nils-herrmann/clean_scirepeval huggingface dataset:
Time trends in primary resistance to HIV drugs in the United Kingdom: multicentre observational study.

To examine whether the level of primary resistance to HIV drugs is increasing in the United Kingdom.



Multicentre observational study.



All virology laboratories in the United Kingdom carrying out tests for HIV resistance as part of routine clinical care.



2357 people infected with HIV who were tested for resistance before receiving antiretroviral therapy.



Prevalence of drug resistance on basis of the Stanford genotypic interpretation system.



Over the study period (February 1996 to May 2003), 335 (14.2%, 95% confidence interval 12.8% to 15.7%) samples had mutations that conferred resistance to one or more antiretroviral drugs (9.3% high level resistance, 5.9% medium level resistance). The prevalence of primary resistance has increased markedly over time, although patterns are specific to drug class; the largest increase was for non-nucleoside reverse transcriptase inhibitors. In 2002-3, the prevalence of resistance to any antiretroviral drug to nucleoside or nucleotide reverse transcriptase inhibitors, to non-nucleoside reverse transcriptase inhibitors, or to protease inhibitors was 19.2% (15.7% to 23.2%), 12.4% (9.5% to 15.9%), 8.1% (5.8% to 11.1%), and 6.6% (4.4% to 9.3%), respectively. The risk of primary resistance was only weakly related to most demographic and clinical factors, including ethnicity and viral subtype.



The United Kingdom has one of the highest reported rates of primary resistance to HIV drugs worldwide. Prevalence seems still to be increasing and is high in all demographic subgroups.
Trilateral retinoblastoma: neuroimaging characteristics and value of routine brain screening on admission

Trilateral retinoblastoma (TRb) is a rare disease associating intraocular retinoblastoma with intracranial primitive neuroectodermal tumor. Treatment is difficult and prognosis is poor. This multicenter study evaluates clinical findings and MR imaging characteristics of associated intracranial tumors in Rb patients. Clinical data of 17 patients (16 TRb and 1 quadrilateral Rb patients) included time intervals between Rb and TRb diagnosis and presence of baseline brain-imaging (BBI). Two reviewers reviewed all images individually and one reviewer per center evaluated their images. Consensus was reached during a joint scoring session. Studies were reviewed for tumor location, size and imaging characteristics (signal intensity (SI) on T1- and T2-weighted images, enhancement pattern and cystic appearance). Of 18 intracranial tumors, 78 % were located in the pineal gland and 22 % suprasellar. All tumors showed well-defined borders with mostly heterogenous enhancement (72 %) and isointense SI on T1- (78 %) and T2-weighted images (72 %) compared to gray matter. The majority of pineal TRbs showed a cystic component (57 %). TRb detected synchronously with the intraocular tumors on BBI (n = 7) were significantly smaller (P = 0.02), and mainly asymptomatic than TRb detected later on (n = 10). Overall, 5-year-survival of TRb patients detected on BBI was 67 % (95 % CI 29–100 %) compared to 11 % (95 % CI 0–32 %) for the group with delayed diagnosis. TRb mainly develops in the pineal gland and frequently presents with a cystic appearance that could be misinterpreted as benign pineal cysts. Routine BBI in all newly diagnosed Rb patients can detect TRb at a subclinical stage.
Colorectal cancer screening among ethnically diverse, low-income patients: a randomized controlled trial.

Patient navigators may increase colorectal cancer (CRC) screening rates among adults in underserved communities, but prior randomized trials have been small or conducted at single sites and have not included substantial numbers of Haitian Creole-speaking or Portuguese-speaking patients.



We identified 465 primary care patients from 4 community health centers and 2 public hospital-based clinics who were not up-to-date with CRC screening and spoke English, Haitian Creole, Portuguese, or Spanish as their primary language. We enrolled participants from September 1, 2008, through March 31, 2009, and followed them up for 1 year after enrollment. We randomly allocated patients to receive a patient navigation-based intervention or usual care. Intervention patients received an introductory letter from their primary care provider with educational material, followed by telephone calls from a language-concordant navigator. The navigators offered patients the option of being screened by fecal occult blood testing or colonoscopy. The primary outcome was completion of any CRC screening within 1 year. Secondary outcomes included the proportions of patients screened by colonoscopy who had adenomas or cancer detected.



During a 1-year period, intervention patients were more likely to undergo CRC screening than control patients (33.6% vs 20.0%; P < .001), to be screened by colonoscopy (26.4% vs 13.0%; P < .001), and to have adenomas detected (8.1% vs 3.9%; P = .06). In prespecified subgroup analyses, the navigator intervention was particularly beneficial for patients whose primary language was other than English (39.8% vs 18.6%; P < .001) and black patients (39.7% vs 16.7%; P = .004).



Patient navigation increased completion of CRC screening among ethnically diverse patients. Targeting patient navigation to black and non-English-speaking patients may be a useful approach to reducing disparities in CRC screening.
Integrated care for asthma: a clinical, social, and economic evaluation. Grampian Asthma Study of Integrated Care (GRASSIC)

To evaluate integrated care for asthma in clinical, social, and economic terms.



Pragmatic randomised trial.



Hospital outpatient clinics and general practices throughout the north east of Scotland.



712 adults attending hospital outpatient clinics with a diagnosis of asthma confirmed by a chest physician and pulmonary function reversibility of at least 20%.



Use of bronchodilators and inhaled and oral steroids; number of general practice consultations and hospital admissions for asthma; sleep disturbance and other restrictions on normal activity; psychological aspects of health including perceived asthma control; patient satisfaction; and financial costs.



After one year there were no significant overall differences between those patients receiving integrated asthma care and those receiving conventional outpatient care for any clinical or psychosocial outcome. For pulmonary function, forced expiratory volume was 76% of predicted for integrated care patients and 75% for conventional outpatients (95% confidence interval for difference -3.6% to 5.0%). Patients who had experienced integrated care were more likely to select it as their preferred course of future management (75% (251/333) v 62% (207/333) (6% to 20%)); they saved 39.52 pounds a year. This was largely because patients in conventional outpatient care consulted their general practitioner as many times as those in integrated care, who were not also visiting hospital.



Integrated care for moderately severe asthma patients is clinically as effective as conventional outpatient care, cost effective, and an attractive management option for patients, general practitioners, and hospital consultants.
Contribution of posture to the maintenance of anal continence

The anorectal angle (ARA) is believed to provide one of the most important contributions to anal continence. The normal resting angle is approx. 90°, but the erect position may modify the ARA and other parameters usually considered in a proctometrogram. We compared the proctometrogram in different postures to elucidate the role of changes in the ARA in maintaining fecal continence. Sixty-three patients with constipation underwent static proctography. Variations in the ARA, perineal descent, puborectalis muscle length, and pubococcygeal distance were determined during resting, squeezing, and pushing with the patient in the Sims' position (SP); further evaluations used radiographs in resting position but with straight legs, in erect and sitting positions. The resting mean ARA was 95.3±15° in SP and 79.8±14° standing erect; the latter value was also significantly less during squeezing (84±11°). The mean ARA during pushing was 118±16°. A systematic and statistically significant difference in the mean resting ARA was demonstrated using the baseline of the rectal shape instead of the major rectal axis when measuring the anorectal angle. When sitting on a toilet, the mean resting ARA was significantly wider than in SP. The length of the puborectalis sling at rest did not change but was significantly reduced during squeezing and increased during pushing. The descent of the perineum at rest was near to 0 (–0.089±1.76 cm) in SP and significantly less when standing (–0.65±1.9 cm) and during squeezing (–0.97±1.7 cm). Perineal descent during pushing was +2.94±2.2 cm. The mean pubococcygeal distance did not change significantly in SP and in the erect position. The erect position thus contributes significantly to the maintenance of fecal continence by sharpening the ARA. This effect is stronger than any active contraction of the puborectalis muscle and is not related to shortening of the puborectalis sling but is secondary to lifting of the pelvic floor.
Acute and Long-Term Increase in Fracture Risk after Hospitalization for Vertebral Fracture

The aims of this study were to determine the magnitude of the increase in risk of further fracture following hospitalization for vertebral fracture, and in particular to determine the time course of this risk. The records of the Swedish Patient Register were examined from 1987 to 1994 to identify all patients who were admitted to hospital for thoracic or lumbar vertebral fractures. Vertebral fractures were characterized as due to high- or low-energy trauma. Patients were followed for subsequent hospitalizations for hip fracture, and for all fractures combined. A Poisson model was used to determine the absolute risk of subsequent nonvertebral fracture and compared with that of the general population. We analyzed 13.4 million hospital admissions from which 28.869 individuals with vertebral fracture were identified, of which 60% were associated with low-energy trauma. There was a marked increase in subsequent incidence of hip and all fractures within the first year following hospitalization for vertebral fracture in both men and women. Thereafter, fracture incidence declined toward, but did not attain, baseline risk. Increased risks were particularly marked in the young. The increase in fracture risk was more marked following low-energy vertebral fracture than in the case of high-eneergy trauma. We conclude that the high incidence of new fractures within a year of hospitalization for vertebral fractures, irrespective of the degree of trauma involved, indicates that such patients should be preferentially targeted for treatment. It is speculated that short courses of treatment at the time of first vertebral fracture could provide important therapeutic dividends.
Paclitaxel, carboplatin, and extended-schedule oral etoposide for small-cell lung cancer.

We evaluated the feasibility and efficacy of combination paclitaxel (Taxol) (via 1-hour infusion), carboplatin (Paraplatin), and oral etoposide (VePesid) in the first-line treatment of patients with small-cell lung cancer. Between June 1993 and July 1996, 117 patients with small-cell lung cancer. were treated in two sequential phase II studies. The first 38 patients received a lower-dose regimen: paclitaxel 135 mg/m2, via 1-hour infusion; carboplatin dosed to an area under the concentration-time curve (AUC) of 5.0, and oral etoposide 50 mg alternating with 100 mg on days 1 through 10. Based on a very favorable toxicity profile, the paclitaxel and carboplatin doses were increased in the subsequent cohort of 79 patients (paclitaxel 200 mg/m2 by 1-hour infusion; carboplatin target AUC increased to 6.0). Thoracic radiation therapy (1.8 Gy/day; total dose, 45 Gy) was administered concurrently with courses 3 and 4 of chemotherapy in patients with limited-stage small-cell lung cancer. The combination of paclitaxel 200 mg/m2, carboplatin to an AUC of 6.0, and extended-schedule oral etoposide 50 or 100 mg alternating days 1 through 10 is highly active and well tolerated in patients with small-cell lung cancer. The regimen can be administered concurrently with radiation therapy with no unusual side effects, although a minority of patients develop esophagitis. Median survival rates in patients with both extensive- and limited-stage disease compare favorably with other reported regimens.
Female Sex Worker Client Behaviors Lead to Condom Breakage: A Prospective Telephone-Based Survey in Bangalore, South India

We examined condom breakage rates and predictors of breakage in a prospective telephone-based study of female sex workers (FSWs) in Bangalore, India. We obtained data on 3,257 condom-use sex acts, and breakage occurred in 2.1 % of these. Situational factors, especially those associated with male clients’ behaviors, were the most important predictors of breakage, including sexual inexperience, roughness and violence. Breakage was also associated with having vaginal and anal sex at the same encounter and with poor-fitting condoms. Despite lower than expected breakage rates, the high client volume of FSWs means that there are many unprotected sex acts caused by breakage. Discussions should be held around new education messages, and how programs can respond quickly when sex workers encounter clients who are inebriated, violent or unusually sexually charged. More work is urgently needed with police, and on FSW empowerment, the use of help lines, and counseling for the most vulnerable women.
Use of thoracic radiotherapy for extensive stage small-cell lung cancer: a phase 3 randomised controlled trial

Most patients with extensive stage small-cell lung cancer (ES-SCLC) who undergo chemotherapy, and prophylactic cranial irradiation, have persistent intrathoracic disease. We assessed thoracic radiotherapy for treatment of this patient group.



We did this phase 3 randomised controlled trial at 42 hospitals: 16 in Netherlands, 22 in the UK, three in Norway, and one in Belgium. We enrolled patients with WHO performance score 0-2 and confirmed ES-SCLC who responded to chemotherapy. They were randomly assigned (1:1) to receive either thoracic radiotherapy (30 Gy in ten fractions) or no thoracic radiotherapy. All underwent prophylactic cranial irradiation. The primary endpoint was overall survival at 1 year in the intention-to-treat population. Secondary endpoints included progression-free survival. 
We randomly assigned 498 patients between Feb 18, 2009, and Dec 21, 2012. Three withdrew informed consent, leaving 247 patients in the thoracic radiotherapy group and 248 in the control group. Mean interval between diagnosis and randomisation was 17 weeks. Median follow-up was 24 months. Overall survival at 1 year was not significantly different between groups: 33% (95% CI 27-39) for the thoracic radiotherapy group versus 28% (95% CI 22-34) for the control group (hazard ratio [HR] 0.84, 95% CI 0.69-1.01; p=0.066). However, in a secondary analysis, 2-year overall survival was 13% (95% CI 9-19) versus 3% (95% CI 2-8; p=0.004). Progression was less likely in the thoracic radiotherapy group than in the control group (HR 0.73, 95% CI 0.61-0.87; p=0.001). At 6 months, progression-free survival was 24% (95% CI 19-30) versus 7% (95% CI 4-11; p=0.001). We recorded no severe toxic effects. The most common grade 3 or higher toxic effects were fatigue (11 vs 9) and dyspnoea (three vs four).



Thoracic radiotherapy in addition to prophylactic cranial irradiation should be considered for all patients with ES-SCLC who respond to chemotherapy.



Dutch Cancer Society (CKTO), Dutch Lung Cancer Research Group, Cancer Research UK, Manchester Academic Health Science Centre Trials Coordination Unit, and the UK National Cancer Research Network.
Zoomorphic design

Zoomorphic shapes are man-made shapes that possess the form or appearance of an animal. They have desirable aesthetic properties, but are difficult to create using conventional modeling tools. We present a method for creating zoomorphic shapes by merging a man-made shape and an animal shape. To identify a pair of shapes that are suitable for merging, we use an efficient graph kernel based technique. We formulate the merging process as a continuous optimization problem where the two shapes are deformed jointly to minimize an energy function combining several design factors. The modeler can adjust the weighting between these factors to attain high-level control over the final shape produced. A novel technique ensures that the zoomorphic shape does not violate the design restrictions of the man-made shape. We demonstrate the versatility and effectiveness of our approach by generating a wide variety of zoomorphic shapes.
Evaluation of haptotherapy for patients with cancer treated with chemotherapy at a day clinic.

The purpose of this study was to evaluate a haptotherapeutic treatment and its effects on the perceived well-being of patients with cancer treated with chemotherapy in day care.



The study had a pre-test-post-test semi-experimental design, with 31 patients in the intervention group and 26 in the control group. Patients in the control group were matched with patients in the experimental condition with respect to age, gender, type of cancer, type of chemotherapy, prognosis and the period between pre- and post-test. Standardized questionnaires were used measuring perceived well-being and satisfaction with care (haptotherapy). Indicators of well-being measured were quality of life, mood, meaning in life, general functioning, physical and psychological symptoms, sleep quality and body awareness. The intervention consisted of five haptotherapy sessions of 45 minutes each. Patients in the control condition received standard medical care.



Patients were highly satisfied with the haptotherapy treatment, and especially valued the personal attention and the relaxation they experienced. The haptotherapy treatment improved both the perceived general quality of life and the perceived cognitive and social functioning of patients. No improvement was found for mood, meaning in life, general functioning, physical symptoms, sleep quality and body awareness.



It may be concluded that haptotherapy positively contributes to several indicators of perceived well-being of patients with cancer during the period they receive chemotherapy. More rigorous experimental studies are necessary in this field, especially concerning randomization, number of participants and homogeneity of the sample.



Haptotherapy as a type of complementary medicine is a potentially valuable and effective intervention to raise the well-being of patients with cancer undergoing invasive treatments like chemotherapy.
Preliminary study of surgical audit for overall survival following gastric cancer resection

Previous studies for surgical audit have focused on short-term outcomes, such as perioperative mortality. There has been no gold standard how to evaluate quality of care for long-term outcomes in surgical oncology. This preliminary study aims to propose a method for surgical audit targeting long-term outcome following gastrectomy for gastric cancer. We prospectively investigated a set of variables relating to physiologic conditions, tumor characteristics and operations in patients who underwent gastrectomy for gastric cancer between June 2005 and July 2008 in 18 referral hospitals in Japan. Overall survival (OS) is the endpoint. Cox hazard regression analysis was used to generate a model to predict OS. The calibration and discrimination power of the model were assessed using the Hosmer-Lemeshow (H-L) test and area under the receiver-operating characteristic curve (AUC), respectively. The ratio of observed-to-estimated 5-year OS rates (OE ratio) was defined as a measure of quality. Among 762 patients analyzed, 697 (91 %) completed the 5-year follow-up. The constructed model for OS exhibited a good discrimination power (AUC, 95 % confidence interval 0.89, 0.86–0.91), which was significantly better than that for the UICC stage (0.81, 0.77–0.84). This model also demonstrated a good calibration power (H-L: χ 2 = 27.2, df = 8, P = 0.77). The OE ratios among the participating hospitals revealed no significant variation between 0.74 and 1.1. The current study suggests the possibility of surgical audit for postoperative OS in gastric cancer. Further studies including high-volume centers will be necessary to validate this idea.
High-dose-rate brachytherapy and hypofractionated external beam radiotherapy combined with long-term hormonal therapy for high-risk and very high-risk prostate cancer: outcomes after 5-year follow-up

The purpose of this study was to report the outcomes of high-dose-rate (HDR) brachytherapy and hypofractionated external beam radiotherapy (EBRT) combined with long-term androgen deprivation therapy (ADT) for National Comprehensive Cancer Network (NCCN) criteria-defined high-risk (HR) and very high-risk (VHR) prostate cancer. Data from 178 HR (n = 96, 54%) and VHR (n = 82, 46%) prostate cancer patients who underwent (192)Ir-HDR brachytherapy and hypofractionated EBRT with long-term ADT between 2003 and 2008 were retrospectively analyzed. The mean dose to 90% of the planning target volume was 6.3 Gy/fraction of HDR brachytherapy. After five fractions of HDR treatment, EBRT with 10 fractions of 3 Gy was administered. All patients initially underwent ≥ 6 months of neoadjuvant ADT, and adjuvant ADT was continued for 36 months after EBRT. The median follow-up was 61 months (range, 25-94 months) from the start of radiotherapy. The 5-year biochemical non-evidence of disease, freedom from clinical failure and overall survival rates were 90.6% (HR, 97.8%; VHR, 81.9%), 95.2% (HR, 97.7%; VHR, 92.1%), and 96.9% (HR, 100%; VHR, 93.3%), respectively. The highest Radiation Therapy Oncology Group-defined late genitourinary toxicities were Grade 2 in 7.3% of patients and Grade 3 in 9.6%. The highest late gastrointestinal toxicities were Grade 2 in 2.8% of patients and Grade 3 in 0%. Although the 5-year outcome of this tri-modality approach seems favorable, further follow-up is necessary to validate clinical and survival advantages of this intensive approach compared with the standard EBRT approach.
Clinical characteristics, course and prognosis of spinal multiple sclerosis

Retrospective examination.To define the clinical characteristics and response to therapy of spinal multiple sclerosis (MS).Setting:Italy.Retrospective review was performed on 563 patients with clinical definite MS. Selection criteria were two or more spinal cord lesions in the presence of normal magnetic resonance imaging of the brain.Spinal MS was diagnosed in 13 patients (2.3%) out of 563 with clinical definite MS. There were seven female and six male patients; nine had a relapsing–remitting (RR) and four, a primary progressive (PP) course. All patients were treated with immunosoppressive or immunomodulatory therapy. Mean disease duration in patients with RR–MS was 13.1±10.1 years with a mean age at onset of 29.5±14.3 years; the mean Expanded Disability Status Scale (EDSS) at the time of the study was 3.5±2.5 with a progression index of 0.28. Mean disease duration in patients with PP course was 7±6.2 years with a mean age at onset of 56.7±10.4 years; the mean EDSS at the time of the study was 6.2±2.0 with a progression index of 1.48.Conclusions:Patients with spinal RR–MS are characterised by an early disease onset with minimal or moderate disability progression; patients with spinal PP–MS show a late disease onset and more rapid disability progression. In our series of spinal MS patients, disability progression seems to be mainly due to the disease course and age at onset rather than to the site of lesion.