nils-herrmann/clean_scirepeval huggingface dataset:
Three-year duration of benefit from abciximab in patient receiving stents for acute myocardial infarction in the randomized double-blind ADMIRAL study.

We have read carefully Dr Kanna’s comments trying to perform a critical appraisal of our manuscript, but it appears that most of these critics are inaccurate. Potential confounders such as coronary risk factors are important to consider, but by definition randomization is used to balance the different groups and the ADMIRAL study was randomized and the two study groups were well balanced for all baseline characteristics. Treatment compliance, another concern in Dr Kanna’s letter, is unlikely to be an issue because abciximab is administered intravenously for 12 h during and immediately after PCI and of course there was no further study drug administration during the 3-year follow-up of the ADMIRAL study. Blinded evaluation is another criterion of quality for studies and an issue in the letter; however, this critic does not apply to our study: of all randomized studies testing abciximab in primary stenting of STEMI, ADMIRAL remains, so far, the only double blind study. Moreover, the 3-year follow-up was performed blindly as indicated in  The following concern in the letter is about the validity of self-reporting data in patient questionnaires but as we indicated this was not the only mode of data collection, and physicians were surveyed, medical records consulted . . . and for hard endpoints, especially mortality which was the main objective, self-reporting is clearly not an issue. Finally, the author does not concur with the conclusions of a favourable effect of abciximab in primary stenting of ST-elevation MI. However, ADMIRAL is a positive study for its primary hypothesis showing the superiority of the study drug over placebo to reduce death, re-infarction, and urgent revascularization at 30 days, confirmed also at 6 months. Because we believe that it is important to provide information on the longterm, a three-year follow-up was conducted to determine whether the benefit observed initially was preserved; we acknowledged that the study was not powered to detect a difference in hard clinical endpoints at 3 years. However, the expression of the results with Kaplan–Meier curves demonstrated the preservation of the initial absolute benefit, with two parallel curves for death or MI, over 3 years. Our data along with other studies confirm the benefit of GPIIbIIIa inhibition with abciximab in primary PCI. Meta-analyses have also shown a significant impact on mortality and a greater benefit when the drug is administered early. All guidelines recommend its use in primary PCI.
Clinical Relevance of Nontuberculous Mycobacteria Isolated from Sputum in a Gold Mining Workforce in South Africa: An Observational, Clinical Study

The clinical relevance of nontuberculous mycobacteria (NTM), detected by liquid more than solid culture in sputum specimens from a South African mining workforce, is uncertain. We aimed to describe the current spectrum and relevance of NTM in this population.



An observational study including individuals with sputum NTM isolates, recruited at workforce tuberculosis screening and routine clinics. Symptom questionnaires were administered at the time of sputum collection and clinical records and chest radiographs reviewed retrospectively.



Of 232 individuals included (228 (98%) male, median age 44 years), M. gordonae (60 individuals), M. kansasii (50), and M. avium complex (MAC: 38) were the commonest species. Of 38 MAC isolates, only 2 (5.3%) were from smear-positive sputum specimens and 30/38 grew in liquid but not solid culture. MAC was especially prevalent among symptomatic, HIV-positive individuals. HIV prevalence was high: 57/74 (77%) among those tested. No differences were found in probability of death or medical separation by NTM species.



M. gordonae, M. kansasii, and MAC were the commonest NTM among miners with suspected tuberculosis, with most MAC from smear-negative specimens in liquid culture only. HIV testing and identification of key pathogenic NTM in this setting are essential to ensure optimal treatment.
Defense against the dark arts

Computer science faculty must attract and retain students by offering innovative courses that spark student interest, yet still teach core, computer science concepts. These efforts have become particularly important as computer science enrollments have declined, thus increasing concerns for attracting and retaining students. We describe an innovative course that leverages students' interest in computer security issues to attract and retain technically-oriented students. Our initial vision was to offer a course covering computer viruses - a subject that even a novice computer user has some familiarity. To avoid the controversy associated with teaching students how to write malicious software, we focused the course on techniques for defending against viruses, so we named the course Defense Against the Dark Arts. In teaching the course, we have found the subject matter provides an engaging way to introduce and reinforce many important computer science concepts that other courses often cover, most particularly, the traditional compiler course. We have taught the course three times at two separate institutions, with a third school soon to follow. The course has been well received by students - completely filling each semester with enrollments that are four to five times greater than the compiler course. Furthermore, student surveys indicate that the course raises students' awareness of computer security while introducing students to important program translation and analysis concepts.
Microtubule Destabilization Is Shared by Genetic and Idiopathic Parkinson’s Disease Patient Fibroblasts

Data from both toxin-based and gene-based models suggest that dysfunction of the microtubule system contributes to the pathogenesis of Parkinson's disease, even if, at present, no evidence of alterations of microtubules in vivo or in patients is available. Here we analyze cytoskeleton organization in primary fibroblasts deriving from patients with idiopathic or genetic Parkinson's disease, focusing on mutations in parkin and leucine-rich repeat kinase 2. Our analyses reveal that genetic and likely idiopathic pathology affects cytoskeletal organization and stability, without any activation of autophagy or apoptosis. All parkinsonian fibroblasts have a reduced microtubule mass, represented by a higher fraction of unpolymerized tubulin in respect to control cells, and display significant changes in microtubule stability-related signaling pathways. Furthermore, we show that the reduction of microtubule mass is so closely related to the alteration of cell morphology and behavior that both pharmacological treatment with microtubule-targeted drugs, and genetic approaches, by transfecting the wild type parkin or leucine-rich repeat kinase 2, restore the proper microtubule stability and are able to rescue cell architecture. Taken together, our results suggest that microtubule destabilization is a point of convergence of genetic and idiopathic forms of parkinsonism and highlight, for the first time, that microtubule dysfunction occurs in patients and not only in experimental models of Parkinson's disease. Therefore, these data contribute to the knowledge on molecular and cellular events underlying Parkinson's disease and, revealing that correction of microtubule defects restores control phenotype, may offer a new therapeutic target for the management of the disease.
Efficacy of pulmonary rehabilitation in patients with moderate chronic obstructive pulmonary disease: a randomized controlled trial

Pulmonary Rehabilitation for moderate Chronic Obstructive Pulmonary Disease in primary care could improve patients' quality of life.



This study aimed to assess the efficacy of a 3-month Pulmonary Rehabilitation (PR) program with a further 9 months of maintenance (RHBM group) compared with both PR for 3 months without further maintenance (RHB group) and usual care in improving the quality of life of patients with moderate COPD.We conducted a parallel-group, randomized clinical trial in Majorca primary health care in which 97 patients with moderate COPD were assigned to the 3 groups. Health outcomes were quality of life, exercise capacity, pulmonary function and exacerbations.



We found statistically and clinically significant differences in the three groups at 3 months in the emotion dimension (0.53; 95%CI0.06-1.01) in the usual care group, (0.72; 95%CI0.26-1.18) the RHB group (0.87; 95%CI 0.44-1.30) and the RHBM group as well as in fatigue (0.47; 95%CI 0.17-0.78) in the RHBM group. After 1 year, these differences favored the long-term rehabilitation group in the domains of fatigue (0.56; 95%CI 0.22-0.91), mastery (0.79; 95%CI 0.03-1.55) and emotion (0.75; 95%CI 0.17-1.33). Between-group analysis only showed statistically and clinically significant differences between the RHB group and control group in the dyspnea dimension (0.79 95%CI 0.05-1.52). No differences were found for exacerbations, pulmonary function or exercise capacity.



We found that patients with moderate COPD and low level of impairment did not show meaningful changes in QoL, exercise tolerance, pulmonary function or exacerbation after a one-year, community based rehabilitation program. However, long-term improvements in the emotional, fatigue and mastery dimensions (within intervention groups) were identified.
Fruit and Vegetable Consumption and the Incidence of Hypertension in Three Prospective Cohort Studies.

Increased fruit and vegetable intake lowers blood pressure in short-term interventional studies. However, data on the association of long-term intake of fruits and vegetables with hypertension risk are scarce. We prospectively examined the independent association of whole fruit (excluding juices) and vegetable intake, as well as the change in consumption of whole fruits and vegetables, with incident hypertension in 3 large longitudinal cohort studies: Nurses' Health Study (n=62 175), Nurses' Health Study II (n=88 475), and Health Professionals Follow-up Study (n=36 803). We calculated hazard ratios and 95% confidence intervals for fruit and vegetable consumption while controlling for hypertension risk factors. Compared with participants whose consumption was ≤4 servings/week, the pooled hazard ratios among those whose intake was ≥4 servings/day were 0.92(0.87-0.97) for total whole fruit intake and 0.95(0.86-1.04) for total vegetable intake. Similarly, compared with participants who did not increase their fruit or vegetable consumption, the pooled hazard ratios for those whose intake increased by ≥7 servings/week were 0.94(0.90-0.97) for total whole fruit intake and 0.98(0.94-1.01) for total vegetable. Analyses of individual fruits and vegetables yielded different results. Consumption levels of ≥4 servings/week (as opposed to <1 serving/month) of broccoli, carrots, tofu or soybeans, raisins, and apples was associated with lower hypertension risk. In conclusion, our results suggest that greater long-term intake and increased consumption of whole fruits may reduce the risk of developing hypertension.
The efficacy of 2 different dosages of methylphenidate in treating adults with attention-deficit hyperactivity disorder.

To evaluate the efficacy of methylphenidate in treating adults with attention-deficit hyperactivity disorder (ADHD), using subjective (self-report) and objective (computerized test) measures.



This double-blind crossover trial of placebo vs methylphenidate included subjects with childhood and current ADHD symptoms, IQs above 80, no other psychiatric condition explaining their difficulties or requiring other treatment, and no substance abuse in the previous 6 months. We administered 10 mg 3 times daily of medication (that is, placebo or methylphenidate) for 2 weeks. On the final day, subjects completed self-report measures and were tested on computerized tests. We then increased dosage to 15 mg 3 times daily for 2 weeks and administered a complete reassessment on the final day. Following a 1-week washout, we repeated this process on the second medication (that is, placebo or methylphenidate).



Thirty adults with ADHD participated. Self-report measures and computerized tests showed significant improvements in ADHD symptoms on methylphenidate, compared with placebo. Other psychiatric symptoms (notably, anxiety and depression) were alleviated with methylphenidate. There was no significant difference between the 2 dosages of methylphenidate.



Methylphenidate is effective in improving ADHD symptoms in adults with ADHD, is well tolerated, and has minimal side effects.
Limited clinical utility of a genetic risk score for the prediction of fracture risk in elderly subjects.

It is important to identify the patients at highest risk of fractures. A recent large-scale meta-analysis identified 63 autosomal single-nucleotide polymorphisms (SNPs) associated with bone mineral density (BMD), of which 16 were also associated with fracture risk. Based on these findings, two genetic risk scores (GRS63 and GRS16) were developed. Our aim was to determine the clinical usefulness of these GRSs for the prediction of BMD, BMD change, and fracture risk in elderly subjects. We studied two male (Osteoporotic Fractures in Men Study [MrOS] US, MrOS Sweden) and one female (Study of Osteoporotic Fractures [SOF]) large prospective cohorts of older subjects, looking at BMD, BMD change, and radiographically and/or medically confirmed incident fractures (8067 subjects, 2185 incident nonvertebral or vertebral fractures). GRS63 was associated with BMD (≅3% of the variation explained) but not with BMD change. Both GRS63 and GRS16 were associated with fractures. After BMD adjustment, the effect sizes for these associations were substantially reduced. Similar results were found using an unweighted GRS63 and an unweighted GRS16 compared with those found using the corresponding weighted risk scores. Only minor improvements in C-statistics (AUC) for fractures were found when the GRSs were added to a base model (age, weight, and height), and no significant improvements in C-statistics were found when they were added to a model further adjusted for BMD. Net reclassification improvements with the addition of the GRSs to a base model were modest and substantially attenuated in BMD-adjusted models. GRS63 is associated with BMD, but not BMD change, suggesting that the genetic determinants of BMD differ from those of BMD change. When BMD is known, the clinical utility of the two GRSs for fracture prediction is limited in elderly subjects.
Online Biometric Authentication Using Subject-Specific Band Power features of EEG

Biometric recognition of persons based on unique features extracted from brain signals is an emerging area of research nowadays, on account of the subject-specificity of human neural activity. This paper proposes an online Electroencephalogram (EEG) based biometric authentication system using band power features extracted from alpha, beta and gamma bands, when the subject is in relaxed rest state with eyes open or closed. The most distinct band features are chosen specifically for each subject which are then used to generate subject-specific template during enrollment. During online authentication, recorded test EEG pattern is matched with the respective template stored in the database and degree of matching in terms of its correlation coefficient predicts the genuineness of the claimant. A number of client and imposter authentication tests have been conducted in online framework among 6 subjects using the proposed system, and achieves an average recognition rate of 88.33% using 14 EEG channels. Experimental analysis shows the subject-specificity of distinct bands and features, and highlights the utility of subject-specific band power features in EEG-based biometric systems.
Identification and Pathway Analysis of microRNAs with No Previous Involvement in Breast Cancer

microRNA expression signatures can differentiate normal and breast cancer tissues and can define specific clinico-pathological phenotypes in breast tumors. In order to further evaluate the microRNA expression profile in breast cancer, we analyzed the expression of 667 microRNAs in 29 tumors and 21 adjacent normal tissues using TaqMan Low-density arrays. 130 miRNAs showed significant differential expression (adjusted P value = 0.05, Fold Change = 2) in breast tumors compared to the normal adjacent tissue. Importantly, the role of 43 of these microRNAs has not been previously reported in breast cancer, including several evolutionary conserved microRNA*, showing similar expression rates to that of their corresponding leading strand. The expression of 14 microRNAs was replicated in an independent set of 55 tumors. Bioinformatic analysis of mRNA targets of the altered miRNAs, identified oncogenes like ERBB2, YY1, several MAP kinases, and known tumor-suppressors like FOXA1 and SMAD4. Pathway analysis identified that some biological process which are important in breast carcinogenesis are affected by the altered microRNA expression, including signaling through MAP kinases and TP53 pathways, as well as biological processes like cell death and communication, focal adhesion and ERBB2-ERBB3 signaling. Our data identified the altered expression of several microRNAs whose aberrant expression might have an important impact on cancer-related cellular pathways and whose role in breast cancer has not been previously described.
Molecular targeting of glioblastoma: Drug discovery and therapies.

Despite advances in treatment for glioblastoma multiforme (GBM), patient prognosis remains poor. Although there is growing evidence that molecular targeting could translate into better survival for GBM, current clinical data show limited impact on survival. Recent progress in GBM genomics implicate several activated pathways and numerous mutated genes. This molecular diversity can partially explain therapeutic resistance and several approaches have been postulated to target molecular changes. Furthermore, most drugs are unable to reach effective concentrations within the tumor owing to elevated intratumoral pressure, restrictive vasculature and other limiting factors. Here, we describe the preclinical and clinical developments in treatment strategies of GBM. We review the current clinical trials for GBM and discuss the challenges and future directions of targeted therapies.
Behavioral and psychosocial effects of rapid genetic counseling and testing in newly diagnosed breast cancer patients: Design of a multicenter randomized clinical trial

It has been estimated that between 5% and 10% of women diagnosed with breast cancer have a hereditary form of the disease, primarily caused by a BRCA1 or BRCA2 gene mutation. Such women have an increased risk of developing a new primary breast and/or ovarian tumor, and may therefore opt for preventive surgery (e.g., bilateral mastectomy, oophorectomy). It is common practice to offer high-risk patients genetic counseling and DNA testing after their primary treatment, with genetic test results being available within 4-6 months. However, some non-commercial laboratories can currently generate test results within 3 to 6 weeks, and thus make it possible to provide rapid genetic counseling and testing (RGCT) prior to primary treatment. The aim of this study is to determine the effect of RGCT on treatment decisions and on psychosocial health. In this randomized controlled trial, 255 newly diagnosed breast cancer patients with at least a 10% risk of carrying a BRCA gene mutation are being recruited from 12 hospitals in the Netherlands. Participants are randomized in a 2:1 ratio to either a RGCT intervention group (the offer of RGCT directly following diagnosis with tests results available before surgical treatment) or to a usual care control group. The primary behavioral outcome is the uptake of direct bilateral mastectomy or delayed prophylactic contralateral mastectomy. Psychosocial outcomes include cancer risk perception, cancer-related worry and distress, health-related quality of life, decisional satisfaction and the perceived need for and use of additional decisional counseling and psychosocial support. Data are collected via medical chart audits and self-report questionnaires administered prior to randomization, and at 6 month and at 12 month follow-up. This trial will provide essential information on the impact of RGCT on the choice of primary surgical treatment among women with breast cancer with an increased risk of hereditary cancer. This study will also provide data on the psychosocial consequences of RGCT and of risk-reducing behavior.
[Effect of montelukast on lung function and clinical symptoms in patients with cystic fibrosis].

Inflammatory process contributes to progressive lung tissue damage in cystic fibrosis (CF). Cysteinyl leukotrienes have been found in the sputum of CF patients at concentrations sufficient to cause potent biological effect. This study was designed to assess the effect of anti-inflammatory treatment with montelukast sodium in CF patients. Twelve patients, aged 6-29 were recruited. It was 20 week, placebo-controlled, and randomized, double blind, crossover trial. At first and last week of each treatment course spirometry and whole body plethysmography parameters (FEV1, PEF, FEF25/75%, VC, TGV, Raw and RV) and clinical wheezing and cough scale were measured. In montelukast group significant improvement in FEV1 (mean +/- SD, 54.6 +/- 22.6 before and 62 +/- 19.0 after treatment, p=0.0112) and FEF25/75% (28.9 +/- 23.0 before and 37.5 +/- 25.5 after treatment, p=0.0053) were observed. Compared with placebo montelukast significantly improved FEV1 (p=0.0032), PEF (p=0.0298) and FEF25/75% (p=0.0091). There was no significant difference in VC, TGV, Raw and RV. Montelukast compared with placebo significantly decreased cough (p<0.0001) and wheezing (p=0.0002) score. In summary, therapy with montelukast may provide clinical benefit to patients with CF.
Socioeconomic factors associated with risk of upper aerodigestive tract cancer in Europe.

In the European Union, there are 180,000 new cases of upper aerodigestive tract (UADT) cancer cases per year--more than half of whom will die of the disease. Socioeconomic inequalities in UADT cancer incidence are recognised across Europe. We aimed to assess the components of socioeconomic risk both independently and through their influence on the known behavioural risk factors of smoking, alcohol consumption and diet.



A multicentre case-control study with 2198 cases of UADT cancer and 2141 controls from hospital and population sources was undertaken involving 14 centres from 10 countries. Personal interviews collected information on demographics, lifetime occupation history, smoking, alcohol consumption and diet. Socioeconomic status was measured by education, occupational social class and unemployment. Odds ratios (ORs) and 95% confidence intervals (CIs) were computed using unconditional logistic regression.



When controlling for age, sex and centre significantly increased risks for UADT cancer were observed for those with low versus high educational attainment OR=1.98 (95% CI 1.67, 2.36). Similarly, for occupational socioeconomic indicators--comparing the lowest versus highest International Socio-Economic Index (ISEI) quartile for the longest occupation gave OR=1.60 (1.28, 2.00); and for unemployment OR=1.64 (1.24, 2.17). Statistical significance remained for low education when adjusting for smoking, alcohol and diet behaviours OR=1.29 (1.06, 1.57) in the multivariate analysis. Inequalities were observed only among men but not among women and were greater among those in the British Isles and Eastern European countries than in Southern and Central/Northern European countries. Associations were broadly consistent for subsite and source of controls (hospital and community).



Socioeconomic inequalities for UADT cancers are only observed among men and are not totally explained by smoking, alcohol drinking and diet.