nils-herrmann/clean_scirepeval huggingface dataset:
Synchronized moving aperture radiation therapy (SMART): average tumour trajectory for lung patients.

Synchronized moving aperture radiation therapy (SMART) is a new technique for treating mobile tumours under development at Massachusetts General Hospital (MGH). The basic idea of SMART is to synchronize the moving radiation beam aperture formed by a dynamic multileaf collimator (DMLC) with the tumour motion induced by respiration. SMART is based on the concept of the average tumour trajectory (ATT) exhibited by a tumour during respiration. During the treatment simulation stage, tumour motion is measured and the ATT is derived. Then, the original IMRT MLC leaf sequence is modified using the ATT to compensate for tumour motion. During treatment, the tumour motion is monitored. The treatment starts when leaf motion and tumour motion are synchronized at a specific breathing phase. The treatment will halt when the tumour drifts away from the ATT and will resume when the synchronization between tumour motion and radiation beam is re-established. In this paper, we present a method to derive the ATT from measured tumour trajectory data. We also investigate the validity of the ATT concept for lung tumours during normal breathing. The lung tumour trajectory data were acquired during actual radiotherapy sessions using a real-time tumour-tracking system. SMART treatment is simulated by assuming that the radiation beam follows the derived ATT and the tumour follows the measured trajectory. In simulation, the treatment starts at exhale phase. The duty cycle of SMART delivery was calculated for various treatment times and gating thresholds, as well as for various exhale phases where the treatment begins. The simulation results show that in the case of free breathing, for 4 out of 11 lung datasets with tumour motion greater than 1 cm from peak to peak, the error in tumour tracking can be controlled to within a couple of millimetres while maintaining a reasonable delivery efficiency. That is to say, without any breath coaching/control, the ATT is a valid concept for some lung tumours. However, to make SMART an efficient technique in general, it is found that breath coaching techniques are required.
Preconditions for widespread reuse of code

Preconditions for widespread reuse of code. In [I] Lubars gives a view of the present status of reusable code. He suggests that widespread use of reusable code will require both a change of attitudes by the software industry, and the establishment of convenient cataloging and indexing tools. The hope would be that with such tools programmers could more easily find whether reusable code exists to solve their problem. While I agree with Lubars on the need for cataloging, I suggest that this by itself will not solve the problem. Indeed, even if an excellent, easily available catalogue were available, I suspect that most programmers often would (and perhaps should) code their own solutions, rather than reusing code available via the cataloging. The unpleasant truth is that there is a lot of awfully bad software out there. It is often more efficient to do your own coding than to verify the quality of available reusable code. The IMSL mathematical software library suggests a better approach. IMSL (with which I have no connection or financial interest) supports its FORTRAN library , tests it on new hardware and new compilers, updates with better algorithms where appropriate. The user can thus have some confidence when he uses this software. If reusing code is ever to become commonplace, it will be because of companies such as IMSL. I have seen very little discussion of attributes of a programming language which contribute to reusable code. Two languages which have developed substantial libraries are FORTRAN and C. Many attribute the success of FORTRAN to its age. However other languages have been around for a long time, and have not developed the amount of reusable code that C has. I believe that the nature of the languages is an important factor. In both C and FORTRAN, the principle means of structuring programs is with the separately compilable procedure. As a result programmers think more about the program interface. It is usually a simple operation to convert these modules into reusable library routines. By contrast, in languages such as PASCAL, PL/I, ADA, it is easier to structure programs with internal procedures. It is much harder to convert these internal routines into reusable code, both because they are internal, and because they are usually written with more assumptions about the environment in which they are used. It is regrettable that the designers of the proposed FORTRAN 8x are introducing internal …
Comparison of quantitative and semiquantitative dynamic contrast-enhanced MRI with respect to their correlation to delayed gadolinium-enhanced MRI of the cartilage in patients with early rheumatoid arthritis.

The objective of this study was to investigate the correlation between semiquantitative and quantitative dynamic contrast-enhanced (DCE) parameters with delayed gadolinium-enhanced magnetic resonance imaging (MRI) of the cartilage (dGEMRIC).



Fifteen patients with early rheumatoid arthritis (RA) from the ArthroMark cohort were investigated at a 3-T MRI scanner. The metacarpophalangeal (MCP) joint of the index finger was examined with DCE-MRI and dGEMRIC. Semiquantitative and quantitative DCE perfusion parameters were calculated. The RA MRI score of the second MCP joint and the joint space width were measured.



Significant correlations were noted between both semiquantitative and quantitative DCE parameters and the RA MRI score of the second MCP joint. There was a significant negative correlation between DCE parameters and dGEMRIC. No association between joint space width and DCE parameters was observed.



Semiquantitative and quantitative analyses of perfusion are applicable to show that cartilage damage correlates with the inflammation activity despite the absence of joint space narrowing.
Pre-treatment evaluation of basal cell carcinoma for photodynamic therapy: comparative measurement of tumour thickness in punch biopsy and excision specimens.

Tumour thickness affects the outcome of photodynamic therapy in basal cell carcinoma (BCC). The aim of this study was to evaluate whether punch biopsy provides reliable information on BCC tumour thickness, by comparing corresponding measurements in biopsy and excision specimens for 48 lesions in 43 patients. BCC tumours were between 0.2 and 6.1 mm thick. The mean depth of the excisions were 0.14 mm greater than that of the biopsies. Bland-Altman 95% limits of agreement were (-1.3, 1.6) mm, but the difference between measurements increased with tumour thickness. A punch biopsy tumour thickness of 1.0 mm yielded an upper 95% predicted limit for excision depth within 2.0 mm. In conclusion, there was reasonable overall agreement between corresponding measurements. A biopsy thickness of 1.0 mm suggests that the tumour will most likely be within the current accepted limits for photodynamic therapy. With increasing tumour thickness, however, individual tumour measurements may differ considerably.
Role of magnesium supplementation in the treatment of depression: A randomized clinical trial

Current treatment options for depression are limited by efficacy, cost, availability, side effects, and acceptability to patients. Several studies have looked at the association between magnesium and depression, yet its role in symptom management is unclear. The objective of this trial was to test whether supplementation with over-the-counter magnesium chloride improves symptoms of depression. An open-label, blocked, randomized, cross-over trial was carried out in outpatient primary care clinics on 126 adults (mean age 52; 38% male) diagnosed with and currently experiencing mild-to-moderate symptoms with Patient Health Questionnaire-9 (PHQ-9) scores of 5-19. The intervention was 6 weeks of active treatment (248 mg of elemental magnesium per day) compared to 6 weeks of control (no treatment). Assessments of depression symptoms were completed at bi-weekly phone calls. The primary outcome was the net difference in the change in depression symptoms from baseline to the end of each treatment period. Secondary outcomes included changes in anxiety symptoms as well as adherence to the supplement regimen, appearance of adverse effects, and intention to use magnesium supplements in the future. Between June 2015 and May 2016, 112 participants provided analyzable data. Consumption of magnesium chloride for 6 weeks resulted in a clinically significant net improvement in PHQ-9 scores of -6.0 points (CI -7.9, -4.2; P<0.001) and net improvement in Generalized Anxiety Disorders-7 scores of -4.5 points (CI -6.6, -2.4; P<0.001). Average adherence was 83% by pill count. The supplements were well tolerated and 61% of participants reported they would use magnesium in the future. Similar effects were observed regardless of age, gender, baseline severity of depression, baseline magnesium level, or use of antidepressant treatments. Effects were observed within two weeks. Magnesium is effective for mild-to-moderate depression in adults. It works quickly and is well tolerated without the need for close monitoring for toxicity.
What is the Ideal Route of Administration of Tranexamic Acid in TKA? A Randomized Controlled Trial.

TKA commonly involves substantial blood loss and tranexamic acid has been used to reduce blood loss after TKA. Numerous clinical trials have documented the efficacy and safety of intravenous (IV) or intraarticular (IA) use of tranexamic acid. Combined administration of tranexamic acid also has been suggested; however, there is no consensus regarding the ideal route of tranexamic acid administration.



(1) To compare the efficacy of tranexamic acid in terms of total blood loss and the allogeneic transfusion rate among three routes of administration: IV alone, IA alone, and combined IV and IA. (2) To compare these regimens in terms of venous thromboembolism (VTE) and the frequency of wound complications.



In total, 376 patients undergoing TKA between March 2014 and March 2015 were randomized to four groups by the route of tranexamic acid administration: IV only, IA only, low-dose combined (IV + IA injection of 1 g), and high-dose combined (IV + IA injection of 2 g). The calculated total blood loss, allogeneic transfusion rate, decrease in hemoglobin, the frequency of symptomatic deep vein thrombosis and pulmonary embolism, wound complications, and periprosthetic joint infection were compared among the groups. Total blood loss was calculated using estimated total body blood volume and hemoglobin loss. The decision regarding when to transfuse was determined based on preset criteria.



The high- and low-dose combined groups and the IA-only group had lower total blood loss (564 ± 242 mL, 642 ± 242 mL, and 633 ± 205 mL, respectively) than the IV-only group (764 ± 217 mL; mean differences = 199 mL [95% CI, 116-283 mL], p < 0.001; 121 mL [95% CI, 38-205 mL], p = 0.001; 131 mL [95% CI, 47-214 mL], p < 0.001); no differences were found among the other three groups. No patients in any study group received an allogeneic transfusion. One patient in the IV-only group had a symptomatic pulmonary embolism develop, but no other symptomatic VTE events occurred in any group. In addition, no differences were observed in wound complications, such as superficial wound necrosis (one patient in the IV-only and the high-dose combined group, respectively) and oozing (IV-only, IA-only, low-dose combined, high-dose combined = 3%, 4%, 4%, and 7%; p = 0.572) between the groups. No patients had a periprosthetic joint infection.



IA tranexamic acid administration further reduces blood loss after TKA in comparison to IV use alone; no additional effect in further reducing blood loss was found in combination with IV tranexamic acid. Appropriately powered studies are needed to confirm the safety of this route of administration as the preferred route of administration in TKA.
Evaluation of the Cardio-Ankle Vascular Index, a New Indicator of Arterial Stiffness Independent of Blood Pressure, in Obesity and Metabolic Syndrome

Aortic stiffness is predictive of cardiovascular diseases (CVD) and mortality in lifestyle-related diseases. The cardio-ankle vascular index (CAVI), a new index of arterial stiffness, was recently developed by measuring of pulse wave velocity (PWV) and blood pressure (BP). CAVI is adjusted for BP based on stiffness parameter β and is less influenced by BP, suggesting its superiority over brachial-ankle PWV (baPWV). However, there are currently no reports on the usefulness of CAVI as an atherogenic index in obesity and metabolic syndrome (MS). Among the 325 obese Japanese outpatients enrolled in the multi-centered Japan Obesity and Metabolic Syndrome Study, 216 patients (67%) met the criteria of MS according to the modified National Cholesterol Education Program–Adult Treatment Panel III. CAVI values were significantly higher in MS than in non-MS patients, whereas there was no significant difference in body mass index, total cholesterol, and low-density lipoprotein-cholesterol between both groups. CAVI values were weakly correlated with BP but closely correlated with the severity of MS and MS-related parameters such as hypoadiponectinemia, relative to baPWV. Furthermore, weight-reduction therapy through diet and exercise over a 3-month period significantly decreased CAVI values in parallel with increasing adiponectin. This study demonstrates for the first time that CAVI is a good indicator of arterial stiffness. It is closely correlated with the severity of MS and CVD risks in obesity and independent of BP, and is thus superior to baPWV. Therefore, the determination of arterial stiffness by CAVI may be useful for evaluating and managing the CVD risks of MS patients.
A family history of Type 1 alcoholism differentiates alcohol consumption in high cortisol responders to stress

The differentiation between high and low cortisol responders to stress is of interest in determining the risk factors which may, along with genetic vulnerability, influence alcohol intake.



Thirty-two healthy volunteers, family history positive to alcoholism (FHP, n = 16) and family history negative (FHN, n = 16) attended two laboratory sessions during which alcohol or placebo was offered.



There were no differences in consumption of alcohol or placebo between FHP and FHN subjects. 



Fifty-eight healthy social drinkers, FHP (n = 27) and FHN (n = 31) attended two laboratory sessions. They were administered either alcohol or placebo in both sessions they attended. All subjects underwent either a stress task (the Trier Social Stress Test, TSST) or a stress-free period, at two separate occasions, before being offered beverage. After the salivary cortisol analysis, subjects in each group were divided into high (HCR) or low (LCR) cortisol responders.



After stress, subjects who were FHP-HCR consumed more alcohol than FHN-HCR. There were no differences in the placebo intake between FHP and FHN subjects regardless of their cortisol response.



This result indicates that stress promotes alcohol consumption only in subjects with a family history of Type 1 alcoholism who show an increase in cortisol response to stress. This behaviour is similar to that previously observed in alcohol dependent individuals after stress and thus could represent an endophenotype posing a risk for future development of alcohol use disorders.
Safety, pharmacokinetics and resistant variants of telaprevir alone for 12 weeks in hepatitis C virus genotype 1b infection

Telaprevir in combination with peginterferon and ribavirin is a promising advancement in chronic hepatitis C treatment. However, the safety, tolerability, pharmacokinetics and antiviral profiles of telaprevir alone beyond 2 weeks have not been studied.



In a phase 1b study in Japan, 10 treatment-naïve patients infected with hepatitis C virus genotype 1b with high viral load (>5 log(10) IU/mL) received telaprevir 750 mg every 8 h (q8h) for 12 weeks. We examined the safety, tolerability, pharmacokinetics, hepatitis C virus (HCV) RNA levels and resistant variants of telaprevir.



Neither serious adverse events nor discontinuations of study drug owing to an adverse event occurred. The most common adverse drug reactions were rash (80%) and anaemia (70%). Telaprevir concentration reached its steady state within 2 days after the first administration without abnormal accumulation. Telaprevir alone provided potent antiviral activity: a median log(10) decrease of 2.325 at 16 h and 5.175 on Day 14. During the treatment, HCV RNA levels at the nadir were below the limit of the quantification in seven patients and undetectable in three of 10 patients. Viral breakthrough associated with mainly Ala(156) -substituted variants occurred in eight patients, and only one patient showed end-of-treatment response. The selected variants reverted to the wild-type during the 24-week follow-up period.



Telaprevir alone was well tolerated at 750 mg q8h for up to 12 weeks. The safety profile and emergence of resistant variants of genotype 1b under telaprevir monotherapy for 12 weeks will become increasingly important in evaluating an oral combination of telaprevir with other direct-acting antiviral agents.
Multisystemic engagement & nephrology based educational intervention: a randomized controlled trial protocol on the kidney team at home-study

Living donor kidney transplantation (LDKT) is the most successful form of renal replacement therapy in terms of wait time and survival rates. However, we observed a significant inequality in the number of LDKT performed between the Dutch and the non-Dutch patients. The objective of this study is to adapt, implement and test an educational home-based intervention to contribute to the reduction of this inequality. Our aim is to establish this through guided communication together with the social network of the patients in an attempt that well-informed decisions regarding renal replacement therapy can be made: Multisystemic Engagement & Nephrology. This manuscript is a detailed description of the Kidney Team At Home-study protocol.



All patients (>18 yrs) that are referred to the pre-transplantation outpatient clinic are eligible to participate in the study. Patients will be randomly assigned to either an experimental or a control group. The control group will continue to receive standard care. The experimental group will receive standard care plus a home-based educational intervention. The intervention consists of two sessions at the patient's home, an initial session with the patient and a second session for which individuals from their social network are invited to take part. Based on the literature and behavioural change theories we hypothesize that reducing hurdles in knowledge, risk perception, subjective norm, self-efficacy, and communication contribute to well-informed decision making and reducing inequality in accessing LDKT programs. A change in these factors is consequently our primary outcome-measure. Based on power calculations, we aim to include 160 patients over a period of two years.



If we are able to show that this home-based group educational intervention contributes to 1) achieving well-informed decision regarding treatment and 2) reducing the inequality in LDKT, the quality of life of patients will be improved while healthcare costs are reduced. As the intervention is investigated in a random heterogeneous patient group in daily practice, the transfer to clinical practice in other kidney transplant centers should be relatively easy.
Randomised controlled trial to examine the e V ects of a GP exercise referral programme in Hailsham , East Sussex , on modifiable coronary heart disease risk factors

To examine the eVects of a GP exercise referral programme on modifiable coronary heart disease risk factors. Randomised controlled trial. A battery of validated measures were carried out at 0, 8, 16, 26, and 37 weeks. Two community health centres and a leisure centre in Hailsham, East Sussex. Subjects—389 patients (smokers, hypertensive or overweight) were selected from medical records, screened for contraindications to exercise and 345 were invited into the study. Of 142 patients randomly allocated, 40 (41%) completed the study in the exercise group and 31 (69%) in the control group. Sixty (35%) invited smokers (48% of non-smokers), 71 (38%) invited hypertensive patients (45% of non-hypertensive patients), and 107 (45%) overweight patients (33% of non-overweight patients) were randomised. Of those randomised, 27 (45%) smokers, 52 (48%) overweight, and 43 (61%) hypertensive patients completed the study. The exercise group was oVered 20, half price sessions over 10 weeks at a leisure centre. Patients engaged in moderate and vigorous aerobic type activity on various exercise machines, in a semi-supervised, informal environment. Results—87% of those referred used the prescription and 28% (high adherers)(45% of obese patients) did at least 15 sessions. The exercise group reduced sum of skinfolds by 8.1% (2.9 to 13.3, 95% confidence intervals) more than the control group, up to 16 weeks after baseline. High adherers reduced sum of skinfolds by 9.2% (0.9 to 17.5) more than the control group, up to 26 weeks. High adherers reduced systolic blood pressure by 7.2% (−0.7 to 14.9) (that is, 9 mm Hg) more than low adherers, up to 37 weeks. Non-smokers and obese patients attended more prescribed sessions than smokers and non-overweight patients. Reduction in sum of skinfolds was maintained up to 26 weeks, among high adherers compared with controls. Reduction in systolic blood pressure was evident up to 37 weeks among high adherers, but only in comparison with low adherers. Selection of appropriate referees and use of other strategies to improve exercise adherence will help to maximise the benefits from GP exercise prescription schemes.
Blob manipulation

This paper introduces Blob Manipulation, the interaction technique with fluidic soft matter. Most of the soft matters are substances between liquid and solid and possess viscoelasticity. We focus on this materiality and propose a novel interaction technique. A stirring rod is used as the input tool. When the system detects a user input such as touching, rubbing or tapping, the corresponding transformation will be executed. Six basic operations were designed to transform fluidic soft matter geometrically and topologically. Rheological user interface associated with metamorphose is expected to pioneer new possibilities for design, education and entertainment.