nils-herrmann/clean_scirepeval huggingface dataset:
Nonalcoholic fatty liver may increase the risk of operation in patients with fatty liver and the frequency of cancer in their first-degree relatives

Fatty liver is a common disease in developed countries. We investigated the frequency of operation in patients with fatty liver and the frequency of cancer in their first-degree relatives. In this study, we evaluated 105 patients with biopsy-proven nonalcoholic fatty liver disease (NAFLD), 121 patients with hepatitis C (61 patients with fatty liver and 60 patients without fatty liver), 50 patients with inflammatory bowel disease (IBD), and 109 patients with dyspepsia as a control group. There was no difference for sex, mean age, and marital status among the groups, except that patients with IBD were younger than others (p < 0.001). The frequency of cancer in family was as follows: 18 % in IBD, 9 % in dyspepsia, 28 % in hepatitis C with hepatic steatosis, 21.5 % in hepatitis C without steatosis, and 27 % in NAFLD (p = 0.006). Then, we divided the study group into two groups—group 1: IBD + dyspepsia + hepatitis C without hepatic steatosis, and group 2: hepatitis C with hepatic steatosis + NAFLD—and performed the same analysis. We found that the frequency of cancer in family was 16 % in group 1 (the patients without fatty liver) vs. 24.4 % in group 2 (those with fatty liver; p = 0.037). We also investigated the rate of operation in patients. The results were as follows: 33 % in group 1 vs. 43 % in group 2 (p = 0.043). Independently of the underlying chronic diseases, occurrence of fat in the liver increased the frequency of operation in patients with fatty liver and the rate of cancer in their first-degree relatives. Understanding the underlying causes of fatty liver forms might decrease the cancer frequency in the population and number of operation in patients with fatty liver.
Electroacupuncture inhibits chronification of the acute pain of knee osteoarthritis: study protocol for a randomized controlled trial

Previous studies have shown that electroacupuncture (EA) has a significant effect on acute pain, but it has not solved the clinical problem of the chronification of acute pain. Diffuse noxious inhibitory controls (DNIC) function as a reliable indicator to predict the risk of chronic pain events. DNIC function in knee osteoarthritis (KOA) patients has been demonstrated to gradually decrease during the development of chronic pain. The purpose of this study is to conduct a randomized, controlled clinical trial to determine if EA can repair impaired DNIC function and thus prevent chronification of the acute pain of KOA.



This is a multicenter, single blind, randomized, controlled, three-arm, large-scale clinical trial. A total of 450 KOA patients will be randomly assigned to three groups. The strong EA group will receive EA with high-intensity current (2 mA < current < 5 mA) at the ipsilateral 'Neixiyan' (EX-LE5), 'Dubi'(ST35), 'Liangqiu'(ST34) and 'Xuehai' (SP10). The weak EA group will receive EA with low-intensity current (0 mA < current < 0.5 mA) on the same acupoints. The sham EA group will receive EA with low-intensity current (0 mA < current < 0.5 mA) with fine needles inserted superficially into the sites 2 cm lateral to the above acupoints. The patients will be treated with EA once a day, 30 minutes per session, in 5 sessions per week, for 2 weeks. In order to determine the best stage of KOA for effective EA intervention, patients within the treatment groups also will be divided into four stages. The primary outcomes are Visual Analog Scale (VAS), DNIC function and the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC). Clinical assessments will be evaluated at baseline (before treatment) and after 5 to 10 sessions of treatment.



This trial will be helpful in identifying whether strong EA is more effective than weak EA in reversing chronification of acute pain through repairing the impaired DNIC function and in screening for the best stage of KOA for effective EA intervention.


 The date of registration is 31 October 2014.
Viral Linkage in HIV-1 Seroconverters and Their Partners in an HIV-1 Prevention Clinical Trial

Characterization of viruses in HIV-1 transmission pairs will help identify biological determinants of infectiousness and evaluate candidate interventions to reduce transmission. Although HIV-1 sequencing is frequently used to substantiate linkage between newly HIV-1 infected individuals and their sexual partners in epidemiologic and forensic studies, viral sequencing is seldom applied in HIV-1 prevention trials. The Partners in Prevention HSV/HIV Transmission Study ( was a prospective randomized placebo-controlled trial that enrolled serodiscordant heterosexual couples to determine the efficacy of genital herpes suppression in reducing HIV-1 transmission; as part of the study analysis, HIV-1 sequences were examined for genetic linkage between seroconverters and their enrolled partners.



We obtained partial consensus HIV-1 env and gag sequences from blood plasma for 151 transmission pairs and performed deep sequencing of env in some cases. We analyzed sequences with phylogenetic techniques and developed a Bayesian algorithm to evaluate the probability of linkage. For linkage, we required monophyletic clustering between enrolled partners' sequences and a Bayesian posterior probability of ≥ 50%. Adjudicators classified each seroconversion, finding 108 (71.5%) linked, 40 (26.5%) unlinked, and 3 (2.0%) indeterminate transmissions, with linkage determined by consensus env sequencing in 91 (84%). Male seroconverters had a higher frequency of unlinked transmissions than female seroconverters. The likelihood of transmission from the enrolled partner was related to time on study, with increasing numbers of unlinked transmissions occurring after longer observation periods. Finally, baseline viral load was found to be significantly higher among linked transmitters.



In this first use of HIV-1 sequencing to establish endpoints in a large clinical trial, more than one-fourth of transmissions were unlinked to the enrolled partner, illustrating the relevance of these methods in the design of future HIV-1 prevention trials in serodiscordant couples. A hierarchy of sequencing techniques, analysis methods, and expert adjudication contributed to the linkage determination process.
Pharmacokinetics of modified-release prednisone tablets in healthy subjects and patients with rheumatoid arthritis.

In rheumatoid arthritis (RA), nocturnal release of proinflammatory cytokines is not adequately counteracted by endogenous glucocorticoid and is associated with symptoms of morning stiffness and pain. Taking exogenous glucocorticoid during the night reduces morning stiffness significantly more than treatment at the conventional time in the morning, although waking to take tablets is unacceptable for patients. Modified-release prednisone tablets were developed to allow administration at bedtime for programmed delivery of glucocorticoid during the night. Single-center crossover studies were conducted, each in ≤24 healthy subjects, to compare the pharmacokinetics of a single 5-mg oral dose of modified-release prednisone and conventional prednisone, as well as the effect of food on bioavailability. There was no substantial difference in pharmacokinetic parameters of the formulations apart from the programmed delay in release of glucocorticoid from the modified-release tablets (C(max) 97%, AUC(0-∞) 101%, 90% confidence intervals within the requisite range for bioequivalence). Administration after a full or light meal did not affect pharmacokinetic characteristics, but bioavailability was reduced under fasted conditions. Pharmacokinetic evaluation in 9 patients with RA confirmed that modified-release prednisone tablets taken at bedtime (around 22:00 h) with or after an evening meal result in programmed release of glucocorticoid 4 to 6 hours after intake.
Effect of different doses of nasal salmon calcitonin on bone mass

Forty postmenopausal women with a former Colles' fracture were enrolled in a 1-year study to determine the dose-effect relationship of nasal salmon calcitonin (SCT) on bone mass. They were randomized to receive either placebo, 50, 100, or 200 IU per day of SCT given as a nasal spray. The rate of change in the bone mineral content of the lumbar spine was 0.7, 0.2, 1.1, and 2.0 gHA per year, respectively, and the rate of change in the bone mineral content in the forearm was −0.4, −0.1, 0.0, and −0.1 AU per year, respectively. The rate of change in the bone mineral content of the lumbar spine in patients receiving 200 IU of SCT per day differed significantly from zero (P<0.01). Except for one patient, who experienced intolerable nausea, no systemic side effects were observed. Seven patients withdrew, two patients from nasal intolerance to the spray. These preliminary data suggest that SCT given by the nasal route has a positive and dose-dependent effect on spinal bone mass, but affects forearm bone mass only minimally.
Inspiratory muscle training in patients with cystic fibrosis.

Little information is available about the effects of inspiratory muscle training in patients with cystic fibrosis (CF). In this study the effects of inspiratory-threshold loading in patients with CF on strength and endurance of the inspiratory muscles, pulmonary function, exercise capacity, dyspnoea and fatigue were evaluated. Sixteen patients were assigned to one of two groups using the minimization method: eight patients in the training group and eight patients in the control group. The training was performed using an inspiratory-threshold loading device. Patients were instructed to use the threshold trainer 20 min a day, 5 days a week for 6 weeks. Patients in the training group trained at inspiratory threshold loads up to 40% of maximal static inspiratory pressure (Pimax) and patients in the control group got 'sham' training at a load of 10% of Pimax. No significant differences were found among the two groups in gender, age, weight, height, pulmonary function, exercise capacity, inspiratory-muscle strength and inspiratory-muscle endurance before starting the training programme. Mean (SD) age in the control group was 19 (5.5) years, mean (SD) age in the training group was 17 (5.2) years. Mean FEV1 in both groups was 70% predicted, mean inspiratory-muscle strength in both groups was above 100% predicted. All patients except one, assigned to the training group, completed the programme. After 6 weeks of training, mean inspiratory-muscle endurance (% Pimax) in the control group increased from 50% to 54% (P = 0.197); in the training group mean inspiratory muscle endurance (% Pimax) increased from 49% to 66% (P = 0.003). Statistical analysis showed that the change in inspiratory-muscle endurance (% Pimax) in the training group was significantly higher than in the control group (P = 0.012). After training, in the training group there was a tendency of improvement in Pimax with an increase from 105 to 123% predicted, which just fell short of statistical significance (P = 0.064). After training no significant differences were found in changes from baseline in pulmonary function, exercise capacity, dyspnoea and fatigue. It is concluded that low-intensity inspiratory-threshold loading at 40% of Pimax was sufficient to elicit an increased inspiratory-muscle endurance in patients with CF.
Long-Term Outcome of 4,040 Children Diagnosed With Pediatric Low-Grade Gliomas: An Analysis of the Surveillance Epidemiology and End Results (SEER) Database

Children with pediatric low-grade gliomas (PLGG) are known to have excellent 10-year survival rates; however the outcomes of adult survivors of PLGG are unknown. We identified patients diagnosed with PLGG diagnosed between 1973 and 2008 through the Surveillance Epidemiology and End Results (SEER) database to examine outcomes of adult survivors of PLGG.


PROCEDURE
Four thousand and forty patients with either WHO grade I or II PLGG were identified and outcome data retrieved. Two analyses were performed to assess survival and risk of death from tumor. Competing risks analysis was conducted and cumulative incidence curves of death due to disease were generated. Cox proportional hazards regression was performed, with adjustment for non-disease death. Kaplan-Meier curves for overall cancer specific survival (OS) were also generated.



The 20-year OS was 87% ± 0.8% and the 20-year cumulative incidence of death due to glioma was 12% ± 0.8%. The incidence of death after transition to adulthood (age greater than 22 years) was slightly lower, with 20-year cumulative incidence of disease death of 7% ± 1.8%. Year of diagnosis, age of diagnosis, histology, WHO grade, primary site, radiation, and degree of initial resection were prognostic in univariate analysis, while the administration of radiation was the greatest risk of death in multivariate analysis of OS (hazard ratio = 3.9).



PLGGs are associated with an excellent long-term survival, with a low likelihood of PLGG related death in adult survivors. Treatment strategies for pediatric tumors should therefore aim for disease control during childhood and adolescence with an emphasis on minimizing long-term treatment induced toxicities.
Abnormal Pap smear follow-up in a high-risk population.

Low-income women are at high risk of developing cervical cancer attributable not only to the higher prevalence of risk factors in this population but also to the lack of timely follow-up of abnormal Pap smears. This study evaluates the efficacy of an aggressive follow-up strategy. Women with abnormal Pap smear results after screening in a public hospital emergency department were randomly assigned to follow-up either by a case-managed approach using computerized tracking and universal colposcopy or by traditional care. The main outcome was the proportion of women receiving follow-up in 6 months. A secondary outcome was the proportion of women receiving follow-up by 6 months and diagnostic resolution in 18 months. Of 54 women in the intervention group, 65% kept at least one follow-up appointment in 6 months compared with 41% of the 54 women in the control group (P = 0.012). Half the women in the intervention group versus 19% of women in the control group had follow-up in 6 months and diagnostic resolution in 18 months (P = 0.001). After adjusting for age, initial Pap smear result, and race/ethnicity, the odds of having follow-up in 6 months were four times greater for women in the intervention group (odds ratio = 4.0; 95% confidence interval, 1.6-9.7), and the odds of having both follow-up in 6 months and diagnostic resolution in 18 months were more than six times greater (odds ratio = 6.5; 95% confidence interval, 2.4-17.8). This study demonstrates that an aggressive follow-up strategy significantly improves the rate of both initial follow-up and diagnostic resolution of abnormal Pap smears among low-income women with atypical squamous cells of undetermined significance and atypical glandular cells of undetermined significance when compared with traditional care.
Determining positional bias of MHC class I restricted T-cell epitopes in viral antigens

After viral infection, CD8+ T-cells can rapidly detect their intracellular presence by recognizing peptide fragments presented by MHC class I molecules on the cell surface that are derived from degraded viral protein. This appears to be in conflict with the observation that viral proteins have relatively long half-lives. To explain this, the DRiPs hypothesis (Yewdell and Nicchitta, 2006) was proposed, which states that these epitopes come from Defective Ribosomal Products (DRiPs), rather than degradation of mature protein products. If epitopes do come from defective ribosomal products, this could lead to a positional bias of epitopes in their corresponding antigens. Specifically, if a major source of defective ribosomal products is pre-mature stop in translation, an overrepresentation of CD8+ T-cell epitopes in the N-terminal portion of antigens would be expected. In contrast, if downstream initiation is a major source of defective ribosomal products, C-terminal portions of antigens would be a dominant source of epitopes. In this study, we systematically assess positional bias of epitopes in viral antigens, taking advantage of the large set of immune epitope data available in the Immune Epitope Database. We demonstrate that there is a small degree of positional skewing detectable in the epitope distribution. Epitopes from both ends of antigens tend to be slightly underrepresented, which suggests that both pre-mature stops in translation and downstream initiation play an equal but minor role in shaping the overall viral epitope repertoire.
CXCL13 predicts disease activity in early rheumatoid arthritis and could be an indicator of the therapeutic ‘window of opportunity’

A key phenomenon in rheumatoid arthritis is the formation of lymphoid follicles in the inflamed synovial membrane. C-X-C motif chemokine 13 (CXCL13) is central in this process as it attracts C-X-C chemokine receptor type 5 (CXCR5)-expressing B cells and T follicular helper cells to the follicle. We here examine the role of CXCL13 and its association with disease in patients with treatment-naïve early rheumatoid arthritis.



Plasma samples from patients in the OPERA trial were examined for CXCL13 at treatment initiation and after 6 months of treatment with either methotrexate plus placebo (DMARD) (n = 37) or methotrexate plus adalimumab (DMARD + ADA) (n = 39). Treatment outcome was evaluated after 1 and 2 years. CXCL13 plasma levels in healthy volunteers (n = 38) were also examined.



Baseline CXCL13 plasma levels were increased in early rheumatoid arthritis patients in comparison with healthy volunteers. Also, plasma CXCL13 correlated positively with disease activity parameters; swollen joint count 28 (rho = 0.34) and 40 (rho = 0.39), visual analog score (rho = 0.38) and simplified disease activity index (rho = 0.25) (all P <0.05). CXCL13 levels decreased a significantly twofold more in the DMARD + ADA group than in the DMARD group. Baseline CXCL13 plasma levels in the DMARD group correlated inversely with disease activity parameters; disease activity score in 28 joints, four variables, C-reactive protein based (DAS28CRP) (rho = 0.58, P < 0.05) at 12 months. High baseline CXCL13 was associated with remission (DAS28CRP less than 2.6) after 2 years.



In treatment-naïve early rheumatoid arthritis patients, plasma CXCL13 levels were associated with joint inflammation. Furthermore, patients with high baseline plasma CXCL13 levels had an improved chance of remission after 2 years. We propose that high CXCL13 concentrations indicate recent onset of inflammation that may respond better to early aggressive treatment. Thus, high levels of CXCL13 could reflect the 'the window of opportunity' for optimal treatment effect.
Security: the state of the practice (invited talk)

In the last twenty years our field has grown enormously and a tremendous number of techniques and tools have been developed. The Internet has moved the need for security centerstage. Yet, with some notable exceptions, most of the tools and techniques being developed are simply not being deployed! For instance, consumer PKI has been a non starter to date. In this talk we analyze the reasons for some of these circumstances and suggest guidelines for developing solutions that are more likely to be adopted. Short biography Ravi Ganesan currently serves as Vice Chairman of CheckFree Corporation. He previously served as Chief Technology Officer of CheckFree Corporation. At CheckFree Ravi led the effort to consolidate the development and operations of several companies CheckFree acquired, culminating in the development of CheckFree's Genesis 2000 electronic billing and payment infrastructure. He then led CheckFree's move to expand its electronic billing and payments services to Internet portals and financial transaction sites. He most recently led the effort to extend CheckFree's Genesis infrastructure to encompass all forms of Internet payments, including person-to-person and personto-merchant Internet payments. Before joining CheckFree, Ravi served various roles at Bell Atlantic Corporation, including Senior Manager of the Center of Electronic Commerce, Director of the Center of Internet Services and before leaving to join CheckFree was Vice President of Distributed Operations. Ravi holds a Bachelor of Engineering from Anna University, Madras, India, an MSc from the University of Maryland Baltimore County, and a PhD from The Johns Hopkins University, each in the area of Computer Science. He holds numerous patents in the areas of Internet payments, electronic billing and cryptography.
Electronic alerts for triage protocol compliance among emergency department triage nurses: a randomized controlled trial.

Alerts embedded in electronic health records (EHRs) are designed to improve processes at the point of care.



The aim of this study was to determine if an EHR alert-at emergency department (ED) triage-increases the ED triage nurse's utilization of triage protocols.



ED triage nurses were randomized to receive either a passive EHR alert or no intervention for patients with the following complaints: minor trauma with extremity injuries or female patients with abdominal pain. The EHR alert notified the nurse that the patient was eligible for diagnostic testing: radiographs for patients with injured extremities or urinalysis for female patients with abdominal pain.



Twenty-eight nurses triaged 20,410 patients in the 6 months before the intervention and 19,157 in the 6 months after the intervention. Before the intervention, the urinalysis protocol was implemented in 101/624 (16.2%) patients triaged by the intervention group and 116/711 (16.3%) triaged by the control group. After the intervention, the urinalysis protocol was implemented in 146/530 (27.6%) patients triaged by the intervention group and 174/679 (25.6%) triaged by the control group. Before the intervention, the radiograph protocol was implemented in 58/774 (7.5%) patients triaged by the intervention group and 45/684 (6.6%) triaged by the control group. After the intervention, the radiograph protocol was implemented in 78/614 (12.7%) patients triaged by the intervention group and 79/609 (13.0%) triaged by the control group.



The use of a passive EHR alert to promote ED triage protocols showed little benefit. Before the widespread implementation of EHR alerts for patient care, rigorous studies are required to determine the best alert methods and the impacts of such interventions.
Health-related quality of life among men with HIV infection: effects of social support, coping, and depression.

In a prospective cohort study, baseline data were collected on 226 males with HIV infection attending three infectious disease clinics in a southern state. As a result of advances in HIV treatment, understanding the association between psychosocial factors and health-related quality of life has become an important area of study. The purpose of this study was to assess the total effects of social support and coping as well as the direct and indirect effects of these factors through depression on health-related quality of life. Subjects were interviewed and answered the following standardized questionnaires: The HIV Cost and Services Utilization Study tool, Coping with HIV Questionnaire, Social Support Appraisals Scale, and Centers for Epidemiological Studies Depression instrument. Path models with strictly ordered relationships were fitted to study the effects of the psychosocial variables on each quality of life subscale. We found that coping and social support had total effects on some, but not all dimensions of health-related quality of life, whereas depression was associated with all dimensions of health-related quality of life. Furthermore, the effects of both social support and coping were mainly through the intermediate variable, depression. In the era of highly active antiretroviral therapy (HAART), when quality of life issues are of paramount importance, strategies to improve social support, coping, and particularly, depressive symptoms are strongly encouraged.