nils-herrmann/clean_scirepeval huggingface dataset:
Efficacy of bleeding risk scores in elderly patients with acute coronary syndromes.

The incidence of acute coronary syndromes is high in the elderly population. Bleeding is associated with a poorer prognosis in this clinical setting. The available bleeding risk scores have not been validated specifically in the elderly. Our aim was to assess predictive ability of the most important bleeding risk scores in patients with acute coronary syndrome aged ≥ 75 years.



We prospectively included consecutive acute coronary syndromes patients. Baseline characteristics, laboratory findings, and hemodynamic data were collected. In-hospital bleeding was defined according to CRUSADE, Mehran, ACTION, and BARC definitions. CRUSADE, Mehran, and ACTION bleeding risk scores were calculated for each patient. The ability of these scores to predict major bleeding was assessed by binary logistic regression, receiver operating characteristic curves, and area under the curves.



We included 2036 patients, with mean age of 62.1 years; 369 patients (18.1%) were ≥ 75 years. Older patients had higher bleeding risk (CRUSADE, 42 vs 22; Mehran, 25 vs 15; ACTION, 36 vs 28; P<.001) and a slightly higher incidence of major bleeding events (CRUSADE bleeding, 5.1% vs 3.8%; P=.250). The predictive ability of these 3 scores was lower in the elderly (area under the curve, CRUSADE: 0.63 in older patients, 0.81 in young patients; P=.027; Mehran: 0.67 in older patients, 0.73 in younger patients; P=.340;



0.58 in older patients, 0.75 in younger patients; P=.041).



Current bleeding risk scores showed poorer predictive performance in elderly patients with acute coronary syndromes than in younger patients.
Comparison of outcomes of ambulance users and nonusers in ST elevation myocardial infarction.

In a systematic province-wide evaluation of care and outcomes of ST elevation myocardial infarction (STEMI), we sought to examine whether a previously documented association between ambulance use and outcome remains after control for clinical risk factors. All 82 acute care hospitals in Quebec (Canada) that treated at least 30 acute myocardial infarctions annually participated in a 6-month evaluation in 2008 to 2009. Medical record librarians abstracted hospital chart data for consecutive patients with a discharge diagnosis of myocardial infarction who presented with characteristic symptoms and met a priori study criteria for STEMI. Linkage to administrative databases provided outcome data (to 1 year) and co-morbidities. Of 1,956 patients, 1,222 (62.5%) arrived by ambulance. Compared with nonusers of an ambulance, users were older, more often women, and more likely to have co-morbidities, low systolic pressure, abnormal heart rate, and a higher Thrombolysis In Myocardial Infarction risk index at presentation. Ambulance users were less likely to receive fibrinolysis or to be sent for primary angioplasty (78.5% vs 83.2% for nonusers, p = 0.01), although if they did, treatment delays were shorter (p <0.001). The 1-year mortality rate was 18.7% versus 7.1% for nonusers (p <0.001). Greater mortality persisted after adjusting for presenting risk factors, co-morbidities, reperfusion treatment, and symptom duration (hazard ratio 1.56, 95% confidence interval 1.30 to 1.87). In conclusion, ambulance users with STEMI were older and sicker than nonusers. Mortality of users was substantially greater after adjustment for clinical risk factors, although they received faster reperfusion treatment overall.
Effectiveness of a cognitive behavioural therapy-based rehabilitation programme (Progressive Goal Attainment Program) for patients who are work-disabled due to back pain: study protocol for a multicentre randomised controlled trial

Psychologically informed rehabilitation programmes such as the Progressive Goal Attainment Program (PGAP) have the potential to address pain-related disability by targeting known psychological factors that inhibit rehabilitation progress. However, no randomised controlled trials of this intervention exist and it has not been evaluated in the Irish health service context. Our objective was to evaluate the clinical efficacy and cost-effectiveness of the PGAP in a multicentre randomised controlled trial with patients who are work-disabled due to back pain.



Adult patients (ages 18 years and older) with nonmalignant back pain who are work-disabled because of chronic pain and not involved in litigation in relation to their pain were invited to take part. Patients were those who show at least one elevated psychosocial risk factor (above the 50th percentile) on pain disability, fear-based activity avoidance, fatigue, depression or pain catastrophizing. Following screening, patients are randomised equally to the intervention or control condition within each of the seven trial locations. Patients allocated to the control condition receive usual medical care only. Patients allocated to the PGAP intervention condition attend a maximum of 10 weekly individual sessions of structured active rehabilitation in addition to usual care. Sessions are delivered by a clinical psychologist and focus on graded activity, goal-setting, pacing activity and cognitive-behavioural therapy techniques to address possible barriers to rehabilitation.The primary analysis will be based on the amount of change on the Roland Morris Disability Questionnaire posttreatment. We will also measure changes in work status, pain intensity, catastrophizing, depression, fear avoidance and fatigue. Outcome measures are collected at baseline, posttreatment and 12-month follow-up. Health-related resource use is also collected pre- and posttreatment and at 12-month follow-up to evaluate cost-effectiveness.



This study will be the first randomized controlled trial of the PGAP in chronic pain patients and will provide important information about the clinical and cost effectiveness of the programme as well as its feasibility in the context of the Irish health service.
Impact of non-linear smoking effects on the identification of gene-by-smoking interactions in COPD genetics studies.

The identification of gene-by-environment interactions is important for understanding the genetic basis of chronic obstructive pulmonary disease (COPD). Many COPD genetic association analyses assume a linear relationship between pack-years of smoking exposure and forced expiratory volume in 1 s (FEV(1)); however, this assumption has not been evaluated empirically in cohorts with a wide spectrum of COPD severity.



The relationship between FEV(1) and pack-years of smoking exposure was examined in four large cohorts assembled for the purpose of identifying genetic associations with COPD. Using data from the Alpha-1 Antitrypsin Genetic Modifiers Study, the accuracy and power of two different approaches to model smoking were compared by performing a simulation study of a genetic variant with a range of gene-by-smoking interaction effects.



Non-linear relationships between smoking and FEV(1) were identified in the four cohorts. It was found that, in most situations where the relationship between pack-years and FEV(1) is non-linear, a piecewise linear approach to model smoking and gene-by-smoking interactions is preferable to the commonly used total pack-years approach. The piecewise linear approach was applied to a genetic association analysis of the PI*Z allele in the Norway Case-Control cohort and a potential PI*Z-by-smoking interaction was identified (p=0.03 for FEV(1) analysis, p=0.01 for COPD susceptibility analysis).



In study samples of subjects with a wide range of COPD severity, a non-linear relationship between pack-years of smoking and FEV(1) is likely. In this setting, approaches that account for this non-linearity can be more powerful and less biased than the more common approach of using total pack-years to model the smoking effect.
Class III beta-tubulin isotype predicts response in advanced breast cancer patients randomly treated either with single-agent doxorubicin or docetaxel.

To evaluate the role of microtubule-associated variables as potential predictors of response and clinical outcome in patients with advanced breast cancer receiving single-agent docetaxel or doxorubicin chemotherapy.



The analysis was done on 173 tumor samples from patients with locally advanced or metastatic breast cancer who have participated in the TAX-303 phase III trial in which patients were randomly assigned to receive docetaxel or doxorubicin. Expression of total alpha- and beta-tubulin, classes II to IV beta-tubulin isotypes, and tau protein was evaluated by immunohistochemistry on formalin-fixed, paraffin-embedded tumors from the primary breast cancer.



We observed that patients with "high" expression of class III beta-tubulin isotype had a higher probability of response to docetaxel than to doxorubicin treatment (odds ratio, 1.9; 95% confidence interval, 1.01-3.7; P = 0.05). No difference was observed in terms of time to progression or in terms of overall survival.



This study suggests that the superiority of docetaxel over doxorubicin seems to be confined to the subgroup of patients with "high" expression of class III beta-tubulin isotype.
Mobile VCT: Reaching Men and Young People in Urban and Rural South African Pilot Studies (NIMH Project Accept, HPTN 043)

Mounting evidence exists that mobile voluntary counselling and testing (VCT) is able to extend coverage to new localities and populations. We describe two feasibility and acceptability pilot studies conducted in rural and urban South Africa in preparation for the larger NIMH Project Accept HIV prevention trial. A total of 1,015 individuals participated in the pilot studies. Participants in rural Vulindlela were younger (median 22 years) compared to urban Soweto (p < 0.001). Young people were more likely to be first time testers in both sites (p = 0.01 in Vulindlela, p < 0.001 in Soweto), with significantly more men likely to be first time testers than women (p = 0.01 in Vulindlela, p < 0.001 in Soweto). User satisfaction with mobile VCT was extremely high in both sites. Our study shows that providing mobile, high-quality and easy to access services in a high prevalence context is a feasible way to engage youth, men and more rural populations in HIV counselling and testing.
Comparison of anticraving efficacy of right and left repetitive transcranial magnetic stimulation in alcohol dependence: a randomized double-blind study.

The objective of this study was to compare the anticraving efficacy of high-frequency repetitive transcranial magnetic stimulation (rTMS) of the right versus left dorsolateral prefrontal cortex (DLPFC) in patients with alcohol dependence. Twenty patients with alcohol dependence syndrome were randomly allocated to receive either right or left rTMS over the right DLPFC (10 sessions at 10 Hz frequency; 20 trains per session; 4.9 seconds per train and intertrain interval 30 seconds) and were assessed on the Alcohol Craving Questionnaire (ACQ-NOW) to measure craving. Two-way repeated-measures analysis of variance for ACQ-NOW total score showed no main effect of group (F[1,18] = 0.0001 but significant main effect of time (F[1,18] = 185.91, p<0.0001, η(2) = 0.912). The interaction effect between group and time was not significant. There was significant reduction in craving scores in patients receiving either right or left rTMS with large effect size. However, there was no difference in anticraving efficacy between the two groups.
Not all age-related white matter hyperintensities are the same: a magnetization transfer imaging study.

Our aim was to assess whether presumed histologic heterogeneity of age-related white matter hyperintensities (WMH) is reflected in quantitative magnetization transfer imaging measures.



From a group of patients participating in a double-blind placebo-controlled multicenter study on the effect of pravastatin (PROSPER), we selected 56 subjects with WMH. WMH were classified as periventricular WMH (PVWMH) and deep WMH (DWMH). PVWMH were subclassified as irregular or smooth, depending on the aspect of their border. Signal intensity of WMH on T1-weighted images was scored as iso- or hypointense. The mean magnetization transfer ratio (MTR) value of different types of WMH was assessed and compared. As a control group, we selected 19 subjects with no or limited WMH.



Mean (SE) MTR of PVWMH (frontal, 31.2% [0.2%]; occipital, 32.2% [0.2%]) was lower than that of DWMH (33.7% [0.5%]). The mean MTR of frontal PVWMH (31.2% [0.2%]) was lower than that of occipital PVWMH (32.2% [0.2%]). Compared with occipital PVWMH, frontal PVWMH more often had a smooth lining (72% frontal versus 8% occipital) and an area with low signal intensity on T1-weighted images (76% frontal versus 35% occipital). MTR did not differ between smooth (31.1% [0.3%]) and irregular (31.6% [0.5%]) PVWMH.



Age-related WMH are heterogeneous, despite their similar appearance on T2-weighted images. By taking into account heterogeneity of age-related WMH, both in terms of etiology and in terms of severity of tissue destruction, one may obtain better understanding on the causes and consequences of these lesions.
Trends in quality of non-Hodgkin’s lymphoma care: is it getting better?

This study outlines trends in quality of delivered non-Hodgkin’s lymphoma (NHL) care in the Netherlands between 2007 and 2011 and to what extend this was influenced by the national Visible Care program, which aimed at increasing transparency by providing insight into the quality of healthcare. We analyzed data collected from medical records in two observational studies, combined into 20 validated quality indicators (QIs) of which 6 were included in the national program. A random sample of 771 patients, diagnosed with NHL in 26 Dutch hospitals, was examined. Multilevel regression analyses were used to assess differences in quality of NHL care and to provide insight into the effect of the national program. We reported improved adherence to only 3 out of 6 QIs involved in the national program and none of the other 14 validated QIs. Improvement was shown for performance of all recommended staging techniques (from 26  to  43 %), assessment of International Prognostic Index (from 21  to  43 %), and multidisciplinary discussion of patients (from 23  to  41 %). We found limited improvement in quality of NHL care between 2007 and 2011; improvement potential (<80 % adherence) was still present for 13 QIs. The national program seems to have a small positive effect, but has not influenced all 20 indicators which represent the most important, measurable parts in quality of NHL care. These results illustrate the need for tailored implementation and quality improvement initiatives.
Ba 679 Br, a new long-acting antimuscarinic bronchodilator: a pilot dose-escalation study in COPD.

Preclinical studies with Ba 679 Br have demonstrated a significantly longer duration of action than ipratropium bromide. Following inhalation of single doses, no systemic antimuscarinic effects were noted at doses likely to be bronchodilating in man. The objective of the present pilot-study of Ba 679 Br was to establish the dose-range for its bronchodilatory activity in a small number of chronic obstructive pulmonary disease (COPD) patients, before initiating a formal dose- and time-response study. Employing an open cross-over design, the efficacy of Ba 679 Br was tested, following single inhalational administration of five doses of increasing magnitude on separate days in six patients with COPD. A piezoelectric crystal was used, in order to nebulize an aqueous solution into a mist suitable for inhalation. There was a mean increase in forced expiratory volume in one second (FEV1) of 36% 30 min after inhaling ipratropium bromide 40 micrograms. Pulmonary function tests (FEV1, and specific airways conductance (sGaw)) were performed, at regular time intervals up to 24 h after test drug inhalation. The bronchodilatory activity of Ba 679 Br appeared to be dose-related in the dose-range tested (10-160 micrograms). A peak response was reached in 1.5-2 h, and persisted for 10-15 h in the majority of patients with return to baseline FEV1 approximately 19 h after dosing. No changes in physical examination, electrocardiogram (ECG) and laboratory safety tests from predose values were noted, and no serious adverse events were reported by the patients.(ABSTRACT TRUNCATED AT 250 WORDS)
Discrimination of breast cancer by anti-malignin antibody serum test in women undergoing biopsy.

The anti-malignin antibody serum (AMAS) test (Oncolab, Boston, MA) has been reported as 97% sensitive and 95% specific for malignancies. To objectively assess accuracy of this test for discrimination of breast cancer, we studied a series of women undergoing core breast biopsy.



Seventy-one core-needle breast biopsies were classified as malignant, suspicious, or benign by two independent pathologists blinded to AMAS results. Corresponding sera were read as AMAS positive, negative, or borderline by criteria used by Oncolab and also using criteria derived from receiver-operator curves based on values for slow (S-tag), fast (F-tag), and their difference (Net-tag) antibody reported by Oncolab. We calculated sensitivity and specificity and analyzed distributions by Fisher's exact test.



Biopsies were read as 42 (59%) benign, 12 (17%) suspicious, and 17 (24%) malignant. By Oncolab criteria, sensitivity (59%) and specificity (62%) were maximized by pooling suspicious with malignant and AMAS borderline with positive (P = 0.098). Receiver-operator curves showed best sensitivity (62%) and specificity (69%) for the criterion AMAS positive if Net-Tag > 135 microg/mL or S-Tag > 220 microg/mL (P = 0.015).



The AMAS test discriminates suspicious and malignant from benign lesions, but sensitivity is insufficient to identify patients to be spared biopsy and false-positive rates are too high for population screening.
Extra-uterine renal growth in preterm infants: Oligonephropathy and prematurity

Nephron number in humans is determined during fetal life. The objective of this study was to investigate the effects of preterm birth on nephron number using renal volume as a surrogate for nephron number. This observational study was conducted over 12 months in a tertiary perinatal center. Preterm babies less than 32 weeks of gestation were recruited and followed until discharge. Term infants were recruited for comparison. The babies underwent renal sonography and renal function measurements at 32 and 38 weeks corrected age. The primary outcome measurement was total kidney volume at 38 weeks and the secondary outcome was estimated glomerular filtration rate (eGFR). Forty-four preterm infants and 24 term infants were recruited. At 38 weeks corrected age, premature infants had lower total kidney volume than term infants (21.6 ± 5.7 vs. 25.2 ± 5.7 ml; p = 0.02) and a significantly lower eGFR (73.6 [IQR 68.1–77.6] vs. 79.3 [IQR 72.5–86.6] ml·min−1·1.73 m−2; p = 0.03). There was a significant correlation between total kidney volume and eGFR in premature and term babies. Premature infants have smaller kidney volume and likely decreased nephron number and lower estimated glomerulofiltration rate relative to infants born at term.
Skeletal muscle fatty acid metabolism in association with insulin resistance, obesity, and weight loss.

The current study was undertaken to investigate fatty acid metabolism by skeletal muscle to examine potential mechanisms that could lead to increased muscle triglyceride in obesity. Sixteen lean and 40 obese research volunteers had leg balance measurement of glucose and free fatty acid (FFA) uptake (fractional extraction of [9,10 (3)H]oleate) and indirect calorimetry across the leg to determine substrate oxidation during fasting and insulin-stimulated conditions. Muscle obtained by percutaneous biopsy had lower carnitine palmitoyl transferase (CPT) activity and oxidative enzyme activity in obesity (P < 0.05). During fasting conditions, obese subjects had an elevated leg respiratory quotient (RQ, 0.83 +/- 0.02 vs. 0.90 +/- 0.01; P < 0.01) and reduced fat oxidation but similar FFA uptake across the leg. During insulin infusions, fat oxidation by leg tissues was suppressed in lean but not obese subjects; rates of FFA uptake were similar. Fasting values for leg RQ correlated with insulin sensitivity (r = -0.57, P < 0.001). Thirty-two of the obese subjects were restudied after weight loss (WL, -14.0 +/- 0.9 kg); insulin sensitivity and insulin suppression of fat oxidation improved (P < 0.01), but fasting leg RQ (0.90 +/- 0.02 vs. 0.90 +/- 0.02, pre-WL vs. post-WL) and muscle CPT activity did not change. The findings suggest that triglyceride accumulation in skeletal muscle in obesity derives from reduced capacity for fat oxidation and that inflexibility in regulating fat oxidation, more than fatty acid uptake, is related to insulin resistance.
Validity of a virtual environment for stroke rehabilitation.

Virtual environments for use in stroke rehabilitation are in development, but there has been little evaluation of their suitability for this purpose. We evaluated a virtual environment developed for the rehabilitation of the task of making a hot drink.



Fifty stroke patients undergoing rehabilitation in a UK hospital stroke unit were involved. The performance of stroke rehabilitation patients when making a hot drink had the neurological impairments associated with performance of this task, and the errors observed were compared for standardized task performance in the real world and in a virtual environment. Neurological impairments were measured using standardized assessments. Errors in task performance were assessed rating video recordings and classified into error types.



Real-world and virtual environment performance scores were not strongly associated (rho=0.30; P<0.05). Performance scores in both settings were associated with age, Barthel ADL score, Mini Mental State Examination score, and tests of visuospatial function. Real-world performance only was associated with arm function and sequencing ability. Virtual environment performance only was associated with language function and praxis. Participants made different errors during task performance in the real world and in the virtual environment.



Although this virtual environment was usable by stroke rehabilitation patients, it posed a different rehabilitation challenge from the task it was intended to simulate, and so it might not be as effective as intended as a rehabilitation tool. Other virtual environments for stroke rehabilitation in development require similar evaluation.
Using defect analysis feedback for improving quality and productivity in iterative software development

In today's business where speed is of essence, an iterative development approach that allows the functionality to be delivered in parts has become a necessity and an effective way to manage risks. Iterative development allows feedback from an iteration to influence decisions in future iterations, thereby making software development more responsive to changing user and business needs. In this paper we discuss the role of defect analysis as a feedback mechanism to improve the quality and productivity in an iteratively developed software project. We discuss how analysis of defects found in one iteration can provide feedback for defect prevention in later iterations, leading to quality and productivity improvement. We give an example of its use and benefits on a commercial project