirnas ( tasirnas ) ( gasciolli et al . , 2005 ; moissiard and voinnet , 2006 ; xie et al . , 2004 ) . arabidopsis encodes five double - stranded rna binding ( drb ) proteins ( eamens et al . , 2012 ) . by assisting dcl1 , drb1 and drb2 are involved in mirna biogenesis . as a partner of dcl4 , drb4 functions in small interfering rna ( sirna ) pathways ( curtin et al . , together with dcl4 , drb4 is responsible for the production of tas3 trans - acting sirnas and in the generation of antiviral responses ( adenot et al . , 2006 ; , 2011 ; hiraguri et al . , 2005 ; jakubiec et al . , 2012 ; nakazawa et al . , 2007 ) . drb3 is involved in methylation - mediated antiviral defense with dcl3 and ago4 ( raja et al . ,2014 ) . despite their important roles in gene expression , epigenetic control , and defense , the post - translational regulation of these dcl proteins and their associated proteinshave not been reported until recently , except drb1 , which is also known as hyl1 , and drb4 . hyl1 - 2 mutants displayed pleiotropic developmental disorders , including shorter stature , delayed flowering , leaf upward curling , partial infertility , defective apical shoot , and root growth ( lu and fedoroff , 2000 ) . hyl1 forms a complex with dcl1 and serrate to increase the accuracy of pri - mirna processing into mature mirnas . structural analysis demonstrated that rna - binding domain 1 recognizes the mirna / mirna * region of the precursor as a dimer , mediated by rna - binding domain 2 ( yang et al . , 2010 ) . furthermore , the homo - dimerization of hyl1 is very important for adjusting the cleavage site in pri - mirnas . the activity of hyl1 is also crucial to select the guide strand of mirnas upon ago1 loading ( wu et al . , 2013 ) . hyl1 requires c - terminal domain phosphatase - like 1 ( cpl1 ) , which dephosphorylates hyl1 proteins , for optimal activity ( manavella et al . , 2012 ) . that study showed , for the first time , that the post - translational modification of hyl1 , involving the removal of a phosphate group , is important for mirna processing accuracy and strand selection . recently , using a dna / silver nanocluster sensor - based screening method , cho et al . interestingly , the isolated component was defined as constitutive photomorphogenic 1 ( cop1 ) , which plays a central role in photomorphogenesis . the role of cop1 in maintaining hyl1 expression was shown to be tightly associated with post - translational regulation . levels of hyl1 were clearly increased by mg132 but not by the other specific proteasome inhibitors , clasto - lactacystin - lactone and epoxomicin . furthermore , hyl1 destabilization was not blocked by pry - 41 , an inhibitor of e1 enzyme for the ubiquitin - conjugating process , implying that ups is not responsible for hyl1 degradation . on the other hand , the possible involvement of autophagy was investigated using an autophagy inhibitor , 3 - ma , and an activator , bth . as a resulttaken together , these results showed that neither the ups pathway nor autophagy is responsible for the degradation of hyl1 . interestingly , hyl1 was specifically cleaved into a 26 - kda n - terminal fragment by a crude cytoplasmic extract in vitro . consistently , the cytoplasmic accumulation of hyl1 has been clearly demonstrated following the treatment of hyl1 - cfp transgenic seedlings with mg132 . based on those results , it was suggested that hyl1 may be cleaved by an as yet unknown protease existing in the cytoplasm . more interestingly , cho et al . showed that hyl1 degradation is regulated by the light - to - dark transition . during the daytime , cop1 moves to the cytoplasm stabilizing hyl1 , possibly by inhibiting the protease . in addition , during the night , cop1 migrates into the nucleus and removes the protease activity required for hyl1 degradation . although the protease involved in hyl1 cleavage was not clarified , the study primarily showed that the presence of a third proteolytic regulatory console , distinct to both the ups pathway and autophagy ( fig . ( 2012 ) . found that drb4 protein directly interacts with apc10 / dco1 , a subunit of anaphase promoting complex ( apc / c ) , or cyclosome , a cell cycle - regulated ubiquitin ligase that controls progression of the cell cycle . the dsrna binding domain 2 of drb4 was required for its homodimerization and for the interactions with apc10 and dcl4 . moreover , the level of drb4 was dramatically increased in response to mg132 treatment and in apc10 rnai knockdown mutants , implying that drb4 might be a target of the apc complex - mediated ups pathway . however , to confirm the involvement of ups in the proteolytic regulation of drb4 , further detailed investigations are needed . these should aim to 1 ) investigate the ubiquitination of drb4 in vivo and in vitro by the apc complex , 2 ) test specific proteasome inhibitors such as clasto - lactacystin - lactone and epoxomicin , and 3 ) test the possible involvement of autophagy . in plants , several studies have shed light on the proteolytic regulation of microprocessor components and rna silencing complexes . in the context of virus - host interactions , ago1 protein seems to be regulated either by scf complex - mediated autophagy or by the ups pathway according to the type of infecting viruses ( baumberger et al . , 2007 ; , 2007 ; chiu et al . , 2010 ; derrien et al . , 2012 ; fusaro et al . , 2012 ) . although the degradations of ago2 , ago4 , ago5 , ago6 , and ago9 have also been monitored using transient expression systems , the mechanism of degradation has not been fully elucidated . notably , the level of ago1 protein was significantly diminished in all mutants in which the mirna biogenesis was affected ( derrien et al . , 2012 ) . reduced levels of ago1 protein in hen1 - 1 seedlings were restored by e64d treatment , implying the involvement of autophagy . when gfp - ago1 was co - expressed with rfp - atg8a fusion protein in tobacco cells , gfp - ago1 associated with rfp - atg8a within small intracellular structures like acid vascular organelles ( avo ) . the co - localization was further recapitulated by a co - immunoprecipitation assay in planta , strongly suggesting that ago1 associates with atg8 in the autophagosome . based on those results , derrian et al . ( 2012 ) suggested that the proteolytic regulation of ago1 in the context of non - viral infection may also be attributed to scf complex - mediated autophagy . however , the detailed mechanism of ago1 destabilization needs to be further established considering the possible involvement of an unknown pathway for ago1 degradation . we propose this hypothesis based in the analysis of p0 - induced ago1 degradation ( baumberger et al . , 2007 ) . regardless of whether p0 was expressed , ago1 was cleaved into a 45 - kda polypeptide corresponding to the n - terminal of ago1 , and that fragmenthence , baumberger et al . ( 2007 ) suggested that the 45 - kda protein is evidence of an ago1 degradation pathway that is not strictly dependent on p0 . if ago1 is solely degraded by autophagy or the 26s proteasome , the specific cleavage pattern of ago1 could not be monitored , indicating that an unknown pathway may exist . autophagy involves the digestion of target proteins and the disassembly of polyubiquitinated proteins into short peptide fragments by the 26s proteasome . although in some cases , the 26s proteasome produces biologically active and functional molecules such as antigenic or signaling polypeptides ( rock and goldberg , 1999 ) , the 45 - kda polypeptide is too large to consider it a product of the 26s proteasome . likewise , hyl1 is specifically cleaved into a 25 - kda polypeptide at the n - terminal region by an as yet unknown cytoplasmic protease , which seems to be be not included in the acid compartments because the catalytic activity of the protease is maintained even under neutral ph ( cho et al . , 2014 ) . therefore , we suggest that the cleavage of ago1 by non - avo cytoplasmic proteases can not be ruled out , at least in plants . even though ago1 and hyl1 might be targets of the unidentified cytoplasmic protease or class of proteases , the detailed mechanisms underlying their degradation could be distinct . because the protein levels of hyl1 and ago1 are differentially modulated by chemical inhibitors such as mg132 and 3 - ma , and the half - life of hyl1 ( less than 2h ) is much shorter than that of ago1 ( more than one day ) ( baumberger et al . , 2007 ; cho et al . , 2014 ; derrien et al . , 2012 ) . the pathogen - induced degradation of ago1 is very important for studying plant defense systems . by blocking the major rna - silencing mechanism , viruses are able to escape from the rna interference - based plant defense system and efficiently spread within host plants . therefore , by obtaining detailed knowledge on the proteolytic regulation of ago1 , plant defense systems can be manipulated to confer high viral resistance . furthermore , the proteolytic regulation of hyl1 by the light dark transition must be further investigated in relation to the light signaling pathway . the developmental transition between skotomorphogenesis and photomorphogenesis is essential in the early development of plants , and this has been widely studied in terms of the proteolytic regulation of light receptors and transcription factors . the integration of light signaling into mirna biogenesis , per se , has been scarcely addressed . thus , future studies investigating the crosstalk between two major regulatory pathways , light signaling and mirna biogenesis , could be essential to fully delineate the early development of plants . moreover , to date , the proteolytic regulation of the core microprocessor , dcl1 and se , has not been addressed in plants . hence , to fully understand mirna biogenesis in plants , investigations on the proteolytic pathways of dcl1 and se are envisaged as future challenges .\noutput:\n" }, { "from": "agent", "value": "post - translational modifications ( ptms ) of proteins are essential to increase the functional diversity of the proteome . by adding chemical groups to proteins , or degrading entire proteins by phosphorylation , glycosylation , ubiquitination , neddylation , acetylation , lipidation , and proteolysis , the complexity of the proteome increases , and this then influences most biological processes . although small rnas are crucial regulatory elements for gene expression in most eukaryotes , ptms of small rna microprocessor and rna silencing components have not been extensively investigated in plants . to date , several studies have shown that the proteolytic regulation of agos is important for host - pathogen interactions . drb4 is regulated by the ubiquitin - proteasome system , and the degradation of hyl1 is modulated by a de - etiolation repressor , cop1 , and an unknown cytoplasmic protease . here , we discuss current findings on the ptms of microprocessor and rna silencing components in plants ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: leeches are segmented worms belonging to the phylum annelida . unlike other oligochaeta such as earthworms , they have 2 suckers . the majority of leeches inhabits in freshwater environments , but may also reside in terrestrial environments . they are generally classified into 2 groups : rhyncobdellae ( jawless leeches ) and arhynchobdellae ( jawed leeches ) . jawed leeches are known for blood - feeding habits and can be found in terrestrial and aquatic environments . blanchard established haemadipsidae to distinguish blood - feeding terrestrial leeches from their aquatic sanguivorous and carnivorous counterparts in hirudininae . in addition , blood - feeding land leeches are separated into 2 families , haemadipisidae and xerobdellidae based on their phylogenetic analyses . they exhibit high biodiversity especially in tropical regions with high humidity , such as the damp jungles and forests of south asia , southeast asia , and australia . haemadipsa , trignathous haemadipsid , is mostly abundant in southeast asia . despite its high abundance throughout the range countries , dna barcoding system for animal species identification applies cytochrome c oxidase subunit 1 ( co1 ) sequences as a genetic marker . additionally , other studies analyzed distantly - related lineages of blood - feeding terrestrial leeches using nuclear 18s rrna and 28s rrna marker . the presence of torix tagoi oka , hirudo nipponia whitman 1886 , and whitmania pigra ( murada , 1936 ) were first reported in korea during the first half of the 20th century . it has been known that some land leeches are living in islands of korea , particularly in gageo - do ( island ) , but yet to be documented scientifically . the goal of this study is to identify the taxonomic status of the land leeches newly found in gageo - do based on molecular analysis . this is the first report on the presence of the terrestrial leech species in korea . during july 25 - 28 of 2011 , 40 leeches were collected on mt . dock - sil ( a.s.l .639 m , e 12507 ' , n 3404 ' ) on the gageo - do , shinan - gun ( county ) , jeollanam - do ( province ) , korea ( fig . the island is located at the southwestern part of mokpo city ( 136 km far from mokpo ) , and its geographical coordinates is between n 3406 ' and 3502 ' and between e 12505 ' and 12509 ' ( fig . leech collection was performed walking along the forest path to attract leeches , and then the leeches on legs or other parts were removed with tweezers as soon as possible ( fig . the specimens were preserved in 70 % alcohol for dna extraction ( fig . 2c and d ) . the dneasy blood & tissue kit ( qiagen , hilden , germany ) was used for lysis of tissue and dna extraction . the extracted dna was stored at -20 . pcr amplifications of 18s rrna and coi gene fragments were carried out using the primers listed in table 1 . the initial pcr amplification was conducted using the primers a and b , yielding a 1.8 kb fragment . the subsequent pcr amplification was performed using 2 sets of nested primers a and y or c and b to yield 2 short overlapping dna fragments with approximately 1.2 kb in length each . all pcrs were conducted using the hipi pcr premix ( eplis - biotech inc . , amplification reactions consisted of 1 unit / 4 l hipi thermostable dna polymerase in 250 mm tris - hcl ( ph 9.0 ) , 80 mm ( nh4 ) 2so4 , 10 % dmso , 8.75 mm mgcl2 , 0.05 % bromophenol blue , 12 % glycerol , stabilizer , 0.5 mm each primers , and 10 - 15 ng of dna . all pcr reactions were performed in a ptc - 200 thermal cycler ( mj research inc . , ramsey , minnesota , usa ) . amplified pcr products were separated by electrophoresis on 1.5 % agarose gel and visualized with ethidium bromide under a sl - 20 image visualizer ( seolin scientific co. , seoul , korea ) . the genbank accession numbers of 18s rrna gene and coi gene sequences related to haemadipsoid leeches were listed in table 2 . for 18s rrna sequences , the 2 separated fragments ( 1.2 kb for each ) were edited and reconciled using bioedit version 7.0.9.0 . consequently , both 1.7 kb of 18s rrna and 649 bp of co1 sequences were used for species identification and phylogenetic analysis . analyses of the sequences were comparatively completed using the blast search option for 18s rrna and co1 sequences of leeches in genbank database . the phylogenetic relationships between haplotypes of the leeches were reconstructed using the neighbor - joining ( nj ) method under the kimura 2 - parameter ( k -2-p ) model . as references , corresponding sequences were selected from genbank database ( table 2 ) . also , corresponding sequences ( n = 8 ) were used to root the phylogenetic tree as outgroup ( table 2 ) . confidence in estimated relationship was determined using the bootstrap approach obtained through 1,000 replicates with the same model as mentioned above . both bootstrap analysis and phylogeny reconstructionduring july 25 - 28 of 2011 , 40 leeches were collected on mt . dock - sil ( a.s.l .639 m , e 12507 ' , n 3404 ' ) on the gageo - do , shinan - gun ( county ) , jeollanam - do ( province ) , korea ( fig . the island is located at the southwestern part of mokpo city ( 136 km far from mokpo ) , and its geographical coordinates is between n 3406 ' and 3502 ' and between e 12505 ' and 12509 ' ( fig . leech collection was performed walking along the forest path to attract leeches , and then the leeches on legs or other parts were removed with tweezers as soon as possible ( fig . the specimens were preserved in 70 % alcohol for dna extraction ( fig . 2c and d ) . the dneasy blood & tissue kit ( qiagen , hilden , germany ) was used for lysis of tissue and dna extraction . the extracted dna was stored at -20 . pcr amplifications of 18s rrna and coi gene fragments were carried out using the primers listed in table 1 . the initial pcr amplification was conducted using the primers a and b , yielding a 1.8 kb fragment . the subsequent pcr amplification was performed using 2 sets of nested primers a and y or c and b to yield 2 short overlapping dna fragments with approximately 1.2 kb in length each . all pcrs were conducted using the hipi pcr premix ( eplis - biotech inc . , city , country ) in 20 l total volume . amplification reactions consisted of 1 unit / 4 l hipi thermostable dna polymerase in 250 mm tris - hcl ( ph 9.0 ) , 80 mm ( nh4 ) 2so4 , 10 % dmso , 8.75 mm mgcl2 , 0.05 % bromophenol blue , 12 % glycerol , stabilizer , 0.5 mm each primers , and 10 - 15 ng of dna . all pcr reactions were performed in a ptc - 200 thermal cycler ( mj research inc . , ramsey , minnesota , usa ) . amplified pcr products were separated by electrophoresis on 1.5 % agarose gel and visualized with ethidium bromide under a sl - 20 image visualizer ( seolin scientific co. , seoul , korea ) . the genbank accession numbers of 18s rrna gene and coi gene sequences related to haemadipsoid leeches were listed in table 2 . for 18s rrna sequences , the 2 separated fragments ( 1.2 kb for each ) were edited and reconciled using bioedit version 7.0.9.0 . consequently , both 1.7 kb of 18s rrna and 649 bp of co1 sequences were used for species identification and phylogenetic analysis . analyses of the sequences were comparatively completed using the blast search option for 18s rrna and co1 sequences of leeches in genbank database . the phylogenetic relationships between haplotypes of the leeches were reconstructed using the neighbor - joining ( nj ) method under the kimura 2 - parameter ( k -2-p ) model . as references , , corresponding sequences ( n = 8 ) were used to root the phylogenetic tree as outgroup ( table 2 ) . confidence in estimated relationship was determined using the bootstrap approach obtained through 1,000 replicates with the same model as mentioned above . both bootstrap analysis and phylogeny reconstructionto determine the species identity and to evaluate the genetic relationship of the land leeches in gageo - do , both 1.8 kb 18s rrna and 710 bp co1 gene sequences were amplified from leech samples ( fig .3 ) . of the 29 samples , 26 and 21 sequences were obtained for 18s rrna and co1 gene , respectively . the remaining samples were failed to yield clear sequences or proved to be other species , rather than haemadipsa spp . ( data not shown ) . for determining the species identity of the gageo - do land leeches , all sequences of the leeches were checked using the blast search from genbank database . the results showed that 18s rrna nucleotide sequences have 99.9 % identity to the h. rjukjuana isolate hary ( from taiwan , hq203097 , fig . the sequences were separated into 2 types , h. rjukjuana co1 type a and co1 type b. among 21 co1 sequences that we acquired , type a sequences were 13 and type b sequences were 8 . the type a and type b showed 94.6 % ( 614/649 bp ) and 94.3 % ( 612/649 bp ) similarity to the reference sequence of the h. rjukjuana l00115a ( from taiwan , hq322443 , fig .5 ) , respectively . for evaluating the genetic relationship of gageo - do land leeches , both 18s rrna and co1 gene nucleotide sequencesthe nj trees of terrestrial leech 18s rrna and co1 supported that h. rjukjuana is monophyletic in a single clade with high bootstrap values ( figs . 4 , 5 ) .4 ) , the genetic distance ( ps ) between h. rjukjuana gageo and h. rjukjuana hary was 0.1 % ( data now shown ) . in contrast , the ps between the h. rjukjuana hary and h. sylvestris and between h. rjukjuana gageo and h. sylvestris were 0.4 and 0.5 % , respectively ( data not shown ) .5 ) , the ps betweeen the h. rjukjuana l00115a and h. limuma hach is 14.6 % ( data now shown ) . however , the ps between the h. rjukjuana l00115a and gageo - do land leech 1 or 27 were 5.6 % and 6.0 % , respectively ( data not shown ) . the phylogenetic tree also revealed that co1 sequences of the gageo - do land leeches had the closest relationship with h. rjukjuana in taiwan . in general , leeches are divided into 2 groups , rhynchobdellida blanchard ( jawless ) and arhynchobdellida blanchard ( jawed ) . arhynchobdellid leeches have a muscular jaw for feeding and are classified into the erpobdelliformes caballero and the diverse hirudiniformes caballero . hirudiniformes are subdivided into 5 families ; americobdellidae canallero , cylicobdellidae ringuelet , haemadipsidae blanchard , haemopidae richardson , and hirudinidae whitman . the remaining blood - feeding hirudiniformes can be classified depending on their habitat preference as the semi - aquatic hirudinidae and the terrestrial ( or land ) haemadipsidae . also , saywer further consolidated haemadipsinae with haemadipisidae to create a single family , which is divided into the dougnathous ( 2 - jawed ) and trignathous ( 3 - jawed ) series , and included all land leech species . the trignathous leeches of the genus haemadipsa tennent ( 1859 ) are widespread throughout the indian subcontinent into southeast asia and up to north - east asia . torix tagoi ( oka , 1925 ) , h. nipponia whitman 1886 , w. pigra ( murada , 1936 ) , glossiphonia werevi , and hemiclepsis japonica have been documented in korea . however , these previous studies focused on morphological features of freshwater leeches but not terrestrial leeches . it has been previously known that terrestrial leeches inhabit the gageo - do in korea but none of researchers have done their taxonomy . gageo - do is a west - southernmost island of korea and located over the migratory routes of birds moving from southeast asia to siberia . the total area and coastline length of gageo - do is 9.18 km and 22.0 km , respectively . there is no weather station on gageo - do , and according to the heuksan - do weather station which is the nearest location from gageo - do ( 70 km away ) , the mean temperature is 3.3 - 6.0 during winter and 22 - 27 during summer . the annual average temperature is 13.6 , and the annual total precipitation is 1,126 millimeters . frommay to august , there are lots of foggy weathers , and the fog tends to spread locally . especially , dock - sil mountain ( a.s.l .639 m ) in gageo - do is the highest mountain in shinan - gun , and its internal forest generally shows a very humid condition throughout the year . generally , terrestrial leeches are known to inhabit in tropical regions with high humidity , and in this regard the mt . dock - sil possess an interior and a posterior sucker and move like extremely elastic inchworm . they suck the blood of human legs for about 30 min , after their blood - feeding , a bleeding scar is formed ( fig . they were regarded as the family haemadipsidae but there were no preliminary data comparable to other land leeches . as the result of 18s rrna gene analysis of gageo - do leeches ( n = 28/29 leeches ) ,26 sequences had 99.9 % similarity to the haemadipsa rjukjuana isolate hary ( from taiwan , hq203097 ) . the other 2 sequences were closer to the orobdella tsushimensis ( from japan , ab663653 , data not shown ) . as the result of co1 gene analysis ( n = 24/29 leeches ) , the 21 sequences were further divided into 2 types , gageo 1 and gageo 27 , by only 1 bp . both haplotypes had a 94.6 % or 94.3 % similarity to the h. rjukjuana l00115a ( from taiwan , hq322443 ) . the remaining 3 sequences were similar to the o. tsushimensis ( japan , ab679660 , data not shown ) . the phylogenetic trees also showed that gageo - do leeches were closest to h. rjukjuana ( figs . 4 , 5 ) . it is unclear when the sanguivorous leeches start living on gageo - do , but a possible hypothesis is that they were spread from other regions by humans ( e.g. , fisherman or tourists ) or animals ( e.g. , migratory birds ) . in addition , according to the distribution map of haemadipisidae ( borda and siddall 2010 ) , sub - distribution of the genus haemadipsa which have 3 - jawed are widespread throughout india subcontinent into southeast asia and up to northeast asia . however , the boundary line of northeast asia is lined up to japan . according to results of this studythe main host of haemadipsa land leeches are medium - or large - sized mammals primarily , including humans . we should try to identify animal species blood - sucked by leeches . also , haemadipsa land leeches should be confirmed whether they play as a vector or not for transmitting zoonotic pathogens . the present study supports the presence of blood - feeding terrestrial leeches with a high genetic similarity to h. rjukjuana in korea . this is the first record of sanguivorous land leeches ( hirudiniformes : haemadipisidae ) in korea .\noutput:\n" }, { "from": "agent", "value": "there are 60 species of blood - feeding land leeches , 50 species belonging to the family haemadipsidae and 10 species belonging to the family xerobdellidae . despite recent papers on the land leeches , their taxonomic identification is not fully understood , especially at a species level . in korea , there have been no historical records of the terrestrial leeches , but recently an unrecorded blood - feeding land leech was discovered at gageo - do ( island ) , korea . molecular analysis was used to identify the species of 29 leeches collected from mt . dock - sil in gageo - do . conventional pcr was conducted using nuclear 18s rrna and mitochondrial cytochrome c oxidase subunit 1 ( co1 ) genetic marker . the 18s rrna sequences revealed that the leeches share 99.9 % identity with haemadipsa rjukjuana ( inhabiting taiwan ) , and the co1 sequences revealed that the leeches are very close to h. rjukjuana ( inhabiting taiwan ) . the co1 sequences were separated into 2 categories , 1 with 94.6 % and the other with 94.3 % similarity to the h. rjukjuana l00115a ( inhabiting taiwan ) . this new finding of the land leech is the first record in korea . in addition , the north range of the distribution of the blood - feeding leech ( hirudiniformes : haemadipisidae ) should be reconsidered including korea ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: second , we reviewed published studies identified through a literature review to estimate the components of a typical outpatient visit ( initial evaluation and diagnostics tests and follow - up care ) . finally , we consulted standard cost sources to provide costs for each resource ( initial treatments , adjunctive therapies , visits ) identified . the patients described in the retrospective cohort analysis were receiving prescription benefits and were included in a prescription claims database of a large pharmaceutical benefits manager ( pbm ) . all data were de - identified in accordance with protected health information standards under the health information portability and accountability act 1996 so that no individually identifiable information was included in the study database . therefore , review by an institutional review board was not required . the study cohort included patients who first initiated therapy with one of four prostaglandin analog products ( bimatoprost , latanoprost , travoprost , or bak - free travoprost ) between may 1st , 2007 and october 31st , 2007 . to qualify , patients had to have more than one prostaglandin analog prescription claim and six months of prior claims data in which there were no glaucoma therapy claims . glaucoma therapy claims were defined by therapeutic class plus generic code number ( gcn ) codes . gcns are a system of unique numbers assigned to medications according to strength , formulation , route of administration , and size by drug pricing service first databank . the study population was further defined by requiring patients to have at least 12 months of uninterrupted use of the index prostaglandin analog following the initial prescription . this was operationalized as not having prescriptions for the other prostaglandin analogs during the year and having at least one prescription for the index prostaglandin analog in the fourth quarter of the follow - up period . patients who did not meet these requirements ( sufficient prior claims data , uninterrupted use , and use of the index prostaglandin analog during the fourth quarter of observation ) were excluded from the study database . patients who switched from one formulation of travoprost to the other were also excluded from the analysis . we considered that patients added an adjunctive medication , defined by therapeutic class plus gcn codes , if there was a sequential and subsequent refill of an adjunctive agent in the presence of continued refills for the index agent . the american academy of ophthalmology preferred practice patterns for glaucoma suggest that follow - up care should be based on achievement of target iop and the amount of disease progression ,18 neither of which was available in the prescription database used for this study . therefore , the base case analysis used resource rates from a survey - based study19 while sensitivity analyses explored visits as recommended by other studies and guidelines .18,20 since all patients in the model are assumed to have undergone the same procedures and tests at their visits regardless of the prostaglandin analog they received , the relatively small differences across studies in terms of the components of each visit have minimal impact on study findings . at the initial visit , patients were assumed to have a level 4 ( comprehensive ) evaluation ( cpt 92004 ) . follow - up visits were assumed to be level 2 ( intermediate ) visits ( cpt 92012 ) , with three follow - up visits during the year ( likely but not necessarily at 30 and 90 days following initiation of the index therapy and at 12 months ) . in addition , two follow - up visits were assumed to be associated with the initiation and monitoring of adjunctive medication among patients for whom it was prescribed . table 1 presents the procedures and diagnostic tests that comprised each visit as well as the costs used for each . we use average wholesale price ( awp ) for 2008 as the prescription costs .21 the range of published awps for the prostaglandin analogs was fairly narrow ( us $ 72.20 to $ 76.69 ) .21 for the prostaglandin analogs , the average cost for the agents was used in the model because awp does not take into consideration contract pricing and rebates , which minimize , if not eliminate , differences in cost to the insurer . further , the number of prescriptions for prostaglandin analogs was normalized to a 2.5 ml bottle , as this was the most common size found in the claims database . medical costs were estimated using the 2008 medicare fee schedule .22 all the costs used in the model are presented in table 1 . number of bottles required was rounded to the nearest tenth . the analysis identified patients by the prostaglandin whose prescription they first filled during the study period . statistical comparisons of the demographic characteristics of the four cohorts were conducted in sas software ( v9 .2 ; sas institute , cary , nc ) . gender was compared using a chi - squared test and age was compared using analysis of variance ( anova ) , with bonferroni s correction for multiple comparisons . median and mean number of days to initiation of adjunctive therapy were calculated for each cohort , with the distribution of number of days examined to determine which measure to use in the model . the median numbers of days until patients added adjunctive therapies were compared using the wilcoxon rank sum test and mean times were compared using anova . first , the proportion of patients remaining on monotherapy for the entire year was changed to the lowest and highest values among the initial treatments , that is , the proportion of patients remaining on monotherapy was changed to 79.3 % ( the base case value for bimatoprost ) and then to 91.1 % ( the base case value for bak - free travoprost ) for all treatments . second , the days to initiating adjunctive therapy was varied in two ways : a ) median number of days to the addition of adjunctive medication was changed to the lowest and highest values among the treatments and b ) the mean number of days was substituted for the median . third , the cost of treatments were varied by a ) assuming that the least and most expensive adjunctive therapies were the only therapies used and b ) rounding up bottles of index and adjunctive therapies to whole numbers . fourth , sensitivity analysis was conducted on the cost of visits , using resource use estimates from other published sources .18,20 the preferred practice patterns published by the american academy of ophthalmology were used to establish minimum and maximum values for the frequency of visits and resource visits . the minimum values assumed that patients were meeting iop targets and the maximum values assumed that patients were not meeting iop targets and that there was progression of disease . the patients described in the retrospective cohort analysis were receiving prescription benefits and were included in a prescription claims database of a large pharmaceutical benefits manager ( pbm ) . all data were de - identified in accordance with protected health information standards under the health information portability and accountability act 1996 so that no individually identifiable information was included in the study database . therefore , review by an institutional review board was not required . the study cohort included patients who first initiated therapy with one of four prostaglandin analog products ( bimatoprost , latanoprost , travoprost , or bak - free travoprost ) between may 1st , 2007 and october 31st , 2007 . to qualify , patients had to have more than one prostaglandin analog prescription claim and six months of prior claims data in which there were no glaucoma therapy claims . glaucoma therapy claims were defined by therapeutic class plus generic code number ( gcn ) codes . gcns are a system of unique numbers assigned to medications according to strength , formulation , route of administration , and size by drug pricing service first databank . the study population was further defined by requiring patients to have at least 12 months of uninterrupted use of the index prostaglandin analog following the initial prescription . this was operationalized as not having prescriptions for the other prostaglandin analogs during the year and having at least one prescription for the index prostaglandin analog in the fourth quarter of the follow - up period . patients who did not meet these requirements ( sufficient prior claims data , uninterrupted use , and use of the index prostaglandin analog during the fourth quarter of observation ) were excluded from the study database . patients who switched from one formulation of travoprost to the other were also excluded from the analysis . we considered that patients added an adjunctive medication , defined by therapeutic class plus gcn codes , if there was a sequential and subsequent refill of an adjunctive agent in the presence of continued refills for the index agent . the american academy of ophthalmology preferred practice patterns for glaucoma suggest that follow - up care should be based on achievement of target iop and the amount of disease progression ,18 neither of which was available in the prescription database used for this study . therefore , the base case analysis used resource rates from a survey - based study19 while sensitivity analyses explored visits as recommended by other studies and guidelines .18,20 since all patients in the model are assumed to have undergone the same procedures and tests at their visits regardless of the prostaglandin analog they received , the relatively small differences across studies in terms of the components of each visit have minimal impact on study findings . at the initial visit , patients were assumed to have a level 4 ( comprehensive ) evaluation ( cpt 92004 ) . follow - up visits were assumed to be level 2 ( intermediate ) visits ( cpt 92012 ) , with three follow - up visits during the year ( likely but not necessarily at 30 and 90 days following initiation of the index therapy and at 12 months ) . in addition , two follow - up visits were assumed to be associated with the initiation and monitoring of adjunctive medication among patients for whom it was prescribed . table 1 presents the procedures and diagnostic tests that comprised each visit as well as the costs used for each . we use average wholesale price ( awp ) for 2008 as the prescription costs .21 the range of published awps for the prostaglandin analogs was fairly narrow ( us $ 72.20 to $ 76.69 ) .21 for the prostaglandin analogs , the average cost for the agents was used in the model because awp does not take into consideration contract pricing and rebates , which minimize , if not eliminate , differences in cost to the insurer . further , the number of prescriptions for prostaglandin analogs was normalized to a 2.5 ml bottle , as this was the most common size found in the claims database . medical costs were estimated using the 2008 medicare fee schedule .22 all the costs used in the model are presented in table 1 . the analysis identified patients by the prostaglandin whose prescription they first filled during the study period . statistical comparisons of the demographic characteristics of the four cohorts were conducted in sas software ( v9 .2 ; sas institute , cary , nc ) . gender was compared using a chi - squared test and age was compared using analysis of variance ( anova ) , with bonferroni s correction for multiple comparisons . median and mean number of days to initiation of adjunctive therapy were calculated for each cohort , with the distribution of number of days examined to determine which measure to use in the model . the median numbers of days until patients added adjunctive therapies were compared using the wilcoxon rank sum test and mean times were compared using anova . first , the proportion of patients remaining on monotherapy for the entire year was changed to the lowest and highest values among the initial treatments , that is , the proportion of patients remaining on monotherapy was changed to 79.3 % ( the base case value for bimatoprost ) and then to 91.1 % ( the base case value for bak - free travoprost ) for all treatments . second , the days to initiating adjunctive therapy was varied in two ways : a ) median number of days to the addition of adjunctive medication was changed to the lowest and highest values among the treatments and b ) the mean number of days was substituted for the median . third , the cost of treatments were varied by a ) assuming that the least and most expensive adjunctive therapies were the only therapies used and b ) rounding up bottles of index and adjunctive therapies to whole numbers . fourth , sensitivity analysis was conducted on the cost of visits , using resource use estimates from other published sources .18,20 the preferred practice patterns published by the american academy of ophthalmology were used to establish minimum and maximum values for the frequency of visits and resource visits . the minimum values assumed that patients were meeting iop targets and the maximum values assumed that patients were not meeting iop targets and that there was progression of disease . figure 1 provides a brief flow chart of the patient selection process for the retrospective cohort analysis . of more than 75 million plan participantsapproximately 6 % of these patients switched from their index prostaglandin analog within the 12 - month study period to another glaucoma therapy . additionally , about 54 % of the patients stopped taking all glaucoma medications within the 12 - month period . the analysis examined only those newly initiating patients who remained on their initial prostaglandin analog therapy for one year , which represents approximately 41 % of the glaucoma patients newly initiating with prostaglandin analogs identified from the database . there were no statistically significant differences among groups in terms of age or gender . in the bimatoprost , latanoprost , travoprost , and bak - free travoprost treatment groups , 20.7 % , 16.5 % , 13.9 % , and 8.9 % , respectively , initiated adjunctive therapy during the course of the year at significantly different proportions ( p 0.0001 , see table 3 ) . patients on bak - free travoprost were able to continue without adjunctive therapy longer than patients treated with other prostaglandins . the median numbers of days until patients added adjunctive therapies were 158.5 days for patients initiating therapy with bak - free travoprost , 123.0 days for travoprost , 69.5 days for bimatoprost , and 67.0 days for latanoprost ( p 0.05 , wilcoxon rank sum test ) . the mean numbers of days to initiating adjunctive therapy were 156.3 days in the bak - free travoprost group and 131.5 days in the travoprost group . for bimatoprost and latanoprost , the mean number of days was 120.8 and 108.3 , respectively . mean time to initiating adjunctive therapy was not significantly different across the cohorts . as shown in table 4 , patients had an average of 8.0 to 9.7 prescription claims ( normalized to 2.5 ml bottles ) for prostaglandin analog therapy during the 12 - month follow - up period . based on the time to initiating adjunctive therapy , anywhere from 4.6 to 10.5 bottles of adjunctive medication were required for the remainder of the year . reflective of the shorter time to initiation of adjunctive therapy , the number of prescriptions for adjunctive therapies was highest for latanoprost , while fewer bottles were required for bak - free travoprost patients , who began adjunctive therapy later . estimated annual costs for patients initiating travoprost were lowest ( $ 1,278 ) , with increasing annual costs for bak - free travoprost ( $ 1,307 ) , latanoprost ( $ 1,359 ) , and bimatoprost ( $ 1,457 ) . the cost of travoprost was lower than bak - free travoprost primarily due to slightly fewer 2.5 ml equivalent bottles being used on average during the year ( 8.0 vs 8.7 ) findings remained consistent , with travoprost having the lowest annual cost and bimatoprost having the highest cost in all scenarios . the range narrowed ( to less than $ 100 ) when the number of bottles of index prostaglandin was equalized across cohorts or when the cost for visits was based on guidelines and widened ( to more than $ 200 ) when the number of bottles of index prostaglandin was rounded up to the nearest whole number . this analysis adds to a growing body of literature finding consistent differences in treatment patterns and costs for glaucoma patients initiating treatment with prostaglandin analogs with varying rates of use of adjunctive therapy . the cohort analysis found that patients receiving bak - free travoprost remained on monotherapy in greater proportions and for a longer duration compared to other prostaglandin analogs . compared to the previous studies in this series ,9,10 a number of findingsfirst , the high rate of monotherapy adherence in the initial study in the series9 seems to have been an aberration , with both the second10 and present studies finding more than half of the patients identified as discontinuing glaucoma therapies within one year , in agreement with other published studies .3,2325 second , the advantage travoprost demonstrated in terms of less use of adjunctive therapies associated with new patients starting on this therapy was consistent across studies , and the introduction of the bak - free formulation only increased this advantage . a possible explanation for longer duration of monotherapy and fewer patients requiring adjunctive therapy is greater patient adherence due to lower rates of osd associated with bak - free travoprost .13,16,17 the use of pharmacy claims databases alone to estimate adherence poses methodological challenges24 and is further complicated by the fact that assuming appropriate refill patterns do not imply appropriate instillation of eye drops .2631 regardless of the reason , bak - free travoprost has been shown to be at least as safe and efficacious as travoprost13 ,17 and if it can also improve adherence by being a more eye - friendly drug , then real - world effectiveness might be enhanced . while the safety of the bak - free preservative has been widely demonstrated , various reports have identified cystoid macular edema after treatment with prostaglandin analogs .3235 bak - free travoprost is associated with less osd , but high - risk patients must still be monitored for other adverse events , as with any of the medications in the class . the patients in this analysis , while generally reflective of the larger glaucoma patient population in terms of demographic characteristics ,36 may not reflect the larger population in other facets . the study attempted to identify only patients who were new to therapy , although even a criterion as simple as this is difficult to implement .24 these patients had prescription coverage , and since finances are one reason cited for nonadherence with glaucoma therapy ,2 this may be an important difference . also , based on the study methodology , patients may have had poor adherence ; patients in the cohort analysis were required to have a minimum of two glaucoma prescriptions filled during the follow - up period , but no attempt was made to assess medication possession ratio or to evaluate persistence with therapy over time . as shown in multiple other studies , more than half of the patients identified in studies of glaucoma therapy discontinue .10,2325,37 the subset of patients identified through this analysis may not be representative of glaucoma patients in other aspects . the use of a large claims database offers an important strength in terms of sample size . however , there are also disadvantages to the use of a pharmaceutical claims database without additional clinical input . patients are not randomly - assigned to treatment and although sample size should help minimize any bias , it is possible that there are systematic preferences for treatments that can not be detected without additional clinical information . the reasons for adding adjunctive therapy or switching or discontinuing therapies can not be surmised from the claims database alone . knowing more about these reasons might inform the study question however , it is impossible to know these answers . in addition , claims databases report on prescriptions filled , but can not be used as a definitive statement of adherence .26,2830 this is further complicated with the study of eye drops , where effective instillation of drops is a problem even among patients who try to adhere to therapy .27,31 the patient population in any given database may not match the overall population of patients with the condition in question nor were patients randomized to treatment , although age and gender distributions here were similar across treatment groups and seem comparable with the glaucoma population . finally , claims databases also may contain coding biases or errors , although there is no reason to believe that these errors would be different across index treatments also . adjunctive therapies were found to be a relatively small contributor to costs in this analysis ; however , it is one of the few areas in which products can be differentiated . these findings showed that prostaglandin analogs with a greater proportion of patients remaining on monotherapy and a longer time to initiation of adjunctive agents had lower first - year direct medical costs from a third party payer s perspective . accordingly , costs from the patient s perspective ( eg , co - pay for visits and prescriptions ) would also be lower with longer duration of monotherapy . further study is needed to identify to what extent tolerability , specifically the absence of bak , contributes to use of adjunctive medications among glaucoma patients .\noutput:\n" }, { "from": "agent", "value": "objective : to estimate first - year costs among new initiators of topical prostaglandin analogs in a managed care population.research design and methods : we developed a model to estimate first - year direct medical costs . we derived treatment patterns from a claims database analysis . published studies were used to estimate visit - related resource use . costs were obtained from standard sources.results : the database analysis identified 9,063 patients meeting study criteria , 41 % ( n = 3,672 ) of whom remained on their initial prostaglandin therapy for 12 months after initiation . adjunctive intraocular pressure lowering therapy was needed in 20.7 % , 16.5 % , 13.9 % , and 8.9 % of bimatoprost , latanoprost , travoprost , and bak - free travoprost patients , respectively . median numbers of days to the first prescription filled for adjunctive therapy ( if required ) were 69.5 , 67.0 , 123.0 , and 158.5 for patients initiating on bimatoprost , latanoprost , travoprost , and bak - free travoprost . total estimated first - year costs were $ 1,457 , $ 1,360 , $ 1,278 , and $ 1,307 for patients initiating therapy with bimatoprost , latanoprost , travoprost , and bak - free travoprost . findings were consistent through sensitivity analysis.conclusions : a bak - free prostaglandin analog may permit longer duration of monotherapy and be associated with lower first - year direct medical costs . use of a claims database and the selection of new initiators of prostaglandin analogs limit projecting findings to all glaucoma patients ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: in most patients with inherited platelet dysfunction , the underlying molecular and genetic mechanisms remain unknown . end responses of platelet aggregation and secretion studies and the investigation of postulated abnormal pathways and proteins . these approaches have been driven by existing knowledge of platelet mechanisms and come with limitations . at the genetic level , the focus has largely been on delineating mutations in the coding sequence of genes encoding the candidate proteins . evidence is now available that in some patients with inherited platelet dysfunction the primary abnormality is a mutation in a hematopoietic transcription factor ( tf ) , which can lead to altered downstream expression of numerous genes that affect diverse cellular pathways and can result in abnormalities in both platelet number and function . major hematopoietic tfs include the runt - related transcription factor 1 ( runx1 ) , friend leukemia integration 1 ( fli1 ) , gata - binding factor 1 ( gata - 1 ) , and growth factor independent 1b ( gfi1b ) ; these tfs act in a combinatorial manner to regulate hematopoietic lineage differentiation , megakaryopoiesis , and platelet production . tf mutations may be more common in patients with inherited platelet dysfunction than previously considered . for example , stockley and colleagues recently reported results of next - generation sequencing studies in 13 unrelated patients suspected of having an inherited platelet defect from the uk genotyping and phenotyping of platelets ( uk - gapp ) study . heterozygous runx1 or fli1 mutations were uncovered in 6 of the 13 patients with excessive bleeding and impaired dense granule secretion and aggregation on activation ; 5 of these patients also had thrombocytopenia . these findings highlight the importance of tf mutations in the pathogenesis of inherited platelet function defects . runx1also known as core - binding factor subunit alpha - 2 ( cbfa2 ) and acute myeloid leukemia 1 ( aml1 ) is a critical hematopoietic tf required for definitive hematopoiesis encoded by the runx1 gene located on chromosome 21 ( 21q22 .12 ) . in a murine model , generation of homozygous runx1 mutants was lethal in utero because of hemorrhage . in humans , heterozygous runx1 mutation is associated with an autosomal dominant disorder , the familial platelet disorder with predisposition to acute myeloid leukemia ( fpd / aml ) ( mendelian inheritance in man [ mim ] 601399 ) , characterized by impaired megakaryopoiesis , quantitative and qualitative defects in platelet function , and over 40 % risk of development of myelodysplastic syndrome ( mds ) or aml at a median age of 33 years . several distinct runx1 mutations , ranging from point mutations to deletional mutations , have been identified in patients with fpd / aml , and most are in the conserved runt domain near the n - terminus , resulting in impaired binding of runx1 to cis - regulatory dna sequences . in addition to the runt domain , a mutation in the c - terminal transactivating domain ( y260x ) has been identified . most runx1 mutations result in haplodeficiency , whereas some mutations may produce dominant - negative activity that has been proposed to increase leukemia risk . interestingly , several syndromic cases of deletion of chromosome 21q22 including runx1 have also been described , and affected individuals may have congenital thrombocytopenia and platelet dysfunction but develop mds or aml at a much lower age ( three cases ranging from 5 to 8 years ) than observed in fpd / aml . numerous platelet abnormalities have been reported in patients with runx1 mutation , including dense or - granule storage pool deficiency ( spd ) or both , impaired platelet responses of aggregation and secretion , reduced protein phosphorylation of myosin light chain and pleckstrin , and decreased activation of iib3 . platelet production of 12 - hydroxyeicosatetraenoic acid and one specific protein kinase c isoform ( pkc - ) have also been shown to be decreased . platelet granule deficiency leading to impaired platelet function is an important abnormality associated with runx1 mutations . in 1969 , weiss and colleagues described one of the first families with inherited platelet dysfunction due to reduced platelet adp and atp , indicating a dense granule spd . this affected family and some others described with spd of dense or - granules were later shown to carry runx1 mutations . other studies have also shown decreased - granule contents in association with runx1 mutations . in one patient , platelet albumin and igg , two constituents of the - granule , were decreased , which suggests a possible defect in uptake and storage of these proteins into - granules because neither protein is synthesized by megakaryocytes ( mks ) . platelet transcript profiling of a patient with runx1 haplodeficiency has shown numerous genes relevant to multiple pathways to be downregulated . several of these genes with prominent roles in platelet structure and function have been shown to be direct transcriptional targets of runx1 . these genes include alox12 ( 12 - lipoxygenase ) , pf4 ( platelet factor 4 ) , platelet myl9 ( myosin light chain ) , and prkcq ( protein kinase c - theta ) . low expression of c - mpl ( thrombopoietin receptor ) in runx1 mutation has been documented , providing an additional mechanism for thrombocytopenia in patients with fpd / aml . more recently , nf - e2 , which encodes a tf implicated in platelet granule development and iib3 signaling , has also been shown to be a transcriptional target of runx1 . thus , the defect in platelet number and function associated with runx1 haplodeficiency may result from abnormalities in multiple mechanisms . recently , connelly and colleagues showed that targeted in vitro correction of runx1 mutation could recover the mk defects . the investigators differentiated induced pluripotent stem cells ( ipscs ) from skin fibroblasts of two fpd / aml patients with y260x mutation and showed reduced mk production and abnormalities in mk structure , such as abundance of vacuoles and deficiency of dense and - granules . as compared with the patients with fpd / aml , the two corrected clones resulted in approximately 40 % to 60 % more cd41cd42 mks with rescue of phenotypic features of abnormal mk differentiation . gene expression profiling also showed significant upregulation of mk genes in the corrected clones as compared with one of the patients with fpd / aml , and runx1 accounted for the differences . these studies constitute strong evidence that runx1 mutation is the cause of defective megakaryopoiesis in patients with fpd / aml . the studies also raise the intriguing potential for gene - targeting therapy for these patients in the future . it should be noted that , from a clinical standpoint , defects in platelet number and function in patients with fpd / aml can be heterogenous . patients commonly have mild to moderate thrombocytopenia with normal - sized platelets and , despite the platelet dysfunction , a mild to moderate bleeding tendency . these features have important implications for treatment , as previously described pedigrees have documented recurrence of leukemia following hematopoietic stem cell transplantation from an undiagnosed sibling donor with fpd / aml . fli1 is part of the e - twenty - six ( ets ) family of tfs that plays a major role in megakaryopoiesis through its influence on the expression of multiple genes , including itga2b ( glycoprotein iib ) , gp1ba ( glycoprotein 1b alpha chain ) , gp9 ( glycoprotein 9 ) , and c - mpl ( thrombopoietin receptor ) . distal deletion of either the maternally or paternally derived chromosome 11 that includes the fli1 locus ( 11q23 .3 - 24 ) is associated with a rare autosomal dominant disorder , the jacobsen syndrome ( mim 147791 ) , and its accompanying platelet disorder , the paris - trousseau syndrome ( mim 188025 ) . the clinical features of jacobsen syndrome include mental retardation , abnormal craniofacial appearance , and abnormalities in multiple organ systems . the paris - trousseau syndrome is characterized by congenital macrothrombocytopenia with giant - granules of 1 to 2 m in diameter in a subpopulation of circulating platelets ( 1 % to 5 % ) and bone marrow dysmegakaryopoiesis . on the platelet function aspect , thrombin - induced platelet release of - granule contentsplatelet survival is normal , although there is a substantial expansion of bone marrow mks because of arrested mk development . a dimorphic population of normal and dysmorphic mks is present as a result of only one of the two fli1 alleles being expressed in a single mk precursor in early development . gata - 1 is a member of the gata tf family that binds to the gata sequence on dna . gata - 1 is an important regulator of both mk and erythroid development , and the encoding gene is located on the short arm of the x chromosome ( xp11 .23 ) . two mutations in gata - 1 ( v205 m and d218 g ) have been connected to an x - linked syndrome consisting of macrothrombocytopenia and dyserythropoiesis with or without anemia ( mim 300367 ) . such mutations have resulted in impaired gata - 1 interaction with the essential co - factor friend of gata - 1 ( fog1 ) . multiple platelet defects have been described in this syndrome , including selectively impaired responses to ristocetin and collagen owing to glycoprotein ib and glycoprotein vi abnormalities , respectively . there is also reduced expression of platelet gs mrna and protein suggestive of incomplete maturation of mks . a sex - linked form of the gray platelet syndrome ( gps ) , a congenital platelet disorder characterized by macrothrombocytopenia and deficiency of - granules , in association with gata - 1 r216n mutation has also been described . the r216n mutation is unique in that it results in decreased affinity between gata - 1 and its palindromic site rather than disrupting interaction with its co - factor fog1 . another identified gata - 1 mutation involves a splice site ( 332g - c , v74l ) that produces a truncated variant of gata - 1 and has been associated with the x - linked syndrome of anemia with or without neutropenia or platelet abnormalities or both ( mim 300835 ) . gfi1b is a tf , which functions as a transcriptional repressor , that has been shown to be essential for mk and erythroid development . the encoding gene is located on the long arm of chromosome 9 ( 9q34 .13 ) . two recent studies have implicated mutations in the zinc finger 5 dna - binding domain region of gfi1b in autosomal dominant platelet disorders characterized by dysmegakaryopoiesis , macrothrombocytopenia , - granule deficiency , and variable bleeding tendency through distinct genetic mechanisms that produce a dominant - negative effect . the first study identified a single nucleotide insertion in exon 7 ( c880 - 881insc ) that predicts a frameshift mutation in the fifth zinc finger dna binding domain of gfi1b in a family with a bleeding disorder originally described in 1976 . the family members were also found to have evidence of red cell anisopoikilocytosis , impaired platelet aggregation responses , and decreased platelet p - selectin , fibrinogen , glycoprotein ib , and glycoprotein iiia . the second study uncovered a truncating mutation ( c. 859c t ) , also within the fifth zinc finger dna binding domain of gfi1b , in a family originally reported in 1968 and subsequently diagnosed with gps . the family members also had reduced platelet factor 4 and thromboglobulin as well as evidence of bone marrow myelofibrosis and emperipolesis ( intact cell within cytoplasm of another cell ) . identification of autosomal dominant genetic mechanisms in gps is particularly noteworthy as previously described pedigrees in gps have primarily been autosomal recessive , and three groups have reported biallelic mutations in the nbeal2 gene , which encodes a beach protein involved in vesicular trafficking . interestingly , it was recently demonstrated in a murine knockout model that nbeal2 deficiency results in loss of - granules from platelets after initial formation and proinflammatory mks , which may drive gps features including myelofibrosis , splenomegaly , and emperipolesis , with - granule loss also leading to protection from cancer metastasis . alpha - granule deficiency due to mutations in the gene encoding the vps33b protein ( a member of the sec1 / munc18 protein family ) and the vps16b gene in the arthrogryposis multiplex congenita , renal dysfunction , and cholestasis ( arc ) syndrome has also been described . these studies highlight the heterogeneous mechanisms that can lead to - granule deficiency and gps , including tf mutations involving runx1 , gata - 1 , and gfi1b . from a different perspective , it is clear that these tf mutations are generally associated with a combination of thrombocytopenia and defects in platelet function , although in some instances there are associated abnormalities in red cells as well , as is the case for mutations in gata - 1 and gfi1b . in summary , evidence is now available that in some patients with impaired platelet aggregation and secretion responses on an inherited basis the primary genetic defect may be in a tf . most , but not all , of these patients have a variable degree of thrombocytopenia . the abnormalities in platelet number and function arise because of alterations in multiple pathways regulated by the tf . some of the tf mutations have prognostic and treatment implications beyond the platelet defect , such as the association of myeloid malignancies with mutations in runx1 and donor selection for hematopoietic stem cell transplant .\noutput:\n" }, { "from": "agent", "value": "the molecular and genetic mechanisms in most patients with inherited platelet dysfunction are unknown . there is increasing evidence that mutations in hematopoietic transcription factors are major players in the pathogenesis of defective megakaryopoiesis and platelet dysfunction in patients with inherited platelet disorders . these hematopoietic transcription factors include runx1 , fli1 , gata - 1 , and gfi1b . mutations involving these transcription factors affect diverse aspects of platelet production and function at the genetic and molecular levels , culminating in clinical manifestations of thrombocytopenia and platelet dysfunction . this review focuses on these hematopoietic transcription factors in the pathobiology of inherited platelet dysfunction ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: cerebral venous and sinus thrombosis ( cvst ) is a potentially life - threatening disorder accounting for about 0.5 % among all types of strokes . despite an increasing use of magnetic resonance imaging ( mri ) although generally considered a disease with good outcome in developed countries , in under developed , and low - income countries during the hospitalization mortality rate may be up to 14 % which could be due to delay in diagnosis . on the other hand , the prevalence of cvst in iran was reported to be 12.3 per million of the populations , which seems higher than western countries . regarding the prevalence and higher mortality rate in the developing countries , clarification of variable risk factors of cvst with extensive assessment in these countries is necessary . the aim of this study is to evaluate clinical characteristics including etiology , neuroimaging , and outcome of patients with cvst and address the limitations of previous studies such as the presence of multiple risk factors . this study was conducted in a tertiary general referral hospital affiliated with tehran university of medical sciences in tehran , iran , which serves many patients from all over the country . from july 2004 to september 2007 , retrospective data were gathered for all patients with a diagnosis of cvst ( 2016 icd -10-cm diagnosis code : g08 ) from the documents recorded in the hospital registry system . a prospective study was conducted from october 2007 to november 2010 where all patients with diagnosis of cvst were included in the study . the data included clinical signs and symptoms , from onset of symptoms , hospital admission , month of presentation , medical and drug history , laboratory results in particular hypercoagulable state factors , neuroimaging , cerebrospinal fluid ( csf ) findings , and outcome of patients . the diagnosis of cvst for all these patients was confirmed according to following imaging protocol : consulting with two neurologists and one radiologist , mri / magnetic resonance venography , and / or conventional angiography were used for the confirmation of the diagnosis of cvst in all the patients . in case of any discrepancy between the clinicians regarding the diagnosis of cvst in any patient that cased - dimer was categorized as low ( 0.5 mg / l ) , intermediate ( 0.62.0 mg / l ) , and high ( 2.0 mg / l ) . based on the delay from symptom onset to hospital admission , mode of onsetwas categorized as acute ( 2 days ) , subacute ( 214 days ) , or chronic ( 14 days ) . all assessed prospective patients were asked to sign a written informed consent . in case of retrospective data collection , after calling the patients or their family , permissions for data acquisition were catched . values with normal distribution were analyzed with chi - square and t - test . otherwise , manna total of 53 patients , 13 males and 40 females were observed during this study . of this group , headache was found as the most prevalent clinical feature of cvst among the patients ( n = 44 , 83 % ) followed by papilledema and vomiting ( n = 36 , 68 % , and n = 29 , 55 % , respectively ) . the mode of clinical presentation was acute , sub - acute , and chronic in 14 ( 26.4 % ) , 22 ( 41.5 % ) , and 17 ( 32 % ) patients , respectively . median days from the onset of symptoms to hospital admission were 11 days with the range of one to 92 days . clinical features of patients with cerebral venous and sinus thrombosis distribution of patients with cerebral venous sinus thrombosis in different months the most frequent identified risk factor of cvst patients in this study , both females and males were the underlying disease . from 40 female patients , 40 % ( n = 16 ) had a predisposing condition for cvst and 37.5 % ( n = 15 ) had used oral contraceptive drug ( ocp ) . four patients used ocp and simultaneously had other underlying causes including behcet disease , hypothyroidism , preeclampsia , and postpartum state . moreover , 8 patients had both positive thrombophilic state and ocp consumption . n = 19 ) had more than one contributing factors for cvst and 20 % of them ( n = 11 ) had no identifiable cause ( idiopathic ) . underlying risk factors of cerebral venous thrombosis in patients procoagulatory factors and vasculitis conditions looked for in 32 of the patients and found abnormal results in 16 of them ( 50 % ) . protein s deficiency was the most common abnormal findings ( n = 9 , 28 % ) . other results contained hyperhomocysteinemia ( n = 2 ) , antithrombin iii deficiency ( n = 2 ) , mutation in factor v leiden ( n = 1 ) , protein c deficiency ( n = 1 ) , and positive antiphospholipid antibodies ( n = 1 ) . from 14 patients with cvst that d - dimer was assessed in them , 10 patients showed high titer . therefore , the sensitivity of d - dimer was 71.4 % , and 4 patients represented false - negative results . cell count was increased in 4 of the patients ( 5 per cumm ) , and total protein was high ( 45 mg / 100 ml ) in two patients . in cytology was positive in one patient who had interstitial lobular cancer of breast . no cvst patient ( even with infectious causes ) represented the positive culture of csf . a total of 10 patients ( 19 % ) represented supratentorial hemorrhagic infarction in initial brain computed tomography scan . the involvement of different cerebral sinuses and veins in descending order of frequency included transverse and sigmoid ( 20/53 , 37.7 % ) , both superior sagittal and lateral ( 19/53 , 35.8 % ) , cavernous ( 6/53 , 11.3 % ) , bilateral transverse and sigmoid ( 4/53 , 7.5 % ) , isolated superior sagittal ( 2/53 , 3.7 % ) , and isolated straight and galen sinuses ( 2/53 , 3.7 % ) . a total of 45 patients had favorable outcome that defined as improvement without any serious complication ( 84 % ) . two patients had intracranial hemorrhage ( ich ) due to intravenous heparin , but finally recovered and were discharged . death and recurrence were occurred in 2 ( 3.7 % ) and 3 ( 5.6 % ) patients , respectively . motor and sensory focal neurological deficits and multicranial nerve palsy were associated with poor outcome that defined as death , recurrence , and ich due to anticoagulation ( p = 0.050 and 0.004 , respectively ) . the underlying disease of patients had no statistically significant association with outcome , 81 % of the patients who had an accompanying disease improved versus 86 % patients who did not . there was also no significant association between the outcome of the patients and the number and type of involved sinuses in chi - square test [ table 3 ] . as shown in table 3 , 4 of 6 patients with cavernous sinus thrombosis were improved ( p = 0.05 ) . on the other handheadache was found as the most prevalent clinical feature of cvst among the patients ( n = 44 , 83 % ) followed by papilledema and vomiting ( n = 36 , 68 % , and n = 29 , 55 % , respectively ) . the mode of clinical presentation was acute , sub - acute , and chronic in 14 ( 26.4 % ) , 22 ( 41.5 % ) , and 17 ( 32 % ) patients , respectively . median days from the onset of symptoms to hospital admission were 11 days with the range of one to 92 days . clinical features of patients with cerebral venous and sinus thrombosis distribution of patients with cerebral venous sinus thrombosis in different monthsthe most frequent identified risk factor of cvst patients in this study , both females and males were the underlying disease . from 40 female patients ,40 % ( n = 16 ) had a predisposing condition for cvst and 37.5 % ( n = 15 ) had used oral contraceptive drug ( ocp ) . four patients used ocp and simultaneously had other underlying causes including behcet disease , hypothyroidism , preeclampsia , and postpartum state . moreover , n = 19 ) had more than one contributing factors for cvst and 20 % of them ( n = 11 ) had no identifiable cause ( idiopathic ) . underlying risk factors of cerebral venous thrombosis in patients procoagulatory factors and vasculitis conditions looked for in 32 of the patients and found abnormal results in 16 of them ( 50 % ) . protein s deficiency was the most common abnormal findings ( n = 9 , 28 % ) . other results contained hyperhomocysteinemia ( n = 2 ) , antithrombin iii deficiency ( n = 2 ) , mutation in factor v leiden ( n = 1 ) , protein c deficiency ( n = 1 ) , and positive antiphospholipid antibodies ( n = 1 ) . from 14 patients with cvst that d - dimer was assessed in them , 10 patients showed high titer . therefore , the sensitivity of d - dimer was 71.4 % , and 4 patients represented false - negative results . cell count was increased in 4 of the patients ( 5 per cumm ) , and total protein was high ( 45 mg / 100 ml ) in two patients . in cytologyno cvst patient ( even with infectious causes ) represented the positive culture of csf . a total of 10 patients ( 19 % ) represented supratentorial hemorrhagic infarction in initial brain computed tomography scan . the involvement of different cerebral sinuses and veins in descending order of frequency included transverse and sigmoid ( 20/53 , 37.7 % ) , both superior sagittal and lateral ( 19/53 , 35.8 % ) , cavernous ( 6/53 , 11.3 % ) , bilateral transverse and sigmoid ( 4/53 , 7.5 % ) , isolated superior sagittal ( 2/53 , 3.7 % ) , and isolated straight and galen sinuses ( 2/53 , 3.7 % ) . a total of 45 patients had favorable outcome that defined as improvement without any serious complication ( 84 % ) . two patients had intracranial hemorrhage ( ich ) due to intravenous heparin , but finally recovered and were discharged . death and recurrencewere occurred in 2 ( 3.7 % ) and 3 ( 5.6 % ) patients , respectively . motor and sensory focal neurological deficits and multicranial nerve palsy were associated with poor outcome that defined as death , recurrence , and ich due to anticoagulation ( p = 0.050 and 0.004 , respectively ) . the underlying disease of patients had no statistically significant association with outcome , 81 % of the patients who had an accompanying disease improved versus 86 % patients who did not . there was also no significant association between the outcome of the patients and the number and type of involved sinuses in chi - square test [ table 3 ] . as shown in table 3 , 4 of 6 patients with cavernous sinus thrombosis were improved ( p = 0.05 ) . on the other handin our patients , females predominance and a female to male ratio of 3 was observed like other previous studies in developed countries . western countries and the frequency of ocp usage among women with cvst has been reported up to 68 % . unlike other studies , the most frequent risk factor of cvst in our patients was their underlying condition that was detected in 40 % of patients . this was also true in women as 40 % of them had a predisposing underlying state and 37.5 % used ocp . the importance of attention to underlying disease in cvst patients is more emphasized because cvst was presenting feature in some of our patients ( polycythemia vera and hypothyroidism ) and their disease was uncovered after appropriate work up . the higher number of cvst patients in the context of a disease in this survey could be due to the setting that study has been performed . it was in a general referral hospital with different departments of internal medicine and gynecology that serves patients from all over the country . compared thrombophilic risk factors in age - matched patients with cvst and deep venous thrombosis / pulmonary thromboembolism patients ( dvt / pe ) . they found that there was not any difference in thrombotic profile between two groups . while ocp intake was more frequent in cvst patients , it was suggested that additional unknown risk factors should be considered to explain the different sites of embolism . we suggest that the underlying disease may be one of the contributing factors in the incidence of thrombosis in different sites as dvt / pe mostly occurs in the context of immobilization and surgery . these factors were not seen in this and other studies as underlying cause in cvst . although further studies with emphasize on the underlying condition between cvst and dvt / pte patients should be performed . the presence of multiple risk factors at the same time in patients with cvst was less considered before . in this study , ocp was still a major contributing factor in women with cvst but from 15 patients who have used ocp , 12 had either simultaneous underlying condition or thrombophilia . therefore , the effect of ocp may be enforced in the presence of other factors in developing of cvst . the importance of multiple risk factors in cvst was further discovered regarding the observation of patients over the different month of the year where it showed higher number of patients in warm months of the year which could be due to the role of dehydration in developing of cvst . sensitivity of d - dimer was 71.4 % , and false negative results were detected in 28.5 % of patients . previously reported sensitivity of d - dimer ranged between 58 % and 93 % in a systematic review . isolated headache , longer duration of symptoms , and limited sinus involvement may be related to false negative d - dimer results . these findings show that normal levels of d - dimer could not definitely exclude the diagnosis of cvst , because still there may be true cvst patients with negative result . however , the positive and high titer of d - dimer test could support the cvst diagnosis in suspicious cases . csf analysis was not performed in all of the patients , but all patients with infectious cause ( n = 7 ) underwent lumbar puncture . this could be due to the source of these infections which were mostly restricted to the nose and ear ( in patients with mucormycosis and acute otitis media ) . the other reason might be the effect of infection in the induction of hypercoagulable state which may explain cvst in the patient with hepatitis b and the patient with a history of bacterial meningitis 1 month before thrombosis . as a limitation to this study , data were collected only from the patients referred to the general hospital . there might have been some cases of cvst patients that had minor presentations , and consequently , they were treated as an outpatient . another limitation was missing data of d - dimer and thrombophilic factors in retrospective assessments . to overcome this scenario , we conducted a prospective phase to evaluate these factors in patients . in this study , no significant association was observed between number and type of thrombosed vein or underlying conditions , and outcome . this could be related to number of enrolled patients , for example , there was 6 patients in cavernous sinus thrombosis group or may be due to potentially inadequate power of the study ; however , cvst is considered a rare disease . further studies with longer period may be needed to evaluate the relationship of underlying disease with outcome . underlying disease was the most common predisposing factor in our patients and cvst was the first presentation in some of the diseases .\noutput:\n" }, { "from": "agent", "value": "introduction : despite increasing the use of magnetic resonance imaging ( mri ) , cerebral venous sinus thrombosis ( cvst ) has remained an under - diagnosed condition . in this study , characteristics and frequency of various risk factors of cvst patients in a tertiary referral hospital were closely assessed.methods : patients with an unequivocal diagnosis of cvst confirmed by mri and magnetic resonance venography during 6 years of the study were included . all data from the onset of symptoms regarding clinical signs and symptoms , hospital admission , seasonal distribution , medical and drug history , thrombophilic profile , d - dimer , neuroimaging , cerebrospinal fluid findings , mortality , and outcome were collected and closely analyzed.result : a total of 53 patients with female to male ratio of 3.07 and mean age of 33.7 years were included in the study . headache and papilledema were the most frequent clinical features ( 44 and 36 patients , respectively ) . an underlying disease ( diagnosed previously or after admission ) was the most common identified risk factor for cvst in both females and males ( 21 patients ) . a total of 15 women used the oral contraceptive pill ( ocp ) where 12 of them had simultaneously other predisposing factors . overall , 19 patients ( 36 % ) had more than one contributing factor . d - dimer had a sensitivity of 71.4 % in cvst patients . the mortality of patients in this study was 3.7 % ( n = 2 ) . focal neurologic deficit and multicranial nerve palsy were associated with poor outcome which defined as death , recurrence , and massive intracranial hemorrhage due to anticoagulation ( p = 0.050 and 0.004 , respectively ) . conclusion : unlike most of the cvst studies in which ocp was the main factor ; in this study , an underlying disease was the most identified cause . considering the high probability of multiple risk factors in cvst that was shown by this study , appropriate work up should be noted to uncover them ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: hearing loss is one of the most common sensorineural defects , which may result from a great variety of genetic and environmental factors . based on the inheritance patterns , the genetic hearing loss can be classified into autosomal recessive , autosomal dominant , and x - linked / mitochondrial , accounting for approximately 80 % , 15 % , and less than 5 % of nonsyndromic hearing loss , respectively . both autosomal dominant ( adnshl ) and autosomal recessive ( arnshl ) nonsyndromic hearing loss have an extremely high degree of heterogeneity . for the former , 35 causative genes and over 60 lociso far , mutations in most adnshl genes were reported based on studies of the individual cases or families . the etiological contribution of the adnshl gene pou4f3 has been rarely studied . in recent years , however , the development of next - generation sequencing ( ngs ) has complemented the traditional sanger sequencing method and made it possible to screen all deafness - associated genes in a high throughout manner . this gene encodes a 338 amino acids ' pou family transcription factor with two conserved dna - binding domains ( the pou - specific domain and the pou homeodomain , amino acids 179256 and 274333 , resp . ) . in mouseinner ear , pou4f3 is strongly expressed in both inner and outer hair cells . it activates the transcription of a downstream target gene gfi1 , whose expression is required for the maintenance of the outer hair cells . to date , only eleven different mutations in pou4f3 have been reported in israeli jewish , dutch , korean , japanese , and chinese adnshl families . the hearing loss caused by pou4f3 mutations was highly variable in the age of onset , the progression course , and the severity of hearing impairment . in the previous ( n = 7 ) and the present ( n = 9 ) studies , we preformed targeted ngs of known deafness genes in 16 chinese han adnshl families and identified novel mutations in pou4f3 as the pathogenic cause in three of them . characterization of the hearing phenotype was performed in the affected family members of these three families in the present study . our results expanded the mutation spectrum of dfna15 and suggested that mutations in pou4f3 are a relatively common cause for adnshl in chinese hans . probands of sixteen chinese han families segregating adnshl were recruited through xinhua hospital , shanghai , china . the pedigrees of the families were shown in figure 1 ( a ) and supplementary figure s1 in supplementary material available online at http://dx.doi.org/10.1155/2016/9890827 . for families p1748 , pd6 , and p59 in which mutations in pou4f3 were identified , 8 , 10 , and 13 additional family members were subsequently recruited , respectively . this study was approved by the ethics committee of xinhua hospital , shanghai jiaotong university school of medicine , shanghai , china . a detailed physical and medical history examination was performed in all probands of the adnshl families . the hearing levels were measured by pure tone audiometry ( pta ) and shown as the average thresholds of 0.5 , 1 , 2 , and 4 khz from the better ear . the hearing levels were classified as normal ( 20 db ) , mild ( 2040 db ) , moderate ( 4170 db ) , severe ( 7190 db ) , and profound ( 90 db ) . targeted ngs of 144 known deafness genes ( see complete list in supplementary table s1 ) was performed using the mygenotics gene enrichment system ( mygenotics , boston , md , usa ) and the illumina hiseq 2000 sequencer ( illumina , san diego , ca , usa ) as previously described . nonsynonymous , on - target variants with maximum minor allele frequency ( maf ) less than 0.001 in public databases nhlbi exome sequencing project ( esp , http://evs.gs.washington.edu/evs/ ) and the exome aggregation consortium ( exac , http://exac.broadinstitute.org/ ) were considered as the candidate pathogenic mutations in compliance with the adnshl inheritance . the pathogenicity of the candidate variants was predicted by computational programs mutation taster ( http://www.mutationtaster.org/ ) , polyphen - 2 ( http://genetics.bwh.harvard.edu/pph2/ ) , provean , and sift ( http://sift.jcvi.org/ , cutoff scores set at 2.5 and 0.05 , resp . ) . cosegregation of the pathogenic mutations and the hearing phenotype was verified in members of families p1748 and pd6 by sanger sequencing . in our previous studies of 7 chinese han adnshl families , a c.603_604delgg ( p.leu201fs12 ) mutation in pou4f3 has been identified by targeted ngs as the pathogenic cause in family p59 . in the present study , we performed a comprehensive mutation screening in probands of another nine chinese han adnshl families ( marked in asterisks in figure 1 ( a ) and supplementary figure s1 ) by targeted ngs of 144 known deafness genes . interestingly , two novel heterozygous variants p.leu311pro ( c. 932t c ) and c. 120 + 1g c in pou4f3 were identified as the candidate pathogenic variants in probands p1748 - iii - 1 and pd6 - iv - 1 , respectively ( table 1 ) , along with a heterozygous tecta p.val1830met and a heterozygous tmc1 p.ser697x variant in proband p1748 - 1 ( table 1 ) . sanger sequencing in the rest of the family members confirmed that p.leu311pro and c. 120 + 1g c were the only two candidate variants segregating with the hearing phenotype in families p1748 and pd6 ( figures 1 ( a ) and 1 ( b ) ) , while the tecta p.val1830met and the tmc1 p.ser697x variants were not seen in any other affected family members of p1748 . the p.leu311pro ( c. 932t c ) and c. 120 + 1g c in pou4f3 were not reported in previous studies , not present in the nhlbi esp ( n = 6503 ) and exac ( n = 60706 ) database , and not seen in 300 chinese han normal hearing controls . the c. 120 + 1g c mutation was predicted to abolish the 5 splice site of introns 1 of pou4f3 ( figure 2 ( a ) ) . the p.leu311pro mutation substituted a conserved amino acid leu311 ( figure 2 ( b ) ) and was predicted to be deleterious by computational programs mutation taster , polyphen - 2 , provean , and sift ( table 1 ) . based on the audiograms and the self - description of the affected individuals with c.603_604delgg , p.leu311pro , and c. 120 + 1g c mutations in pou4f3 , the hearing loss associated with the pou4f3 mutations was typically progressive with considerable variability in ages of onset and degree of severity both interfamilially and intrafamilially . in family p1748 with the p.leu311pro mutation , proband iii - 1 had notable hearing loss since age 10 years . the hearing loss affected high frequency most and gradually progressed to moderate hearing loss at age 29 years ( figure 1 ( c ) ) . the affected individuals in the second generation of family p1748 had hearing loss at the onset age of 10 years to 20 years and all eventually progressed to profound after age 50 years . interestingly , all six female patients in the second generation had significantly decreased hearing levels after giving birth to their children . in family pd6 with the c. 120 + 1g c mutation , proband iv - 1 had congenital , moderate hearing loss with a relatively flat audiometric profile at age 23 years affecting all frequencies ( figure 1 ( c ) ) . other affected individuals in this family demonstrated progressive , moderate - to - profound deafness depending on their ages . the ages of onset ranged from congenital to 40 years . in family p59 with the c.603_604delgg mutation , the proband iii - 8 had only moderate hearing loss at 54 years of age ( figure 1 ( c ) ) and all affected individuals in this family had a rather late age of onset around 40s . for other auditory symptoms , tinnitus has been complained by proband p1748 - iii - 1 . combined with our present and previous studies , we identified mutations in pou4f3 as the pathogenic cause of deafness in 3 of the 16 ( 18 % ) chinese han adnshl families , suggesting that it is a relatively common cause for adnshl in chinese hans . consistently , seven of the ten previously reported pou4f3 mutations from other research groups were also from the east asians ( three in korean , two in japanese , and two in chinese , figure 2 ( a ) ) , suggesting that this gene should be routinely screened in adnshl cases of east asian descent . in contrast , only three ( one in israeli jewish and two in dutch , figure 2 ( a ) ) pou4f3 mutations were previously reported from regions other than east asia . the distinguished mutation spectrum among different ethnical groups has also been reported for other deafness genes such as slc26a4 , in which case biallelic slc26a4 mutations can be identified in 88.4 % of deaf patients with nonsyndromic eva in chinese but only 15 % in caucasians . figure 2 ( a ) summarized the type , position , and associated ethnicity of the thirteen pou4f3 mutations reported to date . four of them , including the c.603_604delgg ( p.leu201fs12 ) mutation reported in our previous study , were truncating mutations that were predicted to lead to prematurely stopped protein product or nonsense - mediated decay of the mrna , while another seven pou4f3 mutations , including the p.leu311pro mutation reported in the present study , were missense mutations leading to single amino acid substitutions . notably , these twelve mutations were all located within or close to the pou - specific domain or the pou homeodomain , the two conserved dna - binding domains of pou4f3 encoded in exon 2 . on the contrary , the c. 120 + 1g c mutation identified in the present study is the only reported mutation outside exon 2 of pou4f3 . consistent with previous reports , the pou4f3 mutations identified in the present study were associated with progressive hearing loss with considerable variability in the ages of onset and the degrees of severity , and this variable hearing phenotype can be seen both interfamilially and intrafamilially . apparently no simple genotype - phenotype correlation can be drawn based on the position or the truncating / nontruncating nature of the pou4f3 mutations . in a previous study of the pou4f3 mutant deaf mice , deficiency of pou4f3 has been found to result in reduced expression of its hair cell specific downstream target gfi1 , which was suggested as the direct cause of the outer hair cell degeneration in the pou4f3 mutant mice . in future studies , therefore , it will be interesting to correlate the presumably reduced levels of the gfi1 transcription with different pou4f3 mutations and the severity of the associated hearing loss . the hearing loss associated with pou4f3 mutations has considerable variability in the ages of onset and the degrees of severity .\noutput:\n" }, { "from": "agent", "value": "autosomal dominant nonsyndromic hearing loss ( adnshl ) is extremely heterogeneous . so far the genetic etiological contribution of the gene pou4f3 associated with adnshl has been rarely reported . in our previous study , a c.603_604delgg mutation in the hair cell specific gene pou4f3 has been identified as the pathogenic cause in one of the seven chinese han adnshl families . in the present study , we performed targeted next - generation sequencing of 144 known deafness genes in another nine chinese han adnshl families and identified two more novel mutations in pou4f3 , p.leu311pro and c. 120 + 1g > c , as the pathogenic cause . clinical characterization of the affected individuals in these three families showed that the three pou4f3 mutations may lead to progressive hearing loss with variable ages of onset and degrees of severity . our results suggested that mutations in pou4f3 are a relatively common cause ( 3/16 ) for adnshl in chinese hans , which should be routinely screened in such cases during genetic testing ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the overall prevalence of type 2 diabetes in isfahan , a centrally located city in iran with a population of almost two million ( 1,986,542 in 2006 ( men 1,017,940 ) ) , was reported as high as 7.76 % in subjects aged over 40 years and 7.54 % in male group . many studies have reported that men with type 2 diabetes , have significantly lower levels of testosterone compared with nondiabetic people as a part of diabetic complications . grossman et al , reported that 43 % of diabetic men had low total testosterone and 57 % had low calculated free testosterone . notably , low free testosterone ( ft ) level , measured by equilibrium dialysis , the gold standard for measuring ft has been reported in 25 % of 57 men with type 2 diabetes . inverse correlation of testosterone and fasting plasma glucose has been shown in large population study . however , both symptoms or signs and biochemical evidence of testosterone deficiency are needed to define hypogonadism . the food and drug administration ( fda ) and the endocrine society recommend to consider hypogonadism in men , if total testosterone ( tt ) concentration is less than or equal to 300 ng / dl ( 10.4 nmol / l ) in addition to related signs and symptoms of androgen deficiency . testosterone in the circulation is in the three major fractions : free ( 2 % 3 % ) , albumin - bound ( 20 % - 40 % ) , and sex hormone - binding globulin ( shbg ) - bound ( 60 % - 80 % ) . both the free and albumin - bound fractions comprise bioavailable testosterone because they are biologically active component that is readily available to the tissues , while shbg - bound testosterone is strongly bound and inactive . obesity , waist circumference , aging , diabetes , and other comorbidities may change shbg levels and influence tt levels . hypertension , body mass index , waist circumference , advanced age , diabetes , current smoking , general health status , and physical activity are considered as the risk factors of low testosterone levels . we studied male patients older than 30 years of age with type 2 diabetes mellitus who had been registered in isfahan endocrine and metabolism research center ( iemrc ) to investigate the prevalence of hypogonadism in type 2 diabetes . the results will help us for future health programming , as the prevalence has a wide range in different areas of the world . on the other hand , diabetic men ( n = 325 ) , aged 30 years , who were registered in iemrc were selected by consecutive patient selection method to enter this cross - sectional study , from june to november 2009 . all patients gave written informed consent , and the ethics committee of isfahan university of medical sciences approved the protocol . those patients who had overt nephrotic syndrome or cirrhosis , breast , and prostate cancer , type1 diabetes , were single or divorced , or were already receiving androgen did not enroll the study ( n = 37 ) . all enrolled patients ( n = 288 ) were asked about their medical history , smoking , marriage status , and medications by one endocrinologist ( mrm ) . blood pressure , height and weight , waist circumference were measured , and bmi was calculated . waist was defined as the middle point between the iliac crest and the lower rib . patients ( n = 288 ) filled in an androgen deficiency in the aging male ( adam ) questionnaire . decreased sexual desire or erectile dysfunction or any three out of eight items of loss of energy , deterioration of work performance , decrease in muscle strength , and sleepiness after dinner , difficulty to sustain erection during sexual intercourse , depressed mood , decreased enjoyment of life , and nontraumatic loss of height , were considered positive adam 's response . symptomatic patients with positive adam 's questionnaire , 265 out of 288 patients ( 92 % ) , were referred to getting 20 ml venous blood sample between 7:30 am and 9:30 a.m. serum samples were separated by centrifugation and immediately freezed at -20 c and stored before analysis . total testosterone ( tt ) was measured by the elisa assay technique ( drg , germany ) with inter - and intra - assay coefficient variation ( cv ) of 3.59 % and 7.13 % , respectively . shbg was measured by the elisa assay method ( diametra , italy ) with both inter and intra assay coefficient variation ( cv ) of 4.4 % . free and bioavailable testosterone were calculated by using total testosterone and shbg via the calculator introduced by www.issam.ch/freetesto.htm . g / l ) , since , patients with marked plasma protein abnormalities , such as in nephrotic syndrome or liver cirrhosis was not initially enrolled . a total testosterone level 8 nmol / l was considered to be low , and it was considered as borderline while it was between 8 and 12total testosterone level 12 nmol / l was considered as normal . a calculated free testosterone ( cft ) level 0.16 nmol / l was postulated low . nmol / l to 4 nmol / l as borderline , and concentrations more than 4 nmol / l as normal . overt hypogonadism was defined as positive adam 's questionnaire and total testosterone level 8 nmol / l or bioavailable concentration 2.5 nmol / l . borderline hypogonadism was defined as positive adam 's questionnaire and total testosterone between 8 nmol / l and 12 nmol / l or bioavailable testosterone between 2.5 values are expressed as percentage or as mean ( sd ) , unless otherwise stated . the effects of clinical variables including decreased sexual desire , difficulty to maintain erection during sexual intercourse , erectile dysfunction , loss of energy , deterioration of work performance , decrease in muscle strength , sleepiness after dinner , depressed mood , decrease enjoyment of life , and nontraumatic loss of height on total , free , bioavailable testosterone and shbg levels were determined . means of total , free , bioavailable testosterone and shbg were compared between different categories of age groups , duration of diabetes , bmi , cholesterol , triglyceride , and ldl levels using t student 's t and anova tests [ table 2 ] . the correlation between tt , cft , and cbt levels with age , shbg , total cholesterol , triglyceride , ldl , hba1c , systolic , and diastolic blood pressure , duration of diabetes , bmi and waist circumference was determined by pearson correlation coefficient . the relationship between hypogonadism and obesity and smoking status was done . both overt and borderlinevalues are expressed as percentage or as mean ( sd ) , unless otherwise stated . the effects of clinical variables including decreased sexual desire , difficulty to maintain erection during sexual intercourse , erectile dysfunction , loss of energy , deterioration of work performance , decrease in muscle strength , sleepiness after dinner , depressed mood , decrease enjoyment of life , and nontraumatic loss of height on total , free , bioavailable testosterone and shbg levels were determined . means of total , free , bioavailable testosterone and shbg were compared between different categories of age groups , duration of diabetes , bmi , cholesterol , triglyceride , and ldl levels using t student 's t and anova tests [ table 2 ] . the correlation between tt , cft , and cbt levels with age , shbg , total cholesterol , triglyceride , ldl , hba1c , systolic , and diastolic blood pressure , duration of diabetes , bmi and waist circumference was determined by pearson correlation coefficient . thirty seven out of 325 selected type 2 diabetic male patients , were not enrolled the study because of already mentioned exclusion criteria . therefore , they were considered clinically eugonadal and were not evaluated further . of those who had positive adam 's questionnaire ( n = 265 , 92 % ) four men were excluded , again , because of the elevated baseline total testosterone , due to unreported exogenous androgen usage . however , the data of 243 hypogonadal diabetic men have been reported . baseline characteristics in diabetic males ( n = 243 ) , clinical and laboratory data the most common symptoms of the diabetic men with low testosterone levels were erectile dysfunction , deterioration of work performance and loss of energy occurring in 211 ( 86.8 % ) , 204 ( 84 % ) , and 199 ( 81.9 % ) , respectively . calculated free testosterone correlates with cbt and tt ( r = 0.6 ; p = 0.001 and r = 0.5 ; p = 0.001 , respectively ) . calculated bioavailable testosterone correlates directly with cft , tt and ldl ( r = 0.6 ; p = 0.001 , r = 0.7 ; p = 001 , r = 0.1 ; p = 0.05 , respectively ) . it was inversely correlated with shbg ( r = -0.3 ; p = 0.001 ) . shbg correlates with tt , systolic and diastolic blood pressure ( r = 0.5 ; p = 0.001 , r = 0.2 ; p = 0.02 and r = 0.2 ; p = 0.02 , respectively ) and also with cbt , bmi and triglyceride ( r = 0.3 ; p = 0.001 , r = 0.2 ; p = 0.003 and r = 0.3 ; p = 0.001 ) . eighteen men ( 7.4 % ) had overt hypogonadism ( total testosterone 8 nmol / l ) and 24 men ( 9.9 % ) had borderline hypogonadism ( total testosterone between 8 nmol / l and 12 nmol / l ) . overt hypogonadism based on calculated bioavailable testosterone which defined as level 2.5 nmol / l was seen in 149 men ( 61.6 % ) and calculated bioavailable testosterone between 2.5 nmol / l and 4 nmol / l found in 89 men ( 36 % ) , as borderline hypogonadism . two hundred twenty seven men ( 96 % ) had calculated free testosterone0 .16 nmol / l . the age distribution by decades and the mean of total , calculated free and bioavailable testosterone and shbg levels were shown in table 2 . those patients less than 50 years were 18.6 % , between 50 and 59 years were 34.7 % , between 60 and 69 years were 31.4 % and more than 69 years were 15.3 % of all hypogonadal men [ table 2 ] . association of shbg and testosterone levels with of some variable categories in hypogonadal type 2 diabetic men with advancing age , the concentration of shbg increased ( r = 0.4 ; p = 0.001 ) and cbt decreased ( r = -0.3 ; p = 0.001 ) . total testosterone and shbg decreased by obesity ( bmi30kg / m ) ( p = 0.02 and p = 0.006 , respectively ) , however , cft and cbt were not be affected by obesity [ table 2 ] . both cbt and cft , inversely , correlated with age ( r = -0.2 ; p = 0.04 and r = -0.2 ; p = 0.04 , respectively ) . nmol / l ) was not correlated with obesity , smoking status , age , duration of diabetes , systolic and diastolic blood pressure , waist circumference , bmi , hba1c , shbg , and lipid profile . some , but not all cross - sectional studies have reported the association between low total testosterone and type 2 diabetes . our study has shown that the prevalence of hypogonadism in men with type 2 diabetes is high , especially , if it was defined based on calculated free and bioavailable testosterone . the design of kapoor et al , study was very similar to ours . the prevalence of overt hypogonadism , derived from tt , in our study was 7.4 % versus 17 % in kapoor et al , study and the borderline hypogonadism was 9.9 % versus 25 % , respectively . according to cbt , the prevalence of overt hypogonadism in our research was 61.6 % versus 14 % in their study and the borderline hypogonadism was 36 % versus 29 % , respectively . the prevalence of hypogonadism was 96 % in our patients and 42 % of kaoor et al , study . the lower prevalence of hypogonadism in kapoor study based on cft , would not be due to different cut off point , as it was higher than ours . there are just a few studies , which have reported the prevalence of hypogonadism according to cbt and cft . measurement of free testosterone by equilibrium dialysis technique is difficult and not available everywhere , but cft values are reliable by vermeulen equation , and can also be used instead of free testosterone , in a clinical setting . the calculator had been designed based on vermeulen et al , method of calculation . in our study , tt had strong correlation with cft and cbt ( r = 0.5 ; p = 0.001 and r = 0.7 ; p = 0.001 , respectively ) . however , the big difference between the prevalence of hypogonadism according to tt and cft ( or cbt ) could not be explained . we observed no correlation between obesity ( bmi30 kg / m ) , age , duration of diabetes , smoking status and hba1c and the prevalence of hypogonadism based on low total testosterone . similar to ours , other studies have found that low testosterone concentrations are not related to glycosylated hemoglobin or duration of diabetes , but had association with obesity . according to a literature review , hypogonadism in diabetes is more related to insulin resistance than glycemic control itself . in a study , recently done in usa , obesity and diabetes were found to be independent risk factors for low free testosterone in men . trials of long duration are required to establish the benefits and risks of testosterone replacement in patients with type 2 diabetes and low testosterone . there is no correlation between obesity , smoking status , age , duration of diabetes , systolic , between hypogonadism of diabetic men and diastolic blood pressure , waist circumference , bmi , hba1c , shbg , and lipid profile .\noutput:\n" }, { "from": "agent", "value": "objective : low testosterone , with or without symptoms , reported in diabetic men in some studies . we investigated the prevalence of hypogonadism in iranian type 2 diabetic men.materials and methods : total testosterone ( tt ) and sex hormone binding globulin ( shbg ) concentrations were measured in 247 diabetic men > 30 years who had symptoms of androgen deficiency , according to adams questionnaire . the correlation between some parameters and total , free and bioavailable testosterone levels was determined using pearson correlation coefficient . free and bioavailable testosterone were calculated by electronic calculator . four patients were excluded because of high testosterone level , due to unreported androgen use . overt hypogonadism was defined as total testosterone 8 nmol / l or calculated bioavailable testosterone ( cbt ) 2.5 nmol / l and borderline hypogonadism was considered as tt 8 - 12 nmol / l or cbt 2.5 - 4nmol / l.results : the mean and sd of age was 59 ( 9.3 ) years . the mean tt , calculated free testosterone ( cft ) , and cbt and shbg levels were 4.81 ( 1.7 ) nmol / l , 0.11 ( 0.06 ) nmol / l , 2.42 ( 1.17 ) nmol / l and 36.15 ( 18.3 ) nmol / l , respectively . according to tt and cbt , overt hypogonadism observed in 7.4 % and 61.6 % of men , respectively , and the prevalence of borderline hypogonadism was 9.9 % and 36 % , respectively . cft 0.16 nmol / l found in 227 diabetic men ( 96 % ) . hypogonadism ( tt 12 nmol / l ) was not correlated with obesity , smoking , age , duration of diabetes , blood pressure , and hba1c.conclusion : hypogonadism is highly prevalent in type 2 diabetes men ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: dogs in the study comprised 3 groups of beagles housed in different rooms of the isolation facility at green cross veterinary products ( yong - in , south korea ) . the virus used was avian - origin canine influenza virus a / canine / 01/2007 , subtype h3n2 , which had been isolated from a pet dog with severe respiratory syndrome . in the first group ( challenge group ) , 4 beagles were inoculated intranasally with a 1050 % egg infectious dose ( eid50 ) . two hours later , the second group of 4 uninfected dogs ( exposure group ) was housed in the same contaminant room . these uninoculated dogs had frequent direct nose - to - nose contact with the inoculated dogs . the third group of 4 dogs ( control group ) was housed separately as uninoculated controls . we monitored clinical signs of infection 7 days postinoculation ( dpi ) and examined nasal swabs obtained 10 dpi for virus shedding ; serum samples were collected at 0 , 3 , 7 , 9 , and 13 dpi . serum antibodies against nucleoprotein were detected by using a commercial competitive elisa ( animal genetics , inc . all organs from the dogs were rapidly immersed in 10 % neutral formalin buffer to prevent autolysis and stored overnight . all animal experiments complied with the current laws of south korea . animal care and treatmentwere conducted in accordance with guidelines established by the seoul national university institutional animal care and use committee . clinical signs , including sneezing , nasal discharge , and coughing , were observed 28 dpi in the challenge group and 58 dpi in the exposure group . twenty - four hours after inoculation , fever developed in dogs in the challenge group ( mean rectal temperature 39.85 c39 .75 c ) that lasted until 3 dpi . fever ( 39.5 c ) developed in dogs in the exposure group 72 hours after exposure ; mean rectal temperature was 38.65 c a day later . necropsy examination found gross lesions in the lung , including multifocal to coalescing reddish consolidations , consistent with influenza - induced lung lesions in other species . these gross lesions were observed in the challenge group on dpi 7 and 13 but in the exposure group only on dpi 13 . infected dogs shared the following histopathologic features ( figure 1 ) : 1 ) severe multilobular or diffuse necrotizing tracheobronchitis with suppurative inflammation in the lumina and squamous metaplasia of the tracheobronchial epithelium and 2 ) severe multilobular bronchiolitis and alveolitis . we observed these histopathologic lesions in the trachea and lungs in the challenge group on dpi 7 and 13 but in the exposure group only on dpi 13 . for the challenge group , mean virus titers in respiratory tract tissues were 10 eid50 / ml on dpi 7 , but no viruses were detected in the tissues on dpi 13 . for the contact group , mean virus titers in respiratory tract tissues were 10 eid50 / ml on dpi 7 , but no viruses were detected in the tissues on dpi 13 . we detected viruses in nasal discharge of dogs in the challenge group on dpi 26 and in the exposure group on dpi 58 ( p 0.01 ) . shedding peaked on dpi 2 in the challenge group and dpi 6 in the exposure group ( figure 2 ) . nucleoprotein - specific elisas showed that all dogs lacked nucleoprotein - specific antibodies before inoculation and that dogs in the control group remained negative throughout the experiment . however , the percentage inhibition values were positive on dpi 7 , 9 , and 13 for dogs in the challenge group ( p 0.01 ) and positive on dpi 9 and 13 for dogs in the exposure group ( p 0.01 , cut - off ratio of percentage inhibition 50 ) ( figure 2 ) . histopathologic appearance of tissue of dogs experimentally exposed to canine influenza virus by contact with infected dogs . severe necrotizing , suppurative tracheitis and bronchioalveolitis were observed in the contact - exposure group on day postinoculation ( dpi ) 13 . however , influenza - associated lesions were not yet present in these dogs on dpi 7 . hematoxylin and eosin stain . virus shedding and serologic response of beagles after experimental contact transmission of canine influenza virus . transmission of virus from 1 host to another species in general , essentially unaltered by direct transfer is an important feature of the ecology of influenza virus ( 2 ) . examples of this interspecies transmission mechanism include the recent human infections with the h5n1 subtype of avian influenza virus ( 3,4 ) . dogs infected with avian subtype h3n2 recently were identified in south korea , suggesting that an avian influenza virus with high pathogenicity that can rapidly spread from dogs to dogs has made the interspecies leap . most whole influenza viruses that are transmitted directly from the natural host species to a different species do not achieve sustained transmission in the new host species ( 5 ) , suggesting that multiple virushost interactions are needed before the virus can replicate and be transmitted horizontally in a new host species ( 2 ) . here we showed that close contact between canine influenza virus - infected and noninfected dogs results in spread of the virus to the uninfected dogs , which then develop clinical signs of the disease . we showed that an avian - origin canine influenza virus isolated from a pet dog can spread from dog to dog by contact infection . we observed a transient rise in rectal temperature in the challenge and exposure dogs and seroconversion in the exposure dogs . these dogs also had viral rna in their nasal swabs and histopathologic changes in their upper and lower respiratory tracts . our results demonstrate that an avian - origin canine influenza virus readily infects dogs and is easily transmissible among dogs .\noutput:\n" }, { "from": "agent", "value": "susceptible dogs were brought into contact with dogs experimentally infected with an avian - origin influenza a virus ( h3n2 ) that had been isolated from a pet dog with severe respiratory syndrome . all the experimentally infected and contact - exposed dogs showed elevated rectal temperatures , virus shedding , seroconversion , and severe necrotizing tracheobronchitis and bronchioalveolitis ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the transcription factor gata2 has a complex role in the development of hematopoiesis and lymphopoiesis but even in differentiation of non - hematopoietic progenitors . it has been previously described that heterozygous mutations in gata2 underlie different syndromes defined by monocytopenia and mycobacterial avium complex infection ( monomac ) , deficiency of dendritic cells , monocytes , b - and nk lymphocytes ( dcml ) , lymphedema , deafness and myelodysplasia ( emberger syndrome ) or familiar myelodysplastic syndrome / acute myeloid leukemia ( mds / aml ) , , . different types of mutations are known to cause loss of function of the mutated allele leading to haploinsufficiency of gata2 , and a correlation with certain clinical symptoms has been described in some cases , , . germline mutations of gata2 are transmitted with autosomal dominant inheritance . however , even among hereditary cases , there is a great variation of clinical findings , time of manifestation and even severity of disease in patients with gata2 mutations . clinical characteristics in most patients include immunodeficiency with susceptibility to human papillomavirus ( hpv ) and non - tuberculous mycobacteria ( ntm ) , predisposition to mds / aml , pulmonary proteinosis ( pap ) and congenital lymphedema . these symptoms might occur with or without preceding cytopenias and different medical specialties are involved in the diagnosis and management of these patients . the only curative treatment so far is allogeneic hematopoietic stem cell transplantation ( allo - hsct ) . therefore , it is crucial to diagnose patients with gata2 mutations as early as possible . we report a case of dcml deficiency and mds in a patient with gata2 mutation who successfully underwent allogeneic stem cell transplantation . a 38 - year old woman presented at the department of hematology , lund university hospital in january 2011 with microcytic anemia . she was referred from the gynecology department where she has been treated for severe and recurrent condylomata . during the last 10 years , she had gone repeatedly through surgical intervention for severe condylomata , that were positive for hpv type 6 . additionally , the patient has been treated for recurrent pneumonia . due to work related reasons , she had moved within europe several times . already at the age of 12 , she was diagnosed with anemia in germany , presumably caused by iron deficiency . due to persisting anemia , a bone marrow biopsy was done in the netherlands in 2008 and she was diagnosed with mds refractory anemia ( ra ) , ipss low , normal karyotype . she has never required blood transfusions . at presentation , she had adapted to a hemoglobin level of 79g / l and had only occasional discrete symptoms of her anemia , as fatigue , other constitutional symptoms were absent . she described her menstruation as mostly normal , but sometimes heavy and prolonged due to known uterine myoma . a lymphocyte profile showed low levels of nk - cells ( 0.0210 ) , cd4 t - cells ( 0.1210 ) and b - cells ( 0.0110 ) . we performed a new bone marrow biopsy in 2012 in which the previous diagnosis of mds ra could be confirmed even if signs of dysplasia were rather discrete with mainly dysplastic megakaryocytes .1 ) . the bone marrow cells still showed a normal karyotype in routine cytogenetics . clinical findings of symptomatic severe hpv infection , recurrent pneumonia and warts / condylomata in combination with the diagnosis of mds ra and monocytopenia / lymphopenia , led to the suspicion of dcml syndrome . in particular , no other family members are known to be affected by any type of hematological malignancy or immunodeficiency ( fig .2 a ) . sequencing of material from both bone marrow and skin biopsy showed a heterozygous frameshift mutation in gata2 ( nm_001145661.1 : c. 404dup ; gly136argfs * 49 ) ( fig . d ) . the patient 's parents were tested but no gata2 mutation could be detected ( fig .2 c ) , suggesting that the patients disorder was caused by a de - novo mutation . to systematically screen for additional mutations , we performed exome sequencing of matched tumor ( bone - marrow ) and normal ( skin biopsy ) samples as described previously , . thereby , we detected a somatic asxl1 mutation ( nm_015338.4 : c. 2077 c t ; arg693 * ) ( fig .2 d ) . since no matched sibling donor was available , a search in the registry was initiated and a suitable unrelated donor with a hla match 16/18 ( difference in hla - dpa - and hla - dpb1 - antigen ) , full blood group match and cmv match could be identified . after reduced conditioning with fludarabine 30 mg / m for 3 days and tbi 2 gy , she underwent allo - hsct with peripheral blood stem cells in june 2013 . already 4 weeks after allo - hsct she achieved an almost normal differential wbc count with monocytes around 110 , total lymphocytes of 0.610 . a new lymphocyte profile showed an almost normal amount of nk - cells ( 0.1510 ) and cd4 t - cells ( 0.1810 ) . eight weeks after allo - hsct , she experienced a severe menstrual bleeding accompanied by some chest discomfort and fatigue . clinical investigation revealed a hemoglobin level of around 70g / l and discrete ecg changes . subsequently , coronary angiography was performed showing a subtotal stenosis of the proximal left anterior descendens ( lad ) coronary artery without any other signs of atherosclerosis . percutaneous transluminal coronary angioplasty ( ptca ) was done and antiplatelet therapy with clopidogrel was initiated . the patient has neither cardiac risk factors nor a family history of heart disease . at 4 monthsshe developed a mild graft - versus host disease ( gvhd grade 1 ) with skin rashes , mild eosinophilia and musculoskeletal pain , responding to an intermediate steroid dose . in this case report we describe a young woman that presented with a long history of condylomata and microcytic anemia due to a combination of mds associated with the dcml syndrome and iron deficiency demonstrating that an overlap of clinical symptoms may complicate diagnosis in patients with gata2 mutations . genetic lesions in gata2 that lead to emberger syndrome seem to be affecting endothelial cells of the lymphatic system , but vascular problems have not been described in patients with gata2 mutations , to our knowledge . our patient suffered from a non - st - elevation myocardial infarction ( nstemi ) caused by a stenosis in the lad in the absence of cardiac risk factors or a family history of heart disease and is , thus , most likely triggered by anemia due to a massive menstrual bleeding aggravated by a uterine myoma . some clinical findings may be associated with distinct type of mutation causing gata2 haploinsufficiency . however , in two large patient cohorts published recently , diversity of phenotype in patients with gata2 mutations was shown for the first time , .84 % of the patients in this study met the diagnostic criteria for mds whereas bone marrow findings in patients with gata2 mutations seem to differ from those with typical mds . instead , patients with gata2 mutations present with a hypocellular bone marrow , increased reticulin fibrosis and atypical megakaryocytes in almost all cases . in addition cytogenetic abnormalities such as monosomy 7 or trisomy 8 are frequent , . in the casepresented here , repeated bone marrow biopsies showed rather discrete changes and considering the absence of cytogenetic aberrations , it was challenging to diagnose mds . myeloid transformation induced by acquired lesions of asxl1 in patients with constitutional gata2 mutations were previously reported , , . this demonstrates that an early diagnosis and evaluation for allo - hsct is crucial for patients with gata2 mutations and genetic counseling should be offered to affected families .\noutput:\n" }, { "from": "agent", "value": "heterozygous mutations in gata2 underlie different syndromes , previously described as monocytopenia and mycobacterial avium complex infection ( monomac ) ; dendritic cell , monocytes , b - and nk lymphocytes deficiency ( dcml ) ; lymphedema , deafness and myelodysplasia ( emberger syndrome ) and familiar myelodysplastic syndrome / acute myeloid leukemia ( mds / aml ) . onset and severity of clinical symptoms vary and preceding cytopenias are not always present.we describe a case of symptomatic dcml deficiency and rather discrete bone marrow findings due to gata2 mutation . exome sequencing revealed a somatic asxl1 mutation and the patient underwent allogeneic stem cell transplantation successfully ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: coronary artery ectasia ( cae ) has been defined as localized or diffuse dilation of the coronary arteries exceeding the 1.5 fold of normal adjacent segment in coronary angiography . cae is a rare finding among coronary artery anomalies and considered to be of either congenital or acquired origin . it is estimated that 50 % of cae is related to atherosclerosis , whereas 20 % 30 % of cases may be due to congenital anomalies . although it has been suggested that ectasia is commonly a variant of atherosclerosis , it is not known clearly why some patients with obstructive coronary artery disease ( cad ) develop cae , whereas others do not . tumor necrosis factor - alpha ( tnf - ) and interleukin - 6 ( il - 6 ) are significantly associated with coronary atherosclerosis . although the increase in the plasma levels of tnf - and il - 6 in obstructive cad is well known , limited data are available in cae . in this study , we aimed to evaluate the plasma levels of the cytokines ; tnf - and il - 6 in cae patients . the study population was selected from a series of 1820 consecutive patients who underwent coronary angiography in our hospital between january 2008 and september 2008 due to the presence of chest pain or positive or equivocal results of noninvasive screening tests for myocardial ischemia . out of the 1820 patients , 36 consecutive patients who had angiographically normal coronary arteries with cae ( group i , 28 male , mean age : 58.212 years ) and accepted to participate to our study after giving informed consent were identified and compared with age , and sex - matched 32 consecutive participants with angiographicallyshow normal coronary arteries without cae ( group ii , 25 male , mean age : 57.210 years ) . no significant difference was present between the two groups regarding the use of acetylsalicylic acid , beta blockers , nitrates , calcium - channel blockers , and statins . the study protocol was approved by the institutional ethics committee , and the study was conducted in accordance with the decleration of helsinki and good clinical practice ( gcp ) / international conference on harmonization ( ich ) guidelines . subjects were excluded if they had evidence of traumatic injury , acute coronary syndrome history , obstructive cad , left ventricular dysfunction , left ventricular hypertrophy , cardiomyopathies , congenital heart disease , valvular heart disease , any abnormality in thyroid function test , arrhythmias , clinically unstable medical illness such as hepatic or renal impairment ; a history of seizure , head trauma , or stroke , active infection , allergy , active inflammation , collagen vascular disease , cancer , and any other primary disease interfering with immune functions . in all patients , coronary angiography was performed using the philips angioscop x - ray ( integris bh 5000 , philips medical systems , best , the netherlands ) using standard judkins technique . two experienced cardiologists , unaware of the patients clinical characteristics and biochemical results , reviewed all of the angiographic images . we used iohexol ( omnipaque , nycomed ireland , cork , ireland ) as contrast agent during coronary angiography in the study patients . a coronary diameter index was defined for each segment as the coronary diameter divided by the body surface area ( bsa ) . a coronary segment with a diameter index 1.5 fold of the control group was defined as ectatic . when there was no identifiable adjacent normal segment , the mean diameter of the corresponding coronary segment in the control group served as normal values . blood samples of all individuals were taken 24 hours after coronary angiography from an antecubital vein . blood samples were centrifuged immediately at 250 g for 10 minutes and stored at + 4c until assay . triglyceride , total cholesterol , low - density lipoprotein ( ldl ) cholesterol , and high - density lipoprotein cholesterol concentrations were measured by automated chemistry analyzer ( aeroset , abbott , ill , usa ) by using commercially available kits . ten ml of heparinized venous blood were collected with the plastic tubes from subjects at 08.00 a.m. blood samples were santrifuged at 3000 rpm ( rotor diameter : 16 cm ) and preserved at 80c . analyses were performed by the immunologists , who were blinded to the condition of the samples . il - 6 , tnf - enzyme - linked immunosorbent assay ( elisa ) kits were purchased by biosource international inc . ( camarillo , calif , usa ) and used according to the recommendations of the manufacturer . the minimum detectable doses of tnf - and il - 6 are 1.1 pg / ml , 2.2 pg / ml , respectively . statistical analysis was performed by using spss for windows 11.0 ( chicago , ill , usa ) . continuous variables were expressed as mean sd , and categorical variables were expressed as percentage . comparison of categorical and continuous variables between groups was performed by using x test and student 's t - test or mann - whitney u - test . the correlation between tnf - and il - 6 levels and the number of ectasic vessels was assessed by the pearson correlation , or the spearman tests were appropriatereproducibility was estimated by analyzing all recordings on 2 separate occasions ( intraobserver variability ) ; to assess interobserver variability , investigators were blinded . baseline demographic , clinical , and angiographic characteristics of the two groups were similar ( table 1 ) . tnf - and il - 6 levels were significantly higher in cae group than controls ( 15.611.2 pg / ml versus 7.83.7 pg / ml , p .001 , and 17.212.6 versus 7.62.1 p .0001 , resp . ) ( table 2 ) . besides no correlation was found between the tnf - , il - 6 levels and the number of ectatic vessels ( r = 0.012 , and r = 0.138 , resp . the main finding of the present study was that patients with isolated cae had significantly higher tnf - alfa and il - 6 levels compared to control subjects with angiographically normal coronary arteries . cae is a well - recognized angiographic finding of abnormal coronary dilatation , and detected in 0.3 % 5.3 % of consecutive angiographic studies . the gold standard for diagnosis of this type of ectasia is coronary angiography , which provides information about the possible size , sample , location , and number of ectasias . clinically , it predisposes to adverse coronary events like vasospasm , thrombosis , and dissection . in some studies , although many etiologies of cae have been reported , the common coexistence with cad has raised the idea that cae may be a variant of cad . individual case reports have shown that isolated cae may be a cause of silent myocardial ischemia . in this study , we found significantly higher levels of il - 6 in cae patients when compared to control subjects with normal coronary arteries . we suggest that this inflammatory state in the cae patiens is responsible for higher tnf - and il - 6 levels in cae . a recently published investigation reported that coronary flow reserve is significantly reduced in patients with cae and put forward that microvascular dysfunction may be the underlying cause of exercise - induced myocardial ischemia . there is now a well - known common aggreement that atherosclerosis is an inflammatory disorder of the vessels . although cause and pathways of atherosclerotic process are probably multiple and different in various clinical settings , the data showed that an inflammatory process was involved in all stages of atherosclerosis including coronary spasm , delayed coronary flow , coronary microvessel dysfunction , silent myocardial ischemia , and restenotic process . as a results of these data , the idea of chronic inflammation as one of the key factors involved in atherosclerosis has come out and broaden into a new area of atherosclerotic diseases . a few recent data have also emphasized that cae is associated with systemic inflammatory response exposed by inreased inflammatory cytokines and c - reactive protein ( crp ) . recently , a study indicated a cytokine - induced tissue inflammation in the pathogenesis of abdominal aortic aneurysms , and it has been documented that circulating il - 6 levels increase in these patients . studied with cae , and found that serum il - 6 levels were significantly higher in patients with cae compared to controls . studied the cae and found that mean fluorescence intensity of cd45 and cd11b on the monocyte surface of patients with cae was significantly higher when compared to controls . they speculated that increased levels of cellular adhesion molecules in patients with cae may be an indicator of endothelial activation and inflammation and are likely to be in the causal pathway leading to coronary artery ectasia . . demonstrated that the levels of crp , a specific marker of chronic inflammation , were significantly higher in patients with isolated cae . a recently published study showed that patients with isolated cae have raised levels of plasma soluble intercellular adhesion molecule - 1 ( icam - 1 ) , vascular cell adhesion molecule - 1 ( vcam - 1 ) , and e - selectin in comparison with patients with obstructive cad without cae and subjects with normal coronary arteries . in addition , turhan et al . evaluated crp levels as a specific marker of inflammation in patients with cae . all these data indicate the presence of a chronic inflammation in the coronary circulation of the patients with cae . accordingly , cae has been suggested to be a destructive inflammatory lesion of the vascular wall . briefly , the approving of the importance of inflammation in atherosclerosis has both theoretical and practical clinical implications . the data have demonstrated that cae is associated with inflammatory response exposed by increased inflammatory cytokines . in conclusion , we found that tnf - and il - 6 levels were significantly higher in cae patients than subjects with normal coronary arteries . we think that tnf - and il - 6 measurements may be a good prognostic value in cae patients as in stenotic ones , suggesting that vascular wall inflammation may play a role in the pathogenesis of cae . further placebo - controlled studies are needed to evaluate the clinical significance of increases in these markers .\noutput:\n" }, { "from": "agent", "value": "background / aim . coronary artery ectasia ( cae ) is considered as a variant of atherosclerosis . tumor necrosis factor - alpha ( tnf - ) and interleukin - 6 ( il - 6 ) are among the sensitive markers of systemic inflammation . the aim of this study was to evaluate the plasma levels of the cytokines ; tnf - and il - 6 in cae patients . methods . plasma concentrations of tnf - and il - 6 were measured in 36 patients with cae ( 28 males , mean age : 58.2 12 years ) , and results were compared with age and sex - matched controls ( n = 32 ) without coronary artery ectasia . tnf - and il - 6 concentrations in blood were assesed by enzyme - linked immunosorbent assay ( elisa ) . results . baseline characteristics of the two groups were similar . tnf - and il - 6 levels were significantly higher in cae group than controls ( 15.6 11.2 pg / ml versus 7.8 3.7 pg / ml , p < .001 , and 17.2 12.6 versus 7.6 2.1 p < .0001 , resp . ) . conclusion . cae patients showed increases in tnf - and il - 6 levels compared to the controls . this study provides evidence for alterations in the proinflamatory cytokines which suggest the involvement of the immune system in the pathophysiology of cae . further placebo - controlled studies are needed to evaluate the clinical significance of this increase in tnf - and il - 6 levels ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: diabetes mellitus is a group of metabolic diseases characterized by hyperglycemia resulting from defects in insulin secretion , insulin action , or both . there are three major types of diabetes : type 1 diabetes , type 2 diabetes , and gestational diabetes . type 1 diabetes mellitus ( t1 dm ) is produced by the destruction of cells of the pancreas . this leads to insulin deficiency , which can be mild initially , but develops quickly towards a complete lack of the hormone . the velocity of - cells destruction is variable and in case of infants it usually progresses rapidly while this loss is somewhat slower in case of adults . a predisposition to develop t1 dm is passed through generations in families , but the inheritance pattern is unknown . moreover , there are also environmental factors related to the probability of developing t1 dm that are still unclear . generally , people with t1 dm present with acute symptoms of diabetes and markedly elevated blood glucose levels .1 the pathophysiology of type 2 diabetes mellitus ( t2 dm ) combines defects that lead finally to hyperglycemia . first of all , there is insulin resistance produced in the striated muscle ( also called peripheral insulin ) and insulin resistance produced in the liver ( also called central insulin resistance ) . however , since the cells fail to maintain sufficient hormone quantity to offset insulin resistance , hyperglycemia arises , which indicates failure in insulin secretion . this form of diabetes accounts for 90 % 95 % of those patients with diabetes , but many cases remain underdiagnosed until complications appear . at the mild stagehowever , as this type of diabetes is progressive and chronic , it requires more intensive therapy as the disease progresses . eventually , patients need to take medication to keep blood glucose at normal levels .1 diabetes mellitus is a worldwide problem , which accounted for 1.3 million lives in 2008.2 this chronic illness requires continuing medical care and patient self - management education . in addition to the consequences of abnormal glucose metabolism , diabetes mellitus can lead to long - term complications ( cardiovascular , peripheral vascular , ocular , neurologic , and renal ) .3,4 in europe , there are about 60 million people with diabetes , approximately 10.3 % of men and 9.6 % of women aged 25 years and over . across countries , germany , spain , and italy were respectively on the second , fourth , and fifth position regarding the highest numbers of people with diabetes in europe in 2013.5 diabetes mellitus has been shown to be an expensive condition , costing the european union over 50 billion per year .6,7 the impact of diabetes can be measured by using the concept of burden of disease ( bod ) , which is used to assess and compare the relative burden of different conditions by quantifying health loss due to the disease and injury that remains after treatment , rehabilitation , or prevention efforts of the health system and society in general .8 the bod can be measured by cost , morbidity , and mortality . in the last few decades , this burden has been increasingly measured across nations for comparability purposes .912 disability - adjusted life years ( dalys ) 13 are a measure that combines the concept of potential years of life lost due to premature death and years ofhealthy life lost in states of less than full health ( disability states ) ; 14 hence , dalys reflect the burden of a condition and facilitate comparisons of different ( in theory all ) types of health conditions or health outcomes . in particular , dalys may be used to include the burden caused by disability and chronic diseases in cost - effectiveness studies .15 compared to quality - adjusted life years ( qalys ) , dalys permit comparisons across different interventions or health areas to understand the effectiveness of a portfolio of interventions by using a standardized set of disability weights .16 the objective of this study was to carry out a literature review to collect data on epidemiology , life expectancy ( le ) , mortality , quality of life ( qol ) , and disability for daly calculation on diabetes for france , germany , italy , spain , and the uk . the data were used to calculate the number of dalys for the total patient population with diabetes for the countries of interested by sex and age group and to compare between countries for 2010 . the daly is a health gap measure that combines information on fatal and nonfatal health outcomes ; hence , the daly measures the health loss . the basic assumption of dalys is that similar events would be treated equally in all populations to ensure comparability ; hence , individual characteristics are restricted to age and sex . this research used the hybrid daly ( h - daly ) approach to calculate the dalys for comparisons .17,18 h - dalys are calculated by adding incidence of years of life lost ( ylls ) to prevalence of years lived with disability ( ylds ) , and thus quantifies both the bod occurring during the reference period and the burden accrued into the future . the hybrid method is a true period - measure because all the data needed to calculate h - dalys can be measured in the time period . the yll is the number of years that death occurred earlier than the age the person was expected to die if he / she had not suffered from the disorder causing death . yll was calculated as follows : ( 1 ) yll = delwith de being the number of deaths related to diabetes as the primary cause in a certain time period and l being the residual le at each year of age8 ( standard le when being in a certain age category ) . the yld is the number of years due to disability and is calculated by multiplying the years lost with a disability weight reflecting the severity of the condition . yld is calculated as follows : ( 2 ) yldpervx = pxdwxwith px being the prevalent cases and dwx being the disability weight . from the prevalence andthe population data , the prevalent cases with diabetes per age category are calculated as the outcome of prevalence multiplied by population ( total ) , which are calculated per country , age group , and sex . then , the daly formula is as follows : ( 3 ) dalys = yldsprevx + ylls in this study , since the incidence of diabetes was not available to calculate the ylds component of the daly , an incidence - based method was not feasible . nonetheless , the data available on prevalence for diabetes of different age categories were available for france , germany , italy , spain , and the uk . moreover , the discounting process is not applicable in this context since this study is a static picture of the burden of diabetes in 2010 . finally , no age - weighting factor was applied to dalys , which is similar to the last version of the global bod by murray et al , which also did not apply any age weights .19 the h - daly avoids both the polio and elvis problems . the polio problem refers to the fact that the incidence is captured at a certain point in time and if there are no new cases in the next year , the burden might be underestimated . the elvis problem refers to the counterfactual assessment that overestimates the prevalence since some cases could be diagnosed many years ago . moreover , only ylls were calculated from an incidence perspective , which makes it easy to choose death as the event and connect all ylls to the moment of death . the hybrid methods consistently combine the projection of the future duration of disability ( incidence part ) and the knowledge of deaths that occurred prior to the time period in question ( prevalence part ) . the demographic data on the population size specified by age and gender were collected for every country from each national statistics database .2024 similar to population size data , le ( which is not related to any specific disease ) by age group , and sex were collected for the five countries from their national statistics . the epidemiological data with reference to prevalence were obtained from each national statistics database , except for france ( ricci et al ) 25 and germany ( heidemann et al ) .26 prevalence data for the uk included region - specific data for england ,27 scotland ,28 wales ,29 and northern ireland .30 to be able to compare the uk with other countries of interest , uniform age categories for the communities within the uk were defined . for the age group 014 years , prevalence data only included t1 dm , as no data on type 2 diabetes for this age category were available . it is assumed that 97 % of the population in this age group was suffering from t1 dm . the demographic data on deaths caused by diabetes from france ,31 germany ,32 italy ,33 spain ,34 and the uk35 were obtained . diabetes mortality rates were obtained by using the number of deaths due to diabetes relative to the total population . figures 1 and 2 contain estimations of mortality due to diabetes for men and women , respectively . in case of men s mortalitydifferences across countries are clear : the uk had the lowest mortality rate while france is the second best - off ; the mortality rates for france were two times higher than the uk rates . at the age range 75 + years , germany and spain had very similar mortality rates . by far the highest value was for italy , where more than 250 out of 100,000 men aged 75 years and over died from diabetes in 2010 . for women ( figure 2 ) , diabetes mortality was quite low for the younger age ranges but there was a steep increment from 6574 years to the 75 + years age range for france , germany , italy and spain . for instance in italy , the mortality rate went from 40 to 263 per 100,000 women . these rates were used to obtain the yll by using the average age of death per age group and le for every age group . the full formula used for yll calculationwas derived from the world health organization ( who ) and fox - rushby and hanson .10,12 furthermore , for this study , the disability weights for the treated population were 0.033 . it is assumed that 2.4 % of the adult population 15 years old and over are not treated for their diabetes based on estimates by hill et al ; the disability weight applied for untreated diabetics was 0.012.36 these disability weights were obtained from the global bod study .9 for children between 014 years old , it is assumed that this population was 100 % treated since they almost always uniquely suffer from t1 dm . for the sensitivity analysis , a disability weight of 0.07 was used for yld calculation based on stouthard et al and mathers et al. 37,38 the demographic data on the population size specified by age and gender were collected for every country from each national statistics database .2024 similar to population size data , le ( which is not related to any specific disease ) by age group , and sex were collected for the five countries from their national statistics . the epidemiological data with reference to prevalence were obtained from each national statistics database , except for france ( ricci et al ) 25 and germany ( heidemann et al ) .26 prevalence data for the uk included region - specific data for england ,27 scotland ,28 wales ,29 and northern ireland .30 to be able to compare the uk with other countries of interest , uniform age categories for the communities within the uk were defined . for the age group 014 years , prevalence data only included t1 dm , as no data on type 2 diabetes for this age category were available . it is assumed that 97 % of the population in this age group was suffering from t1 dm . the demographic data on deaths caused by diabetes from france ,31 germany ,32 italy ,33 spain ,34 and the uk35 were obtained . diabetes mortality rates were obtained by using the number of deaths due to diabetes relative to the total population . figures 1 and 2 contain estimations of mortality due to diabetes for men and women , respectively . in case of men s mortalitydifferences across countries are clear : the uk had the lowest mortality rate while france is the second best - off ; the mortality rates for france were two times higher than the uk rates . at the age range 75 + years , germany and spain had very similar mortality rates . by farthe highest value was for italy , where more than 250 out of 100,000 men aged 75 years and over died from diabetes in 2010 . for women ( figure 2 ) , diabetes mortality was quite low for the younger age ranges but there was a steep increment from 6574 years to the 75 + years age range for france , germany , italy and spain . for instance in italy , the mortality rate went from 40 to 263 per 100,000 women . these rates were used to obtain the yll by using the average age of death per age group and le for every age group . the full formula used for yll calculationwas derived from the world health organization ( who ) and fox - rushby and hanson .10,12 furthermore , for this study , the disability weights for the treated population were 0.033 . it is assumed that 2.4 % of the adult population 15 years old and over are not treated for their diabetes based on estimates by hill et al ; the disability weight applied for untreated diabetics was 0.012.36 these disability weights were obtained from the global bod study .9 for children between 014 years old , it is assumed that this population was 100 % treated since they almost always uniquely suffer from t1 dm . for the sensitivity analysis , a disability weight of 0.07 was used for yld calculation based on stouthard et al and mathers et al. 37,38 detailed results of yll , yld , and daly for 2010 are presented in table 1 . estimates for france , germany , italy , spain , and the uk were calculated as a rate per 1,000 inhabitants ( inh ) in order to compare results between countries . overall , the relative burden of diabetes was shown to be the highest for germany and italy : their estimates were 5.9 and 5.8 dalys per 1,000 inh , respectively . on the contrary , the uk had the lowest value of total dalys lost , at 2.94 dalys per 1,000 inh . in between these extremes , the negative impact of diabetes in france and spain caused 3.70 and 4.36 dalys per 1,000 inh , respectively . as has been mentioned , each component of the daly reflects the health losses associated with diabetes . the yll is the difference between the expected age at death ( le ) and actual age at death ( mortality due to diabetes ) . regardless of sex , estimates of yll were greater than yld for france , germany , italy , and spain ; in contrast , ylds were greater than ylls for the uk . the differences were driven by the values of yll for both sexes . for instance , for men , although ylds values could be considered that follow a similar pattern , the uk has one - third of germany s yll . indeed , the difference between the highest and the lowest yld was 0.49 , while the disparity in yll values was 2.49 points . this suggests that there is a higher burden caused by mortality due to diabetes for france , germany , italy , and spain , whereas in the uk , the burden due to disability was higher . differences in daly values indicate that the burden of diabetes was higher for women compared to men in germany , italy , and spain in 2010 . conversely , dalys in france and the uk were higher for men , suggesting a higher burden of diabetes for men compared to women in these two countries of interest . the total number of dalys per age group for men and women are shown in figures 3 and 4 , respectively . diabetes dalys lost for men were very low for the younger age ranges , for all countries . however , in the uk , for those aged 3544 years , the burden increased substantially , while diabetes dalys remained low for the rest of these countries of interest . diabetes was shown to consistently increase the burden of the disease across all age groups in france , germany , italy , and spain with the exception of the uk , whose burden did not start to expand again until the 5564 years age group upwards ( figure 3 ) . diabetes dalys for women were very low for the younger age ranges in 2010 ( figure 4 ) . the impact of diabetes continued quite constantly until the 4554 years age group , after which diabetes burden became notable . although increments of dalys lost for the 4554 and 6574 years age groups were modest , diabetes burden increased heavily in the older age groups , for all five countries . for all five countries , dalys due to diabetes of the elderly population ( 6574 and 75 + years ) were divergent across countries for both men and women , which suggests that burden of the disease is quite different across countries for the oldest groups . indeed , the uk s values were almost one - third of the dalys in germany . the increasing number of dalys along with older ages might be explained due to the increasing prevalence and mortality of diabetes in older age groups ( figures 1 and 2 ) . thus , it is straightforward to distinguish different patterns : italy , germany , and spain had a steep increment in diabetes burden as age increases , while the uk was shown to have the mildest burden , and france was in between the two trends . in the sensitivity analysis , the disability weight used was 0.07 for the treated and untreated diabetics ; 25 the results are shown in table 2 . this fact is reflected in the dalys estimates : the loss of dalys due to diabetes was higher for all countries in comparison with the base case . the ranking is unaltered : germany has the highest daly loss , italy is the second worse - off , the third position was held by spain , and the fourth and fifth positions were held by france and the uk , respectively . despite the unaltered burden ranking , germany also has the biggest difference if we compared estimates of the sensitivity analysis and the base case ( 2.87 daly per 1,000 inh ) . the second biggest difference was for the uk , which had 2.17 dalys extra per 1,000 inh . the smallest difference was for france , with a difference of only 1.6 daly lost per 1,000 inh . in the sensitivity analysis , the disability weight used was 0.07 for the treated and untreated diabetics ; 25 the results are shown in table 2 . this fact is reflected in the dalys estimates : the loss of dalys due to diabetes was higher for all countries in comparison with the base case . the ranking is unaltered : germany has the highest daly loss , italy is the second worse - off , the third position was held by spain , and the fourth and fifth positions were held by france and the uk , respectively . despite the unaltered burden ranking , germany also has the biggest difference if we compared estimates of the sensitivity analysis and the base case ( 2.87 daly per 1,000 inh ) . the second biggest difference was for the uk , which had 2.17 dalys extra per 1,000 inh . the smallest difference was for france , with a difference of only 1.6 daly lost per 1,000 inh . the present study provides a reliable image of the burden of diabetes for france , germany , italy , spain , and the uk in 2010 according to the methodology by the who .19,20 we provide estimates on diabetes itself , not based on the comorbidities due to diabetes . the approach used presents a broad insight of the burden of this condition because it makes comparison between countries feasible . using the h - daly method , with incidence ylls and prevalence ylds , dalys due tothe major part of the burden was caused by premature mortality in france , germany , italy , and spain . however , disability due to diabetes was shown to be the primary contributor to the burden for the uk . a possible explanation for the lowest daly due to diabetes in the uk could be that the age - specific mortality has been decreasing , with considerably fewer numbers of deaths due to diabetes from the age of 65 years in men and women compared to the mortality rates of the other countries of interest . further , given that ylds are quite similar across countries , the results suggest that diabetes is better managed in the uk , avoiding fatal events associated with this condition . given these results , to determine in which country the burden of diabetes was the largest , dalys seemed necessary since the burden is not mainly driven by epidemiological frequency ( mortality ) . additionally , it was possible to compare the burden of diabetes in men and women . overall , men had a higher number of dalys ( 46.46 per 1,000 ) compared to women ( 35.52 per 1,000 ) despite the steep increase in the number of dalys in women from 75 + years . regarding the methodological aspects , h - dalys have the advantage of avoiding both the polio and elvis problems , and only ylls were calculated from an incidence perspective , which makes it easy to choose death as the event and connect all ylls to the moment of death .20 all the data needed to calculate h - dalys can be measured at the time in question , so these dalys are a true period measureprevalence data were not directly available for all districts from one national statistics database in the uk . therefore , prevalence data were taken from different sources and adjusted to the relevant age categories . in case prevalence informationwas missing for an age category , it was estimated based on the mean prevalence of an equivalent age category from another country of interest . secondly , disability weights were equal for all age categories and for both sexes as no direct qol data were available to obtain individual disability weights that could have affected ylds . in general , diabetes might be perceived differently at different ages ,39 which could vary the estimates . therefore , either different disability weights should be applied for each age range or age weighting should be introduced . both alternatives are controversial , and so far , there is no agreement of consistent estimates of potential weights ( murray and acharya , 1996 ; anand and hanson , 1997 ) . moreover , in this study , a sensitivity analysis was performed with alternative disability weights , which was shown to vary results significantly , and estimates indicate a greater burden of diabetes for all countries included in this analysis . thirdly , the assumptions of this study are consistent with hill et al , whose estimates suggested that 2.4 % of diabetics in the us are not being treated .36 we were aware that this percentage might be different due to region - specific characteristics though . the estimates of dalys from this study for treated and untreated patients are pooled in a single number and further research is needed in order to estimate more specific dalys , since diabetes is a heterogeneous disease . results of this study suggest that mortality due to diabetes has been postponed until older ages in most cases . while the burden of diabetes due to premature death was still significant in 2010 , it is also important to remark the substantial burden of diabetes whose medical consequences lead to disability problems . therefore , greater allocation of resources to prevent diabetes or to reduce its impact on qol may be necessary in the upcoming years . this study estimated the burden of diabetes for france , germany , italy , spain , and the uk in 2010 by using the h - daly method . the results show that germany has the highest number of total dalys lost , with a rate of 5.9 for 2010 in their population due to diabetes , while the uk has the lowest number of dalys due to diabetes . with reference to the male population , diabetes health loss estimates show that germany has the highest number of dalys , while the uk had the lowest number of dalys . these results are equivalent for the female population : germany had the biggest burden measured by 9.32 dalys due to diabetes and the uk had 4.72 dalys , which were also the lowest compared to the other countries of interest . furthermore , dalys lost to diabetes for men and women are relatively lower at younger ages and significantly increase from the 3544 years age group in all the populations of the countries of interest . this pattern may be explained by the increasing prevalence and mortality of diabetes among the older age groups . it is worth mentioning that for all countries except for the uk , a significant increase in dalys lost to diabetes in women is observed for the 75 years and over population , which may lead to a higher burden of diabetes for the national health system due to a higher likelihood of elderly women in developing comorbidities at these ages . dalys have been increasingly cited as a powerful tool to estimate the burden of different conditions and these results could be useful for the policy making process , since dalys seem to be a necessary measure to determine which country has the largest burden of diabetes . however , as for other measures , dalys should not be used as a cookbook recipe to implement public policies .\noutput:\n" }, { "from": "agent", "value": "aimsto compare the burden of disease ( bod ) attributable to diabetes expressed in disability - adjusted life years ( dalys ) for five european countries in 2010 . methodsdalys lost to diabetes as the sum of years of life lost and years lived with disability were estimated by sex and age using country - specific epidemiological data and global disability weights . data from various secondary sources were combined to estimate health loss due to diabetes for france , germany , italy , spain , and the uk . national statistical databases were used and if necessary , community studies were used to derive the prevalence of diabetes by sex and age group , which were weighted proportionately for a national population burden of disease estimate . all identified data were adapted to the global burden of disease methodology ( 2010 ) to calculate the burden attributable to diabetes . no age weighting and discounting was applied . sensitivity to different sources of variation was examined . germany and italy lost the largest number of dalys due to diabetes , with 5.9 and 5.8 per 1,000 inhabitants , respectively , followed by spain ( 4.4 ) , france ( 3.7 ) , and the uk ( 2.9 ) . the highest burden was caused by mortality due to diabetes , with the exception of the uk , for which the burden due to disability of diabetes was higher . mean dalys lost were higher for women in germany , italy , and spain and shown to increase with age for all countries . sensitivity analysis in variation in disability weights and uncertainty in epidemiological data were shown to have effects on dalys lost.conclusionin spite of data limitations , the estimates reported here show that daly loss due to diabetes imposes a substantial burden on countries . cross - national variation in disease epidemiology was the largest source of variation in the burden of diabetes between countries ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: a 3 - step method was used to establish the distribution of spirochetes in rice - water stool : 1 ) the presence of spirochetes in rice - water stool was determined by using dark - field microscopy ; 2 ) the diversity of brachyspira spp . within a subset of these patients was quantified by 16s rdna analysis ; and 3 ) the genetic diversity within the most abundant species was determined by analysis of nadh oxidase ( nox ) . rice - water stool samples were collected from symptomatic cholera patients ( 15 years of age with no history of antimicrobial drug therapy ) during the spring cholera outbreak of 2006 in dhaka , bangladesh , at the international centre for diarrheal disease research , bangladesh , as part of a larger study ( 14 ) . samples were examined by dark - field microscopy for v. cholerae and other bacteria , and the presence of v. cholerae , lytic vibriophage , and etec was determined by using standard methods ( 14 ) . samples were preserved at 4c in formalin , or cell pellets were resuspended in phosphate - buffered saline and 15 % glycerol and stored at 80c . analysis showed that 36 % ( 23/64 ) of samples that were positive for only v. cholerae also harbored spirochetes ( technical appendix , panels aspirochetes were also found in 4/11 and 5/15 samples that harbored etec alone or both etec and v. cholerae , respectively . when we removed etec - positive samples as potential confounders , the presence of spirochetes was independent of lytic vibriophage in v. cholerae positive stool samples ( technical appendix , panel g ) , which is in contrast to the documented trend concerning non v . the ratio of spirochetes to v. cholerae was 1 and independent of lytic vibriophage ( technical appendix , panel h ) . in the second step ,10 samples were chosen for molecular analysis on the basis of a large amount of spirochetes . samples were heated ( 99c for 10 min ) , and standard pcr for a diagnostic segment of the 16s rdna gene ( 15 ) was performed by using genus brachyspira specific primers ( 5 - gtcttaagcatgcaagtc - 3 and 5 - aacaggctaataggccg - 3 ) . b. pilosicoli was the most common species , found in all 10 samples ( technical appendix , panel i ) . a second set of panspecific 16s rdna degenerate primers ( 5 - gtttgatyctggctyagarckaacg - 3 and 5 - ccsstacggmtaccttgttacg - 3 ) confirmed the presence of brachyspira spp . and suggested that spirochetes of other genera were not present . culture , purification , and microscopy of b. pilosicoli from glycerol stocks was used to cross - validate the molecular approach . standard fastidious anaerobe agar ( faa ) supplemented with bovine blood ( 10 % ) , spectinomycin ( 400 g / ml ) , and polymyxin b ( 5 g / ml ) was determined empirically to be the optimal medium for isolation of spirochetes . dilutions of glycerol stocks from each patient were plated on faa agar ; single colonies were best obtained with an faa overlay . plates were incubated for 21 days at 37c in an atmosphere of 94 % h2 and 6 % co2 . most colonies gave rise to sigmoidal spiral cell morphotypes similar to the morphotype of the american type culture collection ( atcc ) ( manassas , va , usa ) control strain for b. pilosicoli . consistent with previous studies , b. aalborgi was not cultured from patient samples . in the third step , 5 samples were analyzed by using nox sequence comparisons that yield higher phylogenetic resolution . dna was extracted and a nox segment was amplified by using degenerate primers ( 5 - gcygghacatgggcdgcaaaaac - 3 and 5 - caaatacrcaaatagcrttag - 3 ) . a phylogenetic tree ( figure ) demonstrated that individual patients harbored clonal lines of b. pilosicoli ( patients b , d , and e ) or more diverse strains ( patient a ) . overall , b. pilosicoli strains found in cholera patients were extremely diverse relative to the known outgroup species , which indicates the potential for detection of new species related to intestinal spirochetosis . neighbor - joining ( nj ) phylogeny of nadh oxidase ( nox ) sequences of brachyspira pilosicoli from 5 cholera patients ( a e ) . the nox sequences were pcr amplified , cloned , and sequenced from each patient ( individual clones are appended _ it has been casually observed for a century that stool from cholera patients harbors spirochete - like bacteria . more than one third of the cholera patients had spirochetes in their stools at densities equal to those of v. cholerae . the pathophysiology of intestinal spirochetosis in this setting and its relevance to human health remain unknown . epidemiologic analysis of intestinal spirochetosis has so far relied on retrospective studies of colonic tissue collected for reasons secondary to the disease ( 4 ) . we recommend a community - based prospective study of stool samples from healthy persons and patients with diarrhea by using the techniques described herein ; animal reservoirs should be identified as a potential point of control . in the context of v. cholerae infection , we hypothesize that spirochetes may be present before v. cholerae infection and exacerbate the already devastating clinical course of cholera . conjugated monoclonal antibody ( ab ) to o1 lipopolysaccharide ( panels a and d ) , and nucleic acid was labeled with 4,6 - diamidino -2-phenylindole ( dapi ) ( panels b and e ) , which showed sigmoidal morphology with tapered ends ( 48 m ) indicative of spirochetes . the single curve orthe aggregate ( panel f ) was also stained for mucus ( blue indicates wheat germ agglutinin lectin ) and showed that only a small portion of the aggregate contained mucus . panel g shows spirochetes counted by direct count microscopy in rice - water stool samples relative to the presence or absence of lytic vibriophage . panel h shows the ratio of spirochetes to v. cholerae by direct count microscopy relative to the presence or absence of vibriophage . panel i shows the percentage of spirochetes that were b. pilosicoli as determined by using partial sequence analysis of 16s rdna . pcr amplified products from isolated dnahorizontal bars are median values with interquartile range as whiskers ; medians were not significantly different ( p 0.05 , by mann - whitney u test ) ; scale bars = 10 m .\noutput:\n" }, { "from": "agent", "value": "the microbes that accompany the etiologic agent of cholera , vibrio cholerae , are only now being defined . in this study , spirochetes from the genus brachyspira were identified at high titers in more than one third of cholera patients in bangladesh . spirochetosis should now be tracked in the setting of cholera outbreaks ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: light - cured composite resins ( lccrs ) have been studied extensively in recent years . the formulation proposed by bowen ( 1963 ) , which is still in use today albeit with slight modifications , consists basically of a resin matrix , filler particles , monomers and a photo absorbing compound . the latest development in this field has been the introduction of low shrinkage monomers and nanofiller particles . lccr ( polymerase chain reaction ) materials are present in filtec z350 ( 3m / espe , saint paul , mn , usa ) , which combines nanometric particles and nanoclusters in a conventional resin matrix , and in admira ( voco , cuxhaven , germany ) , whose resin matrix contains ormocer , an organically modified ceramic . the light - curing units ( lcus ) equipped with a light - emitting diode ( led ) , which produces cold light at 450 nm wavelength , is a promising device of costs and efficiency . however , the lcu operating with a halogen lamp is still the first choice of clinicians and extensive research has been dedicated to testing its efficiency . the present research focused on one of the important properties of lccrs - surface free energy ( sfe ) , to study the interaction between the forces of cohesion and the forces of adhesion that determine the occurrence of surface wetting . the wetting performance of etched enamel is important in all types of adhesive restorations because of the close interaction between the surface free energy of the etched enamel and the wettability of the luting and bonding material . the contact angle measurement method is probably the most definite way to determine cell surface hydrophobic . the angle is very high for water if substrata are hydrophobic . if the surface is hydrophilic , the droplet quickly dissipates and the measured angle is low . contact angles values vary with surface topography , surface tension of the liquid , surface energy of the substrate and the level of interaction between the liquid and solid . hydrophobic materials are more color - stable and stain - resistant than hydrophilic materials . gaps formed at the tooth / restoration interface may be caused by inadequate wetting of the tooth surface by the restorative material along the preparation walls during placement . surfaces with a low surface free energy minimize plaque formation . to calculate de sfe , the first step consists of measuring the contact angle ( ca ) between the solid under study and the test liquid , using a contact angle goniometer . the ca which is the macroscopic expression of the micro and macroscopic phenomena occurring between the solid , the test liquid . the acid - base theory involves the multicomponent approach , whereby the sfe occurs through dispersive interactions or lifshitz - van der waals ( lw ) and lewis acid - base ( ab ) interactions . the second approach involves the equation - of - state theory , which is highly criticized from the thermodynamic standpoint . although these theories are based on different concepts , they share the same basic idea , i.e. , they attempt to express the reverse work of adhesion of some of the components of the interfacial tension between liquids and solids . the aim of this work was to evaluate the variations in the surface energy of various composite resins after curing by led and halogen curing devices , based on contact angles and surface free energy . thirty - six test specimens of composite resins ( admira - voco , cuxhaven , germany ; filtec z350 - 3m / espe , saint paul , mn , usa ; grandio - voco , cuxhaven , germany ) were prepared in a 10 mm diameter , 2 - mm thick articulated brass matrix . the specimens were finished with sof - lex discs ( 3m / espe ) and polished with kota diamond paste ( kota dental products , so paulo , brazil ) . the lcus employed were a led device ( elipar freelight ii -1000 mw / cm , 3m / espe ) and a halogen device ( vip tm 500 mw / cm and 600 mw / cm , bisco , inc . , schaumburg , il , usa ) . the light emission control was preset with a radiometer ( demetron 100p / n ; demetron research corp . , the materials ( shade a2 ) were inserted into the matrix in two portions and pressed with two microscope slides to achieve a smooth flat surface , after which they were light - cured in the specimens center for 20 s on each side . twelve samples of each composite were prepared , 6 were light - cured wit a led lcu and 6 with a halogen lamp . all specimens were stored in dark vials at 8c for 1 week , after which they were finished and polished before testing . the static contact angles were measured with a goniometer ( ram - hart 100 - fo , netcong , nj , usa ) using deionized water and glycerol as test liquids ( table 1 ) . the 36 samples were divided into 12 groups of 6 test specimens each , and 6 drops of each liquid were used for the measurements . the computer was set to record 10 contact angle measurements of each drop , so 360 measurements were made for each group , making a total of 4,320 measurements . = relative equilibrium pressure , = interface tension , = interation forces ( london dispersive - debye dipole and keeson dipole - dipole ) = acidic part - acceptor , = basic part - donor the sfe was determined based on the harmonic mean method described by wu ( 1995 ) . because two test liquids are required to calculate the sfe by this method , the samples were divided into 6 groups of 6 test specimens each . a different lcu and test liquidthe contact angle values determined for each group were stored in the computer , and the surface energy was calculated using dropimage standard software , netcong , nj , usa . the values were done by the soft but the calculations can be done by youngs equation : 2 = 12 +1 cos and with the acid - base theory . statistical inter - and intra - group analyses of the data were made using anova and tukey 's test at 0.05 significance level . thirty - six test specimens of composite resins ( admira - voco , cuxhaven , germany ; filtec z350 - 3m / espe , saint paul , mn , usa ; grandio - voco , cuxhaven , germany ) were prepared in a 10 mm diameter , 2 - mm thick articulated brass matrix . the specimens were finished with sof - lex discs ( 3m / espe ) and polished with kota diamond paste ( kota dental products , so paulo , brazil ) . the lcus employed were a led device ( elipar freelight ii -1000 mw / cm , 3m / espe ) and a halogen device ( vip tm 500 mw / cm and 600 mw / cm , bisco , inc . , schaumburg , il , usa ) . the light emission control was preset with a radiometer ( demetron 100p / n ; demetron research corp . , the materials ( shade a2 ) were inserted into the matrix in two portions and pressed with two microscope slides to achieve a smooth flat surface , after which they were light - cured in the specimens center for 20 s on each side . twelve samples of each composite were prepared , 6 were light - cured wit a led lcu and 6 with a halogen lamp . all specimens were stored in dark vials at 8c for 1 week , after which they were finished and polished before testing . the static contact angles were measured with a goniometer ( ram - hart 100 - fo , netcong , nj , usa ) using deionized water and glycerol as test liquids ( table 1 ) . the 36 samples were divided into 12 groups of 6 test specimens each , and 6 drops of each liquid were used for the measurements . the computer was set to record 10 contact angle measurements of each drop , so 360 measurements were made for each group , making a total of 4,320 measurements . = relative equilibrium pressure , = interface tension , = interation forces ( london dispersive - debye dipole and keeson dipole - dipole ) = acidic part - acceptor , = basic part - donorthe sfe was determined based on the harmonic mean method described by wu ( 1995 ) . because two test liquids are required to calculate the sfe by this method , the samples were divided into 6 groups of 6 test specimens each . a different lcu and test liquidthe contact angle values determined for each group were stored in the computer , and the surface energy was calculated using dropimage standard software , netcong , nj , usa . the values were done by the soft but the calculations can be done by youngs equation : 2 = 12 +1 cos and with the acid - base theory . statistical inter - and intra - group analyses of the data were made using anova and tukey 's test at 0.05 significance level . table 2 shows the mean values and standard deviations of the interactions among the various types of lccrs , lcus , and test liquids , as well as the statistically significant differences among the groups as indicated by the tukey 's test . mean values of contact angles ( meansd ) tukey 's multiple comparisons - ( same letters = not statistically significant p 0.05 ) sd = standard deviation the resin admira ( 74.45 ) , using glycerol as the test liquid and the halogen lamp as the lcu , yielded the highest mean ca value , while grandio ( 59.19 ) resin tested with glycerol , using led as the light source , yielded the lowest ca value . the inter - and intra - group ca values showed no significant difference ( p 0.05 ) for the filtec z350 resin , but all values obtained for the resin grandio showed significant differences ( p 0.05 ) . the sfe results listed in table 3 were subjected to tukey 's test , which indicated the absence of statistically significant differences among the groups . mean , standard deviation and standard error for surface free energy ( mj / m ) p 0.05 - not statistically significantthe main controllable variables involved in ca measurements are the light - curing process , the test liquids and the chemical composition of the resin under study . all samples ( shade a2 ) were subjected to 40 s of light incidence upon the center of the sample , which according to lindberg , peutzfeldt and van dijken ( 2004 ) is sufficient to cure the entire surface of such samples . although the intensity of the vip tm ( bisco ) halogen lamp varied from 500 to 600 mw / cm , we do not believe this variation impaired the polymerization of the test specimens of the 3 resins . the intensity of light emitted by a halogen lamp is lower than that emitted by a led unit , but its values still exceed 280 to 300 mw / cm , according to caughman , rueggeberg and curtis ( 1995 ) . in view of the lack of information about the surface energy of these materials , it is difficult to compare our results to those of other author . the test liquids used here had different polarities , in spite of similar values which explains the mean ca values ranging from 59.19 to 74.45 obtained in this study . the degree of purity and the numerous measurements yielded reliable results and low standard deviations . although zisman ( 1964 ) stated that the volume of the drop does not influence ca values , this volume , as well as room temperature and humidity , were standardized in this study in order to reduce the number of variables . the organic matrix of admira resin is composed of ormocer , siloxane organic / inorganic polymer , bis - gma , hema , udma , fe2o3 , tio and 4 - tert - butylcatechol ( tbc ) , and its inorganic matrix contains ba - al borosilicate , a silicon dioxide ( 0.04 - 0.7 m ) - 78 % in weight and 56 % in volume . the presence of these high surface energy particles , which in some samples may have been located close to the surface , could cause a decrease in measured ca values . light curing of the organic material , which closes the carbon chains , also probably interferes in the expression of these particles even in the deepest layers . the diameters of the inorganic particles of filtec z350 and grandio resins are nanometric . wu ( 1973 ) argues that the homogeneous dispersion of inorganic particles in the polymeric matrix is critical , a statement confirmed by von werne and patten ( 2001 ) . hydrophobic polymers and inorganic hydrophilic particles are physically difficult to mix , and phase separation or agglomeration is common in such mixtures , resulting , according to the aforementioned author , in alterations in their mechanical , optical and electrical properties . these particles can be treated chemically used to produce a more hydrophobic or hydrophilic surface . as shown in table 2 , the ca values of the filtek z350 resin showed no major variations in any of the combinations . in view of these results , it is reasonable to assume that the components of the resin in these test specimens were distributed more homogeneously . the ca values of the admira resin revealed greater variations in the two test liquids and the two lcus . among the 3 resins of this study , table 3 lists the mean values of the total sfe calculated for each lccr with respective sd , indicating no significant differences among the groups . the admira resin showed the highest sfe value when light - cured with the led unit ( 40.17 mj / m ) , while the grandio resin displayed the lowest sfe when photo - activated by the conventional halogen lamp ( 34.74 mj / m ) . the statistical analysis of the resins ' sfe data confirmed that the different types of lcu employed to polymerize the resins did not influence these results . this finding is congruent with that reported by glantz and larsson ( 1971 ) , although the resins tested by these authors belong to another generation of composites , whose chemical compositions differ considerably from those used in our study . milosevic ( 1992 ) who studied the adhesion of saliva films on composite resins , stated that polymers are usually known as low - sfe materials with values of about 40 mj / m , and that the particles of their inorganic load have high sfe values . all the results obtained in the present research ( table 3 ) are in agreement with those of this author . the contact angles of the 3 polymers studied here did not differ significantly , as did their wettability . the research recommends the material that showed the highest contact angle ; 2 . polymerization with led or halogen units did not alter the surface free energy of the composite resins .\noutput:\n" }, { "from": "agent", "value": "objectivesthis study evaluated the surface energy and wettability of composite resins polymerized by different light - curing units to ascertain the good wetting of tooth surfaces to achieve adhesion . material and methodfiltek z350 ( 3 m espe ) , admira ( voco ) and grandio ( voco ) resins were selected for the testing procedures . the resins were light cured using led and halogen devices . contact angles were measured goniometrically ( ram - hart f100 ) using water and glycerol as test liquids . surface energy values were calculated with a software program ( dropimage standard ) that uses the harmonic mean method applied to the acid - base theory . the data were analyzed statistically by anova and tukey 's test with a significance of 0.05 . results and conclusionsno statistically significant differences were found between the values of surface energy . the measured wettability differed statistically in most combinations as a function of the type of composite resin , type of light - curing unit , and the test liquid ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: radiological evaluation of the esophagus has the ability to diagnose both structural changes as well as motility disorders .1 while barium esophagography is performed for the detailed evaluation of the esophagus , a timed barium esophagogram ( tbe ) is performed specifically to study the esophageal emptying .2 tbe quantifies the esophageal emptying easily and accurately , and is essential in the initial evaluation of motor dysphagia , commonly caused by achalasia .3 - 5 esophageal scintigraphy , endoscopic evaluation , conventional and high resolution manometry are the other techniques for evaluating esophageal anatomy and functions .6 - 8 however , scintigraphy and manometry are not widely available and endoscopy is not a good modality for the functional assessment of esophagus . scintigraphy technique varies considerably in different institutions including consistency of the radionuclide meal .3 barium studies are cheaper and readily available . various authors have used tbe in predicting response to pneumatic dilation ( pd ) but the technique and interpretation has been variable . moreover , criteria to define response after pd according to esophageal emptying as seen in tbe also need standardization . this review discusses technique of performing tbe , interpretation and its utility in clinical practice . the technique of tbe is similar to the usual barium swallow with some modifications , which include taking multiple sequential films at pre - decided time interval after a single swallow of a fixed volume of a barium suspension of specific density . several techniques of tbe have been described in the literature by various authors with minor variations .3 - 5 patients are advised overnight fasting prior to tbe .9 entire study is performed in the erect posture using standard radiography machine . a low density barium sulphate suspension ( 45 % weight by volume ) is ingested orally within 15 - 20 seconds ( fig .1 ) . the volume of suspension ( usually 100 to 250 ml ) used for this study should be such that patient can tolerate it well without regurgitation or aspiration and the dilated achalasic esophagus can be filled adequately . left posterior oblique films are taken 1 , 2 and 5 minutes after barium ingestion ( fig . usually , three - on - one spot radiographs of 1414 or 1417 inches size are taken . the distance between the fluoroscope carriage and the patient is kept constant during all three spot films . the 2 - minute radiograph is optional , but fluoroscopy is done at 2 - minute to see the state of esophageal emptying . if barium completely clears from the esophagus on the 2 - minute film , the 5 - minute film may be omitted .3 one can choose smaller volume of barium suspension especially for pediatric patients . for sequential studies before and after treatment for achalasia , one should consume the same volume of barium as ingested for the baseline examination to have consistent results .3 in achalasia patients with a massively dilated esophagus , if the barium column can not be fit on a three - on - one spot film , a two - on - one spot film should be taken .3 if the height of the barium column is not fitting length - wise on one film , a spot film is exposed centered over the lower portion of esophagus , followed immediately with another spot film centered over the upper portion of the esophagus . subsequently , a fixed point is located on each film ( usually a vertebral body ) that serves as a reference point for both the films . the barium column above or below the reference point is measured on the respective films and added to estimate the height of the entire barium column . in patients with vigorous achalasia , exposing the spot film at a time when the barium column is continuous is difficult due to prominent tertiary esophageal contractions .3 in such situation , film should be exposed when the esophagus is relaxed . in patients with achalasia , the esophagus usually contains retained food material and secretions , which may form a barium - foam interface after the patient ingests the barium . in such situation , objectively measuring the height of the barium column may be difficult . when a barium - foam interface forms , one should measure the superior aspect of the barium column at a point where the margin is consistent and reasonably well defined ( fig . the degree of esophageal emptying can be assessed both qualitatively as well as quantitatively . for quantitative assessment , the height of the barium column is measured from its distinct superior level to the esophago - gastric junction . in patients with achalasia , two horizontal parallel lines , one at the lowest and the other at the highest barium level are drawn and the distance between the two is measured ( fig . diameter of the esophagus can also be measured at the widest part of the barium column perpendicular to the long axis of the esophagus . while many authors have used height and width of barium column in sequential films to assess the emptying , others have used the area of the barium column .3 - 5,9,10 the tbe is a reproducible technique for estimating esophageal empting with almost perfect inter - observer agreement .3 barium completely empties from esophagus in 1 minute in most and in 5 minutes in all healthy individuals .11 in achalasia , esophageal aperistalsis with incomplete lower esophageal sphincter ( les ) relaxation leads to stasis in esophagus , thus the barium column persists for longer time as compared to healthy person . as the obstruction persists , the esophagus dilates over time ( decompensates ) . persistence of barium in esophagus and incomplete or partial emptying over 5 minutes of the study along with other features like ' bird beak ' appearance of les and tertiary contractions in body of esophagus help in diagnosis of achalasia , which is however , confirmed by manometry . the aim of management in these patients is to facilitate the esophageal emptying by early and effective treatment , and prevention of further esophageal dilatation .5 severity and number of achalasia - related symptoms may not correlate with the radiographic findings observed on routine imaging . hence , for the assessment of severity of achalasia , a physiological assessment of esophageal emptying such as tbe is required .12 the improvement in esophageal emptying after successful therapy can be more accurately evaluated by performing repeated tbe during follow - up using same pre - treatment protocol ( fig .4 ) . the ideal goal of treatment in achalasia is to achieve complete esophageal emptying . such optimal end point , however , may not be achieved due to aperistaltic dilated esophagus . most authors have used criteria of ' 50 % or more reduction in post - treatment height as compared to pre - treatment height on 5 - minute film ' to define response as per tbe .11 less than 50 % height reduction is taken as failure as per tbe . vaezi et al9 ,11 used tbe for assessment of esophageal emptying following pd in patients with achalasia . the mean pre - treatment barium height andwidth were 17.0 and 6.0 cm , respectively . in 72 % of patients , symptoms as well as barium heightlack of symptomatic improvement was highly associated with poor esophageal emptying ( 50 % improvement in barium height ) . in this study , in 30 % patients with near complete symptom resolution , esophageal emptying was poor ; and most of them had recurrent symptoms within one year .9 there may also be mismatch in response as per tbe , manometry and clinical assessment . in patients with significant pre - pd dysphagia , a minor improvement in emptying may be over - interpreted as significant clinical improvement without positive result on tbe ; these patients are likely to experience recurrent symptom , which is predicted early by objective assessment on tbe . the patients with good emptying ( 50 % ) following pd on tbe are unlikely to report significant and persistent dysphagia . thus , tbe proved to be a good objective tool for predicting long term response following pd . kostic et al5 compared pre - and post - myotomy height and width of barium column in relation to symptom improvement following treatment . before myotomy , median height of barium column at 1 , 2 and 5 minutes , were 19 , 17 and 15 cm , and width were 5.2 , 4.8 and 4.5 cm , respectively . severity of dysphagia before myotomy inversely correlated with change in barium width between 1 to 5 - minute radiographs , whereas , regurgitation was related with the height of the barium column .5 successful treatment by myotomy resulted in reduced height and width of the barium column . post - myotomy height and width of barium columnwere related to pre - myotomy width ; lesser the esophageal dilatation before myotomy , the greater was the improvement in height and width following myotomy . post - myotomy symptoms correlated poorly with the tbe findings , therefore , poorly assessed success of therapy . oezcelik et al10 reported that if there was less than 40 % improvement in esophageal clearance following surgical myotomy , moderate to severe dysphagia persisted more often . rohof et al13 observed that esophageal stasis was a good predictor of treatment failure in long - standing achalasia and proposed use of tbe rather than esophageal manometry to decide on re - treatment . other studies have also shown that tbe is as good as high resolution manometry to predict response to pd in patients with achalasia .14,15 baker et al4 used tbe as an initial step in the evaluation of patients with gastroesophageal reflux disease . the rationale behind this was that some patients with symptoms of gastroesophageal reflux disease actually had a misdiagnosed motility disorder . therefore , tbe should be used in patients with suspected or confirmed achalasia and to follow - up those who have been treated with pd , botulinum toxin injection and heller myotomy .\noutput:\n" }, { "from": "agent", "value": "timed barium esophagogram ( tbe ) is a simple and objective method for assessing the esophageal emptying . the technique of tbe is similar to usual barium swallow with some modifications , which include taking multiple sequential films at pre - decided time interval after a single swallow of a fixed volume of a specific density barium solution . while many authors have used height and width of the barium column to assess the esophageal emptying , others have used the area of the barium column . tbe is being used in patients with suspected or confirmed achalasia and to follow - up those who have been treated with pneumatic dilation or myotomy . this review discusses technique of performing tbe , interpretation and its utility in clinical practice ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: intracellular calcium and reactive oxygen species ( ros ) are increased by myocardial cell injury due to ischemia / reperfusion ( i / r ) , then the sarcolemmal lipid peroxidation leads to the loss of cellular integrity and facility of calcium entry . therefore , pretreatment with antioxidant compounds can protect cells against ros injuries . in recent studies , scientists have found that vegetables and fruits are rich sources of antioxidants , which can defend the heart against chd ( 2 ) . in addition , they proved that gallic acid and other antioxidants ( 3 ) play a protective role ( related to their phenolic compounds ) against oxidative stress ( 4 ) . calcium is entered in the mitochondria because of ros generation , during reperfusion ( 5 ) . in intact cells , high calevels can be supplied from ryanodine release receptors ( ryrs ) and 3 - phosphatidylinositol receptors ( ip3r ) . another pathway is calcium entry into the cardiomyocytes through the voltage - dependent ca channel ( vdcc ) ( 5 ) . also the opening of the mitochondrial permeability transition pore ( mptp ) with its accessory components such as cyclophilin d ( cpd ) , and cardiolipin ( cl ) is modulated by calcium ( 6 ) . thus , preservation of mitochondria against oxidative stress can prevent and reduce the cellular damages which are caused by ros . also , priscilla et al . showed that pretreatment with gallic acid reduced the necrosis in the histopathological finding of infarcted cardiac muscle morphology in male wistar rats ( 4 ) . furthermore , another study has reported that apricot - feeding has cardioprotective effects on necrosis and histopathological findings during i / r in rat . the effects of different doses of gallic acid on histopathological changes during i / r on myocardial morphology have been investigated , but there is no research on either col fibers or mitochondrial protection . it has been proved that csa increases dose - dependently ros synthesis at 1 m ( 7 ) , so we chose the lower dose of csa that was not cytotoxic . considering all the above - mentioned issues , we investigated the dual cell and mitochondria membrane protection and their combined effects of gallic acid ( as an antioxidant ) and csa ( as mptp inhibitor , to prevent opening mitochondria pores ) on myocardial morphology and col during i / r in rats . fifty - four male wistar rats ( 250 - 300 g ) obtained from the animal house of ahvaz jundishapur university of medical sciences , ahvaz , iran , were randomly divided into 9 groups ( table 1 ) . control group was divided into 2 subgroups : ca group received saline as the solvent of gallic acid and cb group was pretreated by saline and then perfused with csa . the gallic acid groups were pretreated with different doses of gallic acid in saline ( g1a : 7.5 , g2a : 15 , and g3a : 30 mg / kg / day ) . gallic acid was dissolved in saline and administered to animals using gavage tube for 10 days ( 8 ) . the other groups pretreated both with different doses of gallic acid and perfused with csa during the first 13 minutes of reperfusion ( g1b : 7.5 , g2b : 15 andg3b : 30 mg / kg / day ) . animals were maintained under the same conditions such as controlled room temperature ( 222c ) , with a 12 hours dark - light cycle supplied with food and water ad - libitum . this study was approved by the animal care and ethics committee of the ahvaz jundishapur university of medical sciences . also this study was a quality research , which was done in the physiology research center of the ahvaz jundishapur university of medical sciences during 2012 . abbreviations : c , control ; ca : only ischemia / reperfusion ; g , gallic acid . gallic acid , cyclosporine a ( csa ) , heparin , hematoxylin and eosin , and masson s trichrome alcohol , were purchased from sigma ( st . louis , mo usa ) ; sodium chloride , potassium chloride , magnesium sulfate , sodium hydrogen carbonate , potassium hydrogen phosphate , d - glucose and calcium chloride were obtained from merck laboratories . ketamine and xylazine were bought from alfasan co ( holland ) . with regard to preparation and isolation of heart perfusion , the animals were anesthetized by ketamine hcl ( 50 mg / kg ) , and xylazine ( 5 mg / kg ) which contained heparin ( 1000 u / kg , ip ) . the trachea was cannulated , and the animals were ventilated with room air using a rodent ventilator ( ugo - basile , model : 7025 ) ( 9 ) . chest was opened and the ribs removed , then a steel cannula was placed into the aorta and secured with a suture . the heart was immediately perfused with krebs - henseleit bicarbonate solution ( bubbled with 95 % o2 and 5 % co2 to attain a ph of 7.4 ) . then , the heart was quickly excised and transferred to a langendorff apparatus while continuously perfused with krebs - henseleit solution at a constant pressure ( 60 - 70 mm hg ) at 37c . all hearts were perfused for 30 minutes before the induction of no flow global ischemia ( 30 minutes ) to allow hemodynamic equilibration , followed by 60 minutes of reperfusion ( 10 ) . ischemia was induced by cutting the krebs - henseleit flow using the pressure - flow controller key ( off ) for 30 minutes . csa ( 0.2 m ) was dissolved in ethanol and added to krebs - henseleit solution 13 minutes before the induction of ischemia and continued during reperfusion ( 11 , 12 ) . after the required period of i / r , the heart was removed from the cannula , then preserved in 10 % formalin for histological studies . small pieces of the heart were fixed in 10 % formalin and processed using a standard histological procedure . then , the tissue sections were evaluated for histological changes under olympus bx51 light microscope . in another step ,6 - m sections were stained with masson s trichrome staining to consider changes in col fiber network ( 11 ) . the intensity of the damage was checked by scaling in three levels ( severe , moderate and mild ) ( table 2 ) . comparison between different groups was assessed using pearson s chi - squared test , and data were presented as mean sd ( spss 18 software ) . fifty - four male wistar rats ( 250 - 300 g ) obtained from the animal house of ahvaz jundishapur university of medical sciences , ahvaz , iran , were randomly divided into 9 groups ( table 1 ) . control group was divided into 2 subgroups : ca group received saline as the solvent of gallic acid and cb group was pretreated by saline and then perfused with csa . the gallic acid groups were pretreated with different doses of gallic acid in saline ( g1a : 7.5 , g2a : 15 , and g3a : 30 mg / kg / day ) . gallic acid was dissolved in saline and administered to animals using gavage tube for 10 days ( 8 ) . the other groups pretreated both with different doses of gallic acid and perfused with csa during the first 13 minutes of reperfusion ( g1b : 7.5 , g2b : 15 andg3b : 30 mg / kg / day ) . animals were maintained under the same conditions such as controlled room temperature ( 222c ) , with a 12 hours dark - light cycle supplied with food and water ad - libitum . this study was approved by the animal care and ethics committee of the ahvaz jundishapur university of medical sciences . also this study was a quality research , which was done in the physiology research center of the ahvaz jundishapur university of medical sciences during 2012 . abbreviations : c , control ; ca : only ischemia / reperfusion ; g , gallic acid . gallic acid , cyclosporine a ( csa ) , heparin , hematoxylin and eosin , and masson s trichrome alcohol , were purchased from sigma ( st . louis , mo usa ) ; sodium chloride , potassium chloride , magnesium sulfate , sodium hydrogen carbonate , potassium hydrogen phosphate , d - glucose and calcium chloride were obtained from merck laboratories . ketamine and xylazine were bought from alfasan co ( holland ) . with regard to preparation and isolation of heart perfusion , the animals were anesthetized by ketamine hcl ( 50 mg / kg ) , and xylazine ( 5 mg / kg ) which contained heparin ( 1000 u / kg , ip ) . the trachea was cannulated , and the animals were ventilated with room air using a rodent ventilator ( ugo - basile , model : 7025 ) ( 9 ) . chest was opened and the ribs removed , then a steel cannula was placed into the aorta and secured with a suture . the heart was immediately perfused with krebs - henseleit bicarbonate solution ( bubbled with 95 % o2 and 5 % co2 to attain a ph of 7.4 ) . then , the heart was quickly excised and transferred to a langendorff apparatus while continuously perfused with krebs - henseleit solution at a constant pressure ( 60 - 70 mm hg ) at 37c . all hearts were perfused for 30 minutes before the induction of no flow global ischemia ( 30 minutes ) to allow hemodynamic equilibration , followed by 60 minutes of reperfusion ( 10 ) . ischemia was induced by cutting the krebs - henseleit flow using the pressure - flow controller key ( off ) for 30 minutes . csa ( 0.2 m ) was dissolved in ethanol and added to krebs - henseleit solution 13 minutes before the induction of ischemia and continued during reperfusion ( 11 , 12 ) . after the required period of i / r , the heart was removed from the cannula , then preserved in 10 % formalin for histological studies . small pieces of the heart were fixed in 10 % formalin and processed using a standard histological procedure . then , the tissue sections were evaluated for histological changes under olympus bx51 light microscope . in another step ,6 - m sections were stained with masson s trichrome staining to consider changes in col fiber network ( 11 ) . the intensity of the damage was checked by scaling in three levels ( severe , moderate and mild ) ( table 2 ) . comparison between different groups was assessed using pearson s chi - squared test , and data were presented as mean sd ( spss 18 software ) . tissue from the control ( ca ) rats showed severe edema ( ed ) between muscle fibers , infiltration of many inflammatory cells ( ic ) , pyknotic nuclei ( pkn ) , and absence of contraction band ( cb ) ( figure 1a ) more than either sham or other groups , which were perfused with csa alone ( cb ) ( figure 1b ) . although some normal muscle fibers , ic and the presence of rare contraction bands had shown in the latter group ( cb ) ( figure 1b ) . pretreatment with gallic acid ( 7.5 mg / kg ) ( figure 1c ) showed severe ed , ic and necrosis ( n ) between muscle fibers more than the cases which received gallic acid ( 7.5 mg / kg ) in combination with csa ( figure 1d ) . also , we observed fewer normal cells with normal nuclei in the second group ( g7 .5 + csa ) rather than ones , which perfused with csa alone . pretreatment with gallic acid ( 15 mg / kg ) and reperfusion with csa ( figure 1f ) showed mild edema , normal architecture of myocardium with a lot of contraction bands ( cb ) , and oviform nuclei more than which exposed to gallic acid ( 15 mg / kg ) or csa alone ( figure 1e ) . however , a few necrotic cells with pyknotic nuclei and moderate edema were observed in the latter groups ( g15 , cb ) . pretreatment with gallic acid ( 30 mg / kg ) ( figure 1 g ) and combination of gallic acid ( 30 mg / kg ) and csa ( figure 1h ) showed severe ed , pkn and many wavy fibers ( w ) . in both groups , edema ( ed ) , pyknotic nuclei ( pkn ) , contraction bands ( cb ) , necrosis ( n ) , wavy fibers ( w ) . a , control group received saline ; b , group received csa ; c , group received gallic acid ( 7.5 mg / kg ) ; d , group received gallic acid ( 7.5 mg / kg + csa ) ; e , group received gallic acid ( 15 mg / kg ) ; f , group received gallic acid ( 15 mg / kg + csa ) ; g , group received gallic acid ( 30 mg / kg ) ; h , group received gallic acid ( 30 mg / kg + csa ) . tissue from control rats showed loss of myocardial structure without collagen fibers that represent severe edema between the myocardial cells , so woven myocardial structure was observed in this group that had undergone 30 minutes ischemia and 60 minutes reperfusion ( figure 2a ) . perfused tissue with csa showed a presentation of connective tissue containing diffused but woven collagen ( col ) fibers between some of the normal myocardial cells ( figure 2b ) . pretreatment with gallic acid ( 7.5 mg / kg ) showed a few thin col fibers and necrosis in the majority of the connective tissue cells , compared with the ones received gallic acid ( 7.5 mg / kg ) and csa ( figure 2 c ) ; therefore , general muscle structure has gone wavy mode . pretreatment with gallic acid ( 7.5 mg / kg ) and csa showed some focally and thin col fibers more than those which received csa or gallic acid ( 7.5 mg / kg ) alone ( figure 2d ) . pretreatment with gallic acid ( 15 mg / kg ) and csa showed a normal connective tissue with diffused thick col fibers between the most cells in comparison with the ones perfused with csa alone ( figure 2e and f ) . pretreatment with gallic acid ( 30 mg / kg ) ( figure 2 g ) and combination of gallic acid ( 30 mg / kg ) and csa ( figure 2h ) showed the extensive col damage and loss of normal myocardial architecture with marked waviness ( w ) in the most cells in comparison with groups which perfused with csa alone . sham : a group that did not expose to ischemia , a , control group received saline ; b , group received csa ; c , group received gallic acid ( 7.5 mg / kg ) ; d , group received gallic acid ( 7.5 mg / kg + csa ) ; e , group received gallic acid ( 15 mg / kg ) ; f , group received gallic acid ( 15 mg / kg + csa ) ; g , group received gallic acid ( 30 mg / kg ) ; h , group received gallic acid ( 30 mg / kg + csa ) . tissue from the control ( ca ) rats showed severe edema ( ed ) between muscle fibers , infiltration of many inflammatory cells ( ic ) , pyknotic nuclei ( pkn ) , and absence of contraction band ( cb ) ( figure 1a ) more than either sham or other groups , which were perfused with csa alone ( cb ) ( figure 1b ) . although some normal muscle fibers , ic and the presence of rare contraction bands had shown in the latter group ( cb ) ( figure 1b ) . pretreatment with gallic acid ( 7.5 mg / kg ) ( figure 1c ) showed severe ed , ic and necrosis ( n ) between muscle fibers more than the cases which received gallic acid ( 7.5 mg / kg ) in combination with csa ( figure 1d ) . also , we observed fewer normal cells with normal nuclei in the second group ( g7 .5 + csa ) rather than ones , which perfused with csa alone . pretreatment with gallic acid ( 15 mg / kg ) and reperfusion with csa ( figure 1f ) showed mild edema , normal architecture of myocardium with a lot of contraction bands ( cb ) , and oviform nuclei more than which exposed to gallic acid ( 15 mg / kg ) or csa alone ( figure 1e ) . however , a few necrotic cells with pyknotic nuclei and moderate edema were observed in the latter groups ( g15 , cb ) . pretreatment with gallic acid ( 30 mg / kg ) ( figure 1 g ) and combination of gallic acid ( 30 mg / kg ) and csa ( figure 1h ) showed severe ed , pkn and many wavy fibers ( w ) . in both groups , edema ( ed ) , pyknotic nuclei ( pkn ) , contraction bands ( cb ) , necrosis ( n ) , wavy fibers ( w ) . a , control group received saline ; b , group received csa ; c , group received gallic acid ( 7.5 mg / kg ) ; d , group received gallic acid ( 7.5 mg / kg + csa ) ; e , group received gallic acid ( 15 mg / kg ) ; f , group received gallic acid ( 15 mg / kg + csa ) ; g , group received gallic acid ( 30 mg / kg ) ; h , group received gallic acid ( 30 mg / kg + csa ) . tissue from control rats showed loss of myocardial structure without collagen fibers that represent severe edema between the myocardial cells , so woven myocardial structure was observed in this group that had undergone 30 minutes ischemia and 60 minutes reperfusion ( figure 2a ) . perfused tissue with csa showed a presentation of connective tissue containing diffused but woven collagen ( col ) fibers between some of the normal myocardial cells ( figure 2b ) . pretreatment with gallic acid ( 7.5 mg / kg ) showed a few thin col fibers and necrosis in the majority of the connective tissue cells , compared with the ones received gallic acid ( 7.5 mg / kg ) and csa ( figure 2 c ) ; therefore , general muscle structure has gone wavy mode . pretreatment with gallic acid ( 7.5 mg / kg ) and csa showed some focally and thin col fibers more than those which received csa or gallic acid ( 7.5 mg / kg ) alone ( figure 2d ) . pretreatment with gallic acid ( 15 mg / kg ) and csa showed a normal connective tissue with diffused thick col fibers between the most cells in comparison with the ones perfused with csa alone ( figure 2e and f ) . pretreatment with gallic acid ( 30 mg / kg ) ( figure 2 g ) and combination of gallic acid ( 30 mg / kg ) and csa ( figure 2h ) showed the extensive col damage and loss of normal myocardial architecture with marked waviness ( w ) in the most cells in comparison with groups which perfused with csa alone . so the groups of cells were appeared ( table 2 ) . sham : a group that did not expose to ischemia , a , control group received saline ; b , group received csa ; c , group received gallic acid ( 7.5 mg / kg ) ; d , group received gallic acid ( 7.5 mg / kg + csa ) ; e , group received gallic acid ( 15 mg / kg ) ; f , group received gallic acid ( 15 mg / kg + csa ) ; g , group received gallic acid ( 30 mg / kg ) ; h , group received gallic acid ( 30 mg / kg + csa ) . during mi , activation of anaerobic glycolysis to provide atp leads to accumulation of h and acidosis . in response to elevated levels of h , ca uptake into mitochondria occurred by the mitochondrial ca uniporter . these changes regenerate the required ion gradient for more ca entry into the mitochondria , which causes the long - lasting opening of mptp regulated by cypd and mitochondrial swelling leads ultimately to cellular necrosis ( 13 ) . in accordance with two light microscopy studies , we found some changes between muscle fibers such as edema , degeneration , pyknotic nuclei , wavy contraction bands and loss of the col network after 30 minutes ischemia followed by 60 minutes reperfusion . the results of this study , have shown that pretreatment of the animals with gallic acid as an antioxidant or csa as mptp inhibitor alone , somewhat reduced mentioned changes ; however , a combination of both drugs improved the morphology of cells more than each one of them alone . another study has shown that during acute ischemic phase , matrix metaloproteinas ( mmp ) activity increases due to proteolytic and redox stress . it could be followed by degradation of the extracellular matrix ( ecm ) at the ischemic region , thus tissue inhibitor of metaloproteinases ( timps ) concentration is lowered and the components of ecm ( like collagen ) are degraded . structural remodeling of the infarcted myocardium leads to tissue stretching , hypertrophy and fibrosis ( 14 ) . thus , i / r injury can affect the myocardial function after losing of col and myocardial performance change by mmps in the early stage of cell damage ( 10 ) . during ischemia , collagenolytic activity was increased and followed by decrease in mmp1 activity ( 10 ) . balance between timp inhibition and collagenase activation determines degradation of interstitial matrix and the amount of collagenolysis ( 14 ) . in addition , other enzymes like lysosomal proteases ( such as cathepsin g ) are responsible in this process in infarcted tissues ( 14 ) . likewise , changes in the mitochondrial morphology of cardiac myocytes have been shown in other related studies ( 15 ) . furthermore , hausenloy et al . showed that inhibition of mptp opening reduced both necrotic and apoptotic cells and preserved mitochondrial morphology ( 16 ) ; thus , this effect prevents i / r injury . previous researchers showed that gallic acid preserved the integrity of lysosomal membrane and reduced the level of serum troponin ( a contractile protein ) by keeping the activities of different fraction of lysosomal enzymes in isoproterenol induced cardiotoxicity in rat heart tissue ( 4 , 8 ) . also it was shown that ros leads to cell are organelle membrane lipid peroxidation and mitochondrial enzyme dysfunction . as a result of these events , because of anaerobic metabolism , ros production increases and exacerbates the oxidative stress ( 5 , 17 ) to make a vicious cycle . therefore , hypothesis of this research was to assess the combination effects of csa ( a potent inhibitor of mptp ) with gallic acid ( a potent antioxidant ) on myocytes necrosis and morphology during i / r injury . the results of this study , have shown that pretreatment of the animals with gallic acid or csa alone would reduce edema , regenerative changes and col damage , but a combination would improve the morphology of cells and keeping col fibers more than each one alone . in addition , loss of col and waviness of the myocytes of the control group in the current study , could be attributed to mmps activity ( 14 ) or lysosomal enzymes like cathepsin d and l ( 18 ) that previously mentioned by tiwari et al . the preservation of col and myocyte morphology in treatment groups , may be due to the preservation of mitochondria against oxidative stress with csa as well as the elevation of antioxidant capacity with gallic acid which prevents damage to cell mitochondrial and lysosomal membranes against lipid peroxidation . because , we protected the cell with two mechanisms , it may further prevent damage caused by oxidative stress and the above - mentioned vicious cycle . we observed that collagen had been preserved and regenerative changes decreased remarkably in the heart tissue sections which pretreated by gallic acid at the medium dose ( 15 mg / kg ) , compared with the control group ( 20 ) . similar to priscilla ( 4 ) , we did not find a significant positive effect at the lowest dose of gallic acid ( 7.5 mg / kg ) . but using the highest dose ( 30 mg / kg ) reversed these effects . according to another study , it can be explained by a pro - oxidant effect of gallic acid in high doses , because it has proven that ferric ion can chelate the hydroxyl group in gallic acid molecule and reduces the oxidation potential so it losses its antioxidant activity ( 21 ) . on the other hand , csa increases the ros synthesis in doses higher than 1 m ( 7 ) ; thus , we used safety dose which does not have toxic effects ( 0.2 m ) ( 12 ) . also , we observed that whenever the mitochondria was protected , the tissue damage due to i / r injury would be more reduced . hence , this result can be useful to protect the heart after ischemia and at the onset of reperfusion . in conclusion , the present results approved our hypothesis that the combination of csa and gallic acid preserved the myocardial cell morphology against i / r injuries , which was more effective than using either of them alone . this effect has the best activity in the medium dose of gallic acid ( 15 mg / kg ) with csa .\noutput:\n" }, { "from": "agent", "value": "background : irreversible myocardial ischemic injury begins 20 minutes after the onset of coronary occlusion . then the infarcted cells show signs of necrosis and death.objectives : this study investigated the effects of co - administration of gallic acid ( antioxidant ) with cyclosporine ( mitochondrial permeability transition pore [ mptp ] inhibitor ) on myocardial morphology of rats during ischemia and reperfusion.materials and methods : fifty - four male wistar rats ( 250 - 300 g ) , were randomly divided into 9 groups : sham , control ( ca received saline , 1 ml / kg , cb : perfused with cyclosporine csa 0.2 m ) , 3 groups pretreated with gallic acid in saline ( g1a : 7.5 , g2a : 15 , and g3a : 30 mg / kg / day , and gavage daily for 10 days , n = 6 ) , and the other three groups were pretreated with gallic acid then perfused using csa , ( g1b : 7.5 , g2b : 15 , and g3b : 30 mg / kg / day ) at the first 13 minutes of reperfusion period . after 10 days pretreatment , the rat hearts were isolated and transferred to langendorff apparatus and exposed to 30 minutes ischemia following 60 minutes reperfusion . afterward , the hearts were preserved in 10 % formalin for histological studies at the end of the experiment . finally , hematoxylin and eosin and masson s trichrome staining techniques were used for evaluating the changes in myocardial architecture , degradation of myofibers , and collagen integrity . the differences were analyzed using pearson test.results : cell degenerative changes , pyknotic nuclei , contraction bands , edema , and loosening of collagen in between muscle fibers were observed during ischemia - reperfusion . myocardial architecture and cellular morphology were recovered in co - administration groups , especially in ( gallic acid 15 mg / kg + csa , p < 0.001 ) . conclusions : the results suggest the important role of the antioxidant system potentiation in the prevention of myocardial damage ." } ]