nils-herrmann/clean_scirepeval huggingface dataset:
Impacts of antibiotic and anti-inflammatory therapies on serum prostate-specific antigen levels in the presence of prostatic inflammation: a prospective randomized controlled trial.

The aim of this study was to determine if antibiotic or anti-inflammatory medications lower serum prostate-specific antigen (PSA) in the presence or absence of inflammation in the prostatic secretions of patients with PSA levels between 2.5 and 10 ng/ml and normal digital rectal examinations (DRE).



Patients with PSA levels between 2.5 and 10 ng/ml and normal DRE were candidates for the study. One hundred and eight patients with positive expressed prostate secretion (EPS) were randomized into antibiotics, anti-inflammatory and control groups (groups 1, 2 and 3, respectively), and 108 patients with negative EPS were randomized into similar groups (groups 4, 5 and 6, respectively). Repeat PSA levels of all patients were obtained 6 weeks after randomization and 10 core prostate biopsies were performed.



Median PSA levels in group 1 before and after treatment were 5.2 (4.3-6.4) and 4.0 ng/ml (3.1-4.9), respectively (p < 0.001). The only significant decrease in PSA was observed in group 1. The percent change in PSA levels in group 1 was significantly greater than both in its control group (group 3; p < 0.001) and the EPS- antibiotics group (group 4; p < 0.001).



Antibiotherapy significantly reduces serum PSA only in EPS+ patients, which justifies limiting the use of prebiopsy antibiotics to EPS+ patients with a normal DRE and PSA level between 2.5 and 10 ng/ml, minimizing the major drawbacks of empirical antibiotics usage.
Women, men, and rheumatoid arthritis: analyses of disease activity, disease characteristics, and treatments in the QUEST-RA Study

Gender as a predictor of outcomes of rheumatoid arthritis (RA) has evoked considerable interest over the decades. Historically, there is no consensus whether RA is worse in females or males. Recent reports suggest that females are less likely than males to achieve remission. Therefore, we aimed to study possible associations of gender and disease activity, disease characteristics, and treatments of RA in a large multinational cross-sectional cohort of patients with RA called Quantitative Standard Monitoring of Patients with RA (QUEST-RA).



The cohort includes clinical and questionnaire data from patients who were seen in usual care, including 6,004 patients at 70 sites in 25 countries as of April 2008. Gender differences were analyzed for American College of Rheumatology Core Data Set measures of disease activity, DAS28 (disease activity score using 28 joint counts), fatigue, the presence of rheumatoid factor, nodules and erosions, and the current use of prednisone, methotrexate, and biologic agents.



Women had poorer scores than men in all Core Data Set measures. The mean values for females and males were swollen joint count-28 (SJC28) of 4.5 versus 3.8, tender joint count-28 of 6.9 versus 5.4, erythrocyte sedimentation rate of 30 versus 26, Health Assessment Questionnaire of 1.1 versus 0.8, visual analog scales for physician global estimate of 3.0 versus 2.5, pain of 4.3 versus 3.6, patient global status of 4.2 versus 3.7, DAS28 of 4.3 versus 3.8, and fatigue of 4.6 versus 3.7 (P < 0.001). However, effect sizes were small-medium and smallest (0.13) for SJC28. Among patients who had no or minimal disease activity (0 to 1) on SJC28, women had statistically significantly higher mean values compared with men in all other disease activity measures (P < 0.001) and met DAS28 remission less often than men. Rheumatoid factor was equally prevalent among genders. Men had nodules more often than women. Women had erosions more often than men, but the statistical significance was marginal. Similar proportions of females and males were taking different therapies.



In this large multinational cohort, RA disease activity measures appear to be worse in women than in men. However, most of the gender differences in RA disease activity may originate from the measures of disease activity rather than from RA disease activity itself.
Balance and walking after three different models of stroke rehabilitation: early supported discharge in a day unit or at home, and traditional treatment (control)

To compare the effects on balance and walking of three models of stroke rehabilitation: early supported discharge with rehabilitation in a day unit or at home, and traditional uncoordinated treatment (control).



Group comparison study within a randomised controlled trial.



Hospital stroke unit and primary healthcare.



a score of 2-26 on National Institutes of Health Stroke Scale, assessed with Postural Assessment Scale for Stroke (PASS), and discharge directly home from the hospital stroke unit.



Two intervention groups were given early supported discharge with treatment in either a day unit or the patient's own home. The controls were offered traditional, uncoordinated treatment.



Primary: PASS.  Trunk Impairment Scale-modified Norwegian version; timed Up-and-Go; 5 m timed walk; self-reports on problems with walking, balance, ADL, physical activity, pain and tiredness. The patients were tested before randomisation and 3 months after inclusion.



From a total of 306 randomised patients, 167 were tested with PASS at baseline and discharged directly home. 105 were retested at 3 months: mean age 69 years, 63 men, 27 patients in day unit rehabilitation, 43 in home rehabilitation and 35 in a control group. There were no group differences, either at baseline for demographic and test data or for length of stroke unit stay. At 3 months, there was no group difference in change on PASS (p>0.05). Some secondary measures tended to show better outcome for the intervention groups, that is, trunk control, median (95% CI): day unit, 2 (0.28 to 2.31); home rehabilitation, 4 (1.80 to 3.78); control, 1 (0.56 to 2.53), p=0.044; and for self-report on walking, p=0.021 and ADL, p=0.016.



There was no difference in change between the groups for postural balance, but the secondary outcomes indicated that improvement of trunk control and walking was better in the intervention groups than in the control group.
The effects of low dose intravenous 99-126 atrial natriuretic factor infusion in patients with chronic renal failure.

The aim was to study the renal and hormonal effects of intravenous 99-126 atrial natriuretic factor (ANF) infusion in a mixed group of patients who had moderate to severe chronic renal failure (CRF) and who were not treated with dialysis. The peak mean plasma level of ANF achieved during the experiment was at the upper limit of an absolute range of basal values previously recorded in a larger group of patients with similar degrees of renal impairment. A significant tissue effect was confirmed by rises in plasma and urinary cyclic guanosine monophosphate, the 'second-messenger' of ANF. ANF infusion increased sodium excretion rate by a mean of 68% compared with a fall of 40% in a placebo group, and significant increases in urinary albumin excretion occurred during the peptide infusion. Thus, the high levels of plasma ANF found in CRF may have a role in the maintenance of sodium balance. In addition, the proteinuric effect may be detrimental to long-term renal function.
Use of tissue velocity imaging in the diagnosis of fetal cardiac arrhythmias.

Precise diagnosis of cardiac arrhythmias in the fetus is crucial for a managed therapeutic approach. However, many technical, positional, and gestational age-related limitations may render conventional methods, such as M-mode and Doppler flow methodologies, or newer techniques, such as fetal electrocardiography or magnetocardiography, difficult to apply, or these techniques may be unsuitable for the diagnosis of fetal arrhythmias.



In this prospective study, we describe a novel method based on raw scan-line tissue velocity data acquisition and analysis. The raw data are available from high-frame-rate 2D tissue velocity images and allow simultaneous sampling of right and left atrial and ventricular wall velocities to yield precise temporal analysis of atrial and ventricular events. Using this timing data, a ladder diagram-like "fetal kinetocardiogram" was developed to diagram and diagnose arrhythmias and to provide true intervals. This technique was feasible and fast, yielding diagnostic results in all 31 fetuses from 18 to 38 weeks of gestation. Analysis of various supraventricular and ventricular arrhythmias was readily obtained, including arrhythmias that conventional methods fail to diagnose.



The fetal kinetocardiogram opens a new window to aid in the diagnosis and understanding of fetal arrhythmias, and it provides a tool for studying the action of antiarrhythmic drugs and their effects on electrophysiological conduction in the fetal heart.
Telephone-administered cognitive behavioral therapy for veterans served by community-based outpatient clinics.

Multiple trials have found telephone-administered cognitive behavioral therapy (T-CBT) to be effective for the treatment of depression. The aim of this study was to evaluate T-CBT for the treatment of depression among veterans served by community-based outpatient clinics (CBOCs) outside of major urban areas.



Eighty-five veterans meeting Diagnostic and Statistical Manual of Mental Disorders (4th ed.; American Psychiatric Association, 1994) criteria for major depressive disorder were randomized to receive 16 sessions of T-CBT over 20 weeks or treatment as usual through the CBOC. Veterans were assessed at baseline, 12 weeks, 20 weeks (posttreatment), and 6-month follow-up using the Hamilton Depression Rating Scale (Hamilton, 1960), the Patient Health Questionnaire-9 (Kroenke, Spitzer, & Williams, 2001), and a standardized psychiatric interview.



There were no significant Time × Treatment effects (ps > .20). Patients were compliant, with 38 (92.7%) completing at least 12 sessions, and 32 (78.0%) having no missed sessions whatsoever. Ratings of audiotaped sessions showed the therapists to be highly competent.



This trial yielded negative results for an intervention that has been shown to be effective under other circumstances. We speculate that veterans served within the Veterans Affairs system are more refractory to treatment than other populations, and they may require a more rigorous intervention.
Quantitative measurement of HER2 expression in breast cancers: comparison with ‘real-world’ routine HER2 testing in a multicenter Collaborative Biomarker Study and correlation with overall survival

Accurate assessment of HER2 status is critical in determining appropriate therapy for breast cancer patients but the best HER2 testing methodology has yet to be defined. In this study, we compared quantitative HER2 expression by the HERmark™ Breast Cancer Assay (HERmark) with routine HER2 testing by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH), and correlated HER2 results with overall survival (OS) of breast cancer patients in a multicenter Collaborative Biomarker Study (CBS). Two hundred and thirty-two formalin-fixed, paraffin-embedded breast cancer tissues and local laboratory HER2 testing results were provided by 11 CBS sites. HERmark assay and central laboratory HER2 IHC retesting were retrospectively performed in a blinded fashion. HER2 results by all testing methods were obtained in 192 cases. HERmark yielded a continuum of total HER2 expression (H2T) ranging from 0.3 to 403 RF/mm2 (approximately 3 logs). The distribution of H2T levels correlated significantly (P <0.0001) with all routine HER2 testing results. The concordance of positive and negative values (equivocal cases excluded) between HERmark and routine HER2 testing was 84% for local IHC, 96% for central IHC, 85% for local FISH, and 84% for local HER2 status. OS analysis revealed a significant correlation of shorter OS with HER2 positivity by local IHC (HR = 2.6, P = 0.016), central IHC (HR = 3.2, P = 0.015), and HERmark (HR = 5.1, P <0.0001) in this cohort of patients most of whom received no HER2-targeted therapy. The OS curve of discordant low (HER2 positive but H2T low, 10% of all cases) was aligned with concordant negative (HER2 negative and H2T low, HR = 1.9, P = 0.444), but showed a significantly longer OS than concordant positive (HER2 positive and H2T high, HR = 0.31, P = 0.024). Conversely, the OS curve of discordant high (HER2 negative but H2T high, 9% of all cases) was aligned with concordant positive (HR = 0.41, P = 0.105), but showed a significantly shorter OS than concordant negative (HR = 41, P <0.0001). Quantitative HER2 measurement by HERmark is highly sensitive, accurately quantifies HER2 protein expression and correlates well with routine HER2 testing. When HERmark and local HER2 results were discordant, HERmark more accurately predicted overall survival.
Pulmonary Vascular Distensibility Predicts Pulmonary Hypertension Severity, Exercise Capacity, and Survival in Heart Failure.

Pulmonary vascular (PV) distensibility, defined as the percent increase in pulmonary vessel diameter per mm Hg increase in pressure, permits the pulmonary vessels to increase in size to accommodate increased blood flow. We hypothesized that PV distensibility is abnormally low in patients with heart failure (HF) and serves as an important determinant of right ventricular performance and exercise capacity.



Patients with HF with preserved ejection fraction (n=48), HF with reduced ejection fraction (n=55), pulmonary arterial hypertension without left heart failure (n=18), and control subjects (n=30) underwent cardiopulmonary exercise testing with invasive hemodynamic monitoring and first-pass radionuclide ventriculography. PV distensibility was derived from 1257 matched measurements (mean±SD, 8.3±2.8 per subject) of pulmonary arterial pressure, pulmonary arterial wedge pressure and cardiac output. PV distensibility was lowest in the pulmonary arterial hypertension group (0.40±0.24% per mm Hg) and intermediate in the HF with preserved ejection fraction and HF with reduced ejection fraction groups (0.92±0.39 and 0.84±0.33% per mm Hg, respectively) compared to the control group (1.39±0.32% per mm Hg, P<0.0001 for all three). PV distensibility was associated with change in right ventricular ejection fraction (RVEF, ρ=0.39, P<0.0001) with exercise and was an independent predictor of peak VO2. PV distensibility also predicted cardiovascular mortality independent of peak VO2 in HF patients (n=103; Cox hazard ratio, 0.30; 95% confidence interval, 0.10-0.93; P=0.036). In a subset of patients with HF with reduced ejection fraction (n=26), 12 weeks of treatment with the pulmonary vasodilator sildenafil or placebo led to a 24.6% increase in PV distensibility (P=0.015) in the sildenafil group only.



PV distensibility is reduced in patients with HF and pulmonary arterial hypertension and is closely related to RV systolic function during exercise, maximal exercise capacity, and survival. Furthermore, PV distensibility is modifiable with selective pulmonary vasodilator therapy and may represent an important target for therapy in selected HF patients with pulmonary hypertension.
Computer-aided detection of breast cancer nuclei

A computer-aided detection system for tissue cell nuclei in histological sections is introduced and validated as part of the Biopsy Analysis Support System (BASS). Cell nuclei are selectively stained with monoclonal antibodies, such as the anti-estrogen receptor antibodies, which are widely applied as part of assessing patient prognosis in breast cancer. The detection system uses a receptive field filter to enhance negatively and positively stained cell nuclei and a squashing function to label each pixel value as belonging to the background or a nucleus. In this study, the detection system assessed all biopsies in an automated fashion. Detection and classification of individual nuclei as well as biopsy grading performance was shown to be promising as compared to that of two experts. Sensitivity and positive predictive value were measured to be 83% and 67.4%, respectively. One major advantage of BASS stems from the fact that the system simulates the assessment procedures routinely employed by human experts; thus it can be used as an additional independent expert. Moreover, the system allows the efficient accumulation of data from large numbers of nuclei in a short time span. Therefore, the potential for accurate quantitative assessments is increased and a platform for more standardized evaluations is provided.
Efficacy of n-3 polyunsaturated fatty acids and feasibility of optimizing preventive strategies in patients at high cardiovascular risk: rationale, design and baseline characteristics of the Rischio and Prevenzione study, a large randomised trial in general practice

The optimization of preventive strategies in patients at high risk of cardiovascular events and the evaluation of bottlenecks and limitations of transferring current guidelines to the real world of clinical practice are important limiting steps to cardiovascular prevention. Treatment with n-3 polyunsaturated fatty acids improves prognosis after myocardial infarction, but evidence of this benefit is lacking in patients at high cardiovascular risk, but without a history of myocardial infarction.



Patients were eligible if their general practitioner (GP) considered them at high cardiovascular risk because of a cardiovascular disease other than myocardial infarction, or multiple risk factors (at least four major risk factors in non-diabetic patients and one in diabetics).Patients were randomly allocated to treatment with n-3 polyunsaturated fatty acids (1 g daily) or placebo in a double-blind study and followed up for five years by their GPs to assess the efficacy of the treatment in preventing cardiovascular mortality (including sudden death) and hospitalization for cardiovascular reasons. The secondary, epidemiological, aim of the study is to assess whether it is feasible to adopt current guidelines in everyday clinical practice, with a view to optimizing all the available preventive strategies in people at high cardiovascular risk.A nation-wide network of 860 GPs admitted 12,513 patients to the study between February 2004 and March 2007. The mean age was 64 years and 62% were males. Diabetes mellitus plus one or more cardiovascular risk factors was the main inclusion criterion (47%). About 30% of patients were included because of a history of atherosclerotic cardiovascular disease, 21% for four or more risk factors, and less than 1% for other reasons.



The Rischio and Prevenzione (R&P) project provides a feasible model to test the efficacy of n-3 polyunsaturated fatty acid therapy in patients at high cardiovascular risk with no history of myocardial infarction, and to assess how to implement recommended preventive strategies in general practice.
Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data

Novel methods, both molecular and statistical, are urgently needed to take advantage of recent advances in biotechnology and the human genome project for disease diagnosis and prognosis. Mass spectrometry (MS) holds great promise for biomarker identification and genome-wide protein profiling. It has been demonstrated in the literature that biomarkers can be identified to distinguish normal individuals from cancer patients using MS data. Such progress is especially exciting for the detection of early-stage ovarian cancer patients. Although various statistical methods have been utilized to identify biomarkers from MS data, there has been no systematic comparison among these approaches in their relative ability to analyze MS data.



We compare the performance of several classes of statistical methods for the classification of cancer based on MS spectra. These methods include: linear discriminant analysis, quadratic discriminant analysis, k-nearest neighbor classifier, bagging and boosting classification trees, support vector machine, and random forest (RF). The methods are applied to ovarian cancer and control serum samples from the National Ovarian Cancer Early Detection Program clinic at Northwestern University Hospital. We found that RF outperforms other methods in the analysis of MS data.
Pre-Transplant Cardiovascular Risk Factors Affect Kidney Allograft Survival: A Multi-Center Study in Korea

Pre-transplant cardiovascular (CV) risk factors affect the development of CV events even after successful kidney transplantation (KT). However, the impact of pre-transplant CV risk factors on allograft failure (GF) has not been reported.



We analyzed the graft outcomes of 2,902 KT recipients who were enrolled in a multi-center cohort from 1997 to 2012. We calculated the pre-transplant CV risk scores based on the Framingham risk model using age, gender, total cholesterol level, smoking status, and history of hypertension. Vascular disease (a composite of ischemic heart disease, peripheral vascular disease, and cerebrovascular disease) was noted in 6.5% of the patients. During the median follow-up of 6.4 years, 286 (9.9%) patients had developed GF. In the multivariable-adjusted Cox proportional hazard model, pre-transplant vascular disease was associated with an increased risk of GF (HR 2.51; 95% CI 1.66-3.80). The HR for GF (comparing the highest with the lowest tertile regarding the pre-transplant CV risk scores) was 1.65 (95% CI 1.22-2.23). In the competing risk model, both pre-transplant vascular disease and CV risk score were independent risk factors for GF. Moreover, the addition of the CV risk score, the pre-transplant vascular disease, or both had a better predictability for GF compared to the traditional GF risk factors.



In conclusion, both vascular disease and pre-transplant CV risk score were independently associated with GF in this multi-center study. Pre-transplant CV risk assessments could be useful in predicting GF in KT recipients.
The role of basic health insurance on depression: an epidemiological cohort study of a randomized community sample in Northwest China

Little research has focused on the relationship between health insurance and mental health in the community. The objective of this study is to determine how the basic health insurance system influences depression in Northwest China.



Participants were selected from 32 communities in two northwestern Chinese cities through a three-stage random sampling. Three waves of interviews were completed in April 2006, December 2006, and January 2008. The baseline survey was completed by 4,079 participants. Subsequently, 2,220 participants completed the first follow-up, and 1,888 completed the second follow-up. Depression symptoms were measured by the Center for Epidemiologic Studies Depression Scale (CES-D).



A total of 40.0% of participants had at least one form of health insurance. The percentages of participants with severe depressive symptoms in the three waves were 21.7%, 22.0%, and 17.6%. Depressive symptoms were found to be more severe among participants without health insurance in the follow-up surveys. After adjusting for confounders, participants without health insurance were found to experience a higher risk of developing severe depressive symptoms than participants with health insurance (7 months: OR, 1.40; 95% CI, 1.09-1.82; p = 0.01; 20 months: OR, 1.89; 95% CI, 1.37-2.61; p < 0.001).



A lack of basic health insurance can dramatically increase the risk of depression based on northwestern Chinese community samples.