nils-herrmann/clean_scirepeval huggingface dataset:
Teaching large scale data processing: the five-week course and two years' experiences

We have setup a new course on the large scale data processing using clusters. It introduces the concepts and design of distributed systems. Many newly developed ideas such as Google file system and MapReduce programming framework for processing large scale data sets are introduced. Students will gain practical experience with distributed programming technologies via several small labs and one large multi-week final project. Labs and projects will be completed using Hadoop, an open-source implementation of Google's distributed file system and MapReduce programming model. We have taught this class named "Mass Data Processing Technology on Large Scale Clusters" for two years. This paper will describe the design, perform of the course as well as the experiences and lessons learned.
Tranylcypromine versus venlafaxine plus mirtazapine following three failed antidepressant medication trials for depression: a STAR*D report.

The purpose of this study was to compare the effectiveness and tolerability of tranylcypromine and combination treatment with extended-release venlafaxine and mirtazapine in patients with treatment-resistant major depression whose current depressive episode had not responded adequately to treatment in three prior prospective medication trials.



Adult outpatients with nonpsychotic major depressive disorder who had not achieved remission or had withdrawn from treatment because of intolerance in three previous prospective medication trials were randomly assigned to receive open-label treatment with either tranylcypromine (N=58) or extended-release venlafaxine plus mirtazapine (N=51). The primary outcome measure was whether patients achieved remission, which was defined as a score < or =7 at exit on the 17-item Hamilton Depression Rating Scale (HAM-D). The HAM-D was administered by telephone by raters to whom treatment was masked.



Remission rates were not significantly different between the two treatment groups (6.9% for the tranylcypromine group and 13.7% for the venlafaxine plus mirtazapine group). The mean daily dose at exit for tranylcypromine was 36.9 mg (SD=18.5); for venlafaxine, 210.3 mg (SD=95.2); and for mirtazapine, 35.7 mg (SD=17.6). Tranylcypromine was associated with significantly less symptom reduction and greater attrition due to intolerance.



Remission rates were modest for both the tranylcypromine group and the extended-release venlafaxine plus mirtazapine group, and the rates were not statistically different between groups. The lower side effect burden, lack of dietary restrictions, and ease of use of venlafaxine and mirtazapine suggest that this combination may be preferred over tranylcypromine for patients with highly treatment-resistant depression who have not benefited adequately from several prior treatments.
Effectiveness of adjuvant occupational therapy in employees with depression: design of a randomized controlled trial

Major depressive disorder is among the medical conditions with the highest negative impact on work outcome. However, little is known regarding evidence-based interventions targeting the improvement of work outcomes in depressed employees. In this paper, the design of a randomized controlled trial is presented in order to evaluate the effectiveness of adjuvant occupational therapy in employees with depression. This occupational intervention is based on an earlier intervention, which was designed and proven effective by our research group, and is the only intervention to date that specifically targets work outcome in depressed employees.



In a two-arm randomized controlled trial, a total of 117 participants are randomized to either 'care as usual' or ' care as usual' with the addition of occupational therapy. Patients included in the study are employees who are absent from work due to depression for at least 25% of their contract hours, and who have a possibility of returning to their own or a new job. The occupational intervention consists of six individual sessions, eight group sessions and a work-place visit over a 16-week period. By increasing exposure to the working environment, and by stimulating communication between employer and employee, the occupational intervention aims to enhance self-efficacy and the acquisition of more adaptive coping strategies. Assessments take place at baseline, and at 6, 12, and 18-month follow-ups. Primary outcome measure is work participation (hours of absenteeism and time until work resumption). Secondary outcome measures are work functioning, symptomatology, health-related quality of life, and neurocognitive functioning. In addition, cost-effectiveness is evaluated from a societal perspective. Finally, mechanisms of change (intermediate outcomes) and potential patient-treatment matching variables are investigated.



This study hopes to provide valuable knowledge regarding an intervention to treat depression, one of the most common and debilitating diseases of our time. If our intervention is proven (cost-) effective, the personal, economic, and health benefits for both patients and employers are far-reaching.
Supervised step-down of inhaled corticosteroids in the community--an observational study.

Current asthma guidelines recommend step-down of inhaled corticosteroids (ICS) to the minimum dose required for control of symptoms.



To determine if supervised step-down of (ICS) in the community has any effect on asthmatic inflammation.



119 Community based asthmatics underwent progressive step-down of therapy until they became unstable or reached an (ICS) dose of ≤200 μg beclomethasone dipropionate (BDP) or equivalent. Once unstable, participants stepped back up to the last stable dose of ICS. Exhaled nitric oxide (NO) and mannitol challenge were performed at the start and end of step-down. Asthma Quality of Life Questionnaire (AQLQ) and spirometry were recorded at each step-down visit.



The median (interquartile range) BDP equivalent dose was significantly higher pre vs. post step-down: 400 μg (400-800) and 250 μg (200-400) per day respectively (P < 0.05). Examination of change in PD(10) in individual patients revealed that 34% had an improvement (>+1 dd), 47% had no change (±-1 dd), and 19% had a worsening (<-1 dd). The geometric mean fold ratio in NO for pre vs. post was 0.96 (95% CI 0.87 to 1.06, P = 0.43). Mean (SEM) values for FEV(1) were 86.2% (1.51) vs. 84.5% (1.46) (P = 0.04). There was a significant improvement in AQLQ.



We have demonstrated that a significant reduction in ICS dose may be achieved in a community setting without any worsening of airways inflammation or lung function, and with an associated improvement quality of life in the majority of patients. This apparent disconnect may reflect enhanced adherence due to supervision of step-down.
Preferential Induction of the T Cell Auxiliary Signaling Molecule B7-H3 on Synovial Monocytes in Rheumatoid Arthritis.

B7-H3, a newly identified B7 family member, has functional duality as a co-stimulator and co-inhibitor that fine-tunes T cell-mediated immune responses. Given that B7-H3 expression on human monocytes and dendritic cells is enhanced by inflammatory cytokines, its potential inmmunoregulatory role at sites of inflammation has been suggested. Further, monocytes play crucial roles in the pathophysiology of various inflammatory disorders including autoimmune diseases; however, the immunological role of B7-H3 in rheumatoid arthritis (RA) has not been defined. Thus, we aimed to investigate the possible roles of monocyte B7-H3 in the pathogenesis of RA. Synovial monocytes, but not peripheral monocytes, in RA patients predominantly express surface B7-H3. The 4Ig isoform of B7-H3 is exclusively induced on the cell surface, whereas the 2Ig B7-H3 isoform is constitutively expressed in the intracytoplasmic region of both peripheral and synovial monocytes. B7-H3 knockdown experiments reveal that surface B7-H3 has an inhibitory effect on IFN-γ production in CD4 memory cells. Moreover, surface B7-H3 expression on synovial monocytes inversely correlates with RA clinical parameters. Our findings demonstrate that activation-induced B7-H3 expression on synovial monocytes has the potential to inhibit Th1-mediated immune responses and immunomodulatory roles affecting RA pathogenesis.
Postoperative Impedance–pH Testing is Unreliable After Nissen Fundoplication With or Without Giant Hiatal Hernia Repair

Combined 24-h multichannel intralumenal impedance–pH monitoring (MII-pH) is gaining popularity as a diagnostic tool for gastroesophageal reflux. Since the surgical reduction of hiatal hernias and creation of a fundoplication anatomically restores the gastroesophageal reflux barrier, one would assume that it effectively stops all reflux regardless of composition. Our aim is to evaluate the results of routine MII-pH testing in successful Nissen fundoplication patients. Sixty-two patients with normal acid exposure, confirmed by 24-h pH testing, after Nissen fundoplication were evaluated with symptomatic questionnaire, esophageal manometry and MII-pH testing more than 6 months after surgery. Patients were grouped into normal and abnormal based on postoperative impedance results. Patients with Nissen alone were separately compared to patients with Nissen + giant hiatal hernia (GHH). Twenty-nine (47%) patients exhibited abnormal impedance after successful Nissen fundoplication. Abnormal impedance was associated with GHH repair, lower bolus pressures, and lower distal esophageal contraction amplitudes. Postoperative testing with the standard MII-pH catheters using published normative values seems to be clinically irrelevant. Clinicians should analyze the results of routine MII-pH testing in the setting of a fundoplication critically as the current technology is associated with a high false positive rate.
Wheelchair tilt-in-space and recline does not reduce sacral skin perfusion as changing from the upright to the tilted and reclined position in people with spinal cord injury.

To investigate the effect of various wheelchair tilt-in-space and recline angles on sacral skin perfusion in wheelchair users with spinal cord injury.



Repeated-measures, intervention and outcomes measure design.



University research laboratory.



Power wheelchair users with spinal cord injury (N=11).



Six protocols of various wheelchair tilt-in-space and recline angles were randomly assigned to the participants: (1) 15° tilt-in-space and 100° recline, (2) 25° tilt-in-space and 100° recline, (3) 35° tilt-in-space and 100° recline, (4) 15° tilt-in-space and 120° recline, (5) 25° tilt-in-space and 120° recline, and (6) 35° tilt-in-space and 120° recline. Each protocol consisted of a 5-minute upright sitting and a 5-minute tilted and reclined period.



Skin perfusion over the sacrum (midpoint between the right posterior superior iliac spine and the adjacent spinous process) and right ischial tuberosity was measured using laser Doppler flowmetry.



Sacral skin perfusion did not show a significant difference in all 6 protocols of various tilt-in-space and recline angles when changing from an upright to a tilted and reclined position (not significant). However, as previously reported, skin perfusion over the ischial tuberosity showed a significant increase at 15°, 25°, and 35° tilt-in-space when combined with 120° recline and at 35° tilt-in-space when combined with 100° recline (P<.008).



Our results indicate that wheelchair tilt-in-space and recline enhances skin perfusion over the ischial tuberosities without reducing sacral skin perfusion when changing from an upright to a tilted and reclined position.
Marist college token ring test network

Marist is a small liberal arts college located in Poughkeepsie, New York, on the banks of the Hudson River about 70 miles north of New York City. Marist currently enrolls near 2800 undergraduates and 500 graduate students. The Computer Center facilities support academic, library, and administrative areas. Our mainframe computer is an IBM 3090 model 200E. We have PC facilities with hardware induding IBM PCs, XTs, ATs. and the full family of PSRs. There are major PC and terminal labs in two academic buildings as well as one dormitory. The Computer Center is staffed by 17 full time analysts, programmers, technicians and professionals. We also employ over 60 part time student employees. Forty of these students make up the Student User Support Staff which is the front line of support for all users in the lab areas.
Renal and Vascular Protective Effects of Telmisartan in Patients with Essential Hypertension

It is known that the angiotensin receptor blockers (ARBs) have organ protective effects in patients with heart failure or renal impairment. Several studies have revealed that the ARB telmisartan has an organ protective effect, but there have been few studies directly comparing the effects of telmisartan and calcium antagonists, since most clinical studies on telmisartan have been conducted in treated patients or patients on combination therapy. The present study was conducted to compare the renal and vascular protective effects of telmisartan monotherapy and calcium antagonist monotherapy in untreated hypertensive patients. Forty-three patients with untreated essential hypertension were randomized to receive amlodipine (n=22) or telmisartan (n=21), which were respectively administered at doses of 5 mg and 40 mg once daily in the morning for 24 weeks. The patients were examined before and after treatment to assess changes of renal function, flow-mediated dilation (a parameter of vascular endothelial function), and brachial-ankle pulse wave velocity (baPWV; a parameter of arteriosclerosis). Before treatment, there were no significant differences in these parameters between groups. The decreases of urinary albumin excretion and baPWV, and the increase of flow-mediated dilation were significantly greater in the telmisartan group than the amlodipine group, while the antihypertensive effects were not significantly different between the two groups. In conclusion, these results suggest that telmisartan is more effective at protecting renal function and vascular endothelial function, and at improving arteriosclerosis than the calcium channel blocker in patients with essential hypertension.
Assessment and clinical factors associated with pain in patients undergoing transrectal prostate biopsy.

To quantify the degree of pain experienced by patients who undergo ultrasound-guided transrectal prostate biopsy in standard clinical practice and assess the clinical factors associated with increased pain.



Analysis of a multicenter series of patients with prostate biopsy according to standard clinical practice. The biopsy was performed transrectally with a protocol of local anesthesia on the posterolateral nerve bundle. The pain was assessed at 20minutes into the procedure using the visual analog scale (0-10). The degree of pain was analyzed, and the association was studied using a univariate/multivariate analysis of selected clinical variables and the degree of pain.



A total of 1188 patients with a median age of 64 years were analyzed. Thirty percent of the biopsies were diagnosed with a tumor. The median pain score was 2, with 65% of the patients reporting a pain score ≤2. The multivariate analysis showed that the prostate volume (RR, 1.34; 95% CI 1.01-1.77; P=.04), having a previous biopsy (RR, 2.25; 95% CI 1.44-3.52; P<.01), age (RR, .63; 95% CI .47-.85; P<.01) and feel palpation (RR, 1.95; 95% CI 1.28-2.96; P<.01) were factors independently associated with greater pain during the procedure.



Transrectal biopsy with local anesthesia is a relatively painless technique. Factors such as age, a previous biopsy, pain on being touched and prostate volume were associated with the presence of greater pain during the procedure.
Evaluation of Folksonomy Induction Algorithms

Algorithms for constructing hierarchical structures from user-generated metadata have caught the interest of the academic community in recent years. In social tagging systems, the output of these algorithms is usually referred to as folksonomies (from folk-generated taxonomies). Evaluation of folksonomies and folksonomy induction algorithms is a challenging issue complicated by the lack of golden standards, lack of comprehensive methods and tools as well as a lack of research and empirical/simulation studies applying these methods. In this article, we report results from a broad comparative study of state-of-the-art folksonomy induction algorithms that we have applied and evaluated in the context of five social tagging systems. In addition to adopting semantic evaluation techniques, we present and adopt a new technique that can be used to evaluate the usefulness of folksonomies for navigation. Our work sheds new light on the properties and characteristics of state-of-the-art folksonomy induction algorithms and introduces a new pragmatic approach to folksonomy evaluation, while at the same time identifying some important limitations and challenges of folksonomy evaluation. Our results show that folksonomy induction algorithms specifically developed to capture intuitions of social tagging systems outperform traditional hierarchical clustering techniques. To the best of our knowledge, this work represents the largest and most comprehensive evaluation study of state-of-the-art folksonomy induction algorithms to date.
Beta-trace protein and cystatin c as predictors of major bleeding in non-ST-segment elevation acute coronary syndrome.

Beta-trace protein (BTP) and cystatin C (CysC) are novel biomarkers of renal function. We assessed the ability of both to predict major bleeding (MB) in patients with non-ST-segment elevation acute coronary syndromes (NSTE-ACS), compared to other renal function parameters and clinical risk scores.



We included 273 patients. Blood samples were obtained within 24h of admission. The endpoint was MB. During a follow-up of 760 days (411-1,098 days), 25 patients (9.2%) had MB. Patients with MB had higher concentrations of BTP (0.98 mg/L; 0.71-1.16 mg/L vs. 0.72 mg/L, 0.60-0.91 mg/L, P=0.002), CysC (1.05 mg/L; 0.91-1.30 mg/L vs. 0.90 mg/L, 0.75-1.08 mg/L, P=0.003), higher CRUSADE score (39 ± 16 points vs. 29 ± 15 points, P=0.002) and lower estimated glomerular filtration rate (eGFR; 66 ± 27 vs. 80 ± 30 ml·min(-1)·1.73 m(-2), P=0.02) than patients without MB; there was no difference in creatinine level between the groups (P=0.14). After multivariable adjustment, both were predictors of MB, while eGFR and creatinine did not achieve statistical significance. Among subjects with eGFR >60 ml·min(-1)·1.73 m(-2), those with elevated concentrations of both biomarkers had a significantly higher risk for MB. Net reclassification indexes from the addition of BTP and CysC to CRUSADE risk score were 38% and 21% respectively, while the relative integrated discrimination indexes were 12.5% and 3.8%.



Among NSTE-ACS patients, BTP and CysC were superior to conventional renal parameters for predicting MB, and improved clinical stratification for hemorrhagic risk.
Phase I dose-escalation study of AZD7762, a checkpoint kinase inhibitor, in combination with gemcitabine in US patients with advanced solid tumors

AZD7762 is a Chk1 kinase inhibitor which increases sensitivity to DNA-damaging agents, including gemcitabine. We evaluated the safety of AZD7762 monotherapy and with gemcitabine in advanced solid tumor patients. In this Phase I study, patients received intravenous AZD7762 on days 1 and 8 of a 14-day run-in cycle (cycle 0; AZD7762 monotherapy), followed by AZD7762 plus gemcitabine 750–1,000 mg/m2 on days 1 and 8, every 21 days, in ascending AZD7762 doses (cycle 1; combination therapy). Forty-two patients received AZD7762 6 mg (n = 9), 9 mg (n = 3), 14 mg (n = 6), 21 mg (n = 3), 30 mg (n = 7), 32 mg (n = 6), and 40 mg (n = 8), in combination with gemcitabine. Common adverse events (AEs) were fatigue [41 % (17/42) patients], neutropenia/leukopenia [36 % (15/42) patients], anemia/Hb decrease [29 % (12/42) patients] and nausea, pyrexia and alanine aminotransferase/aspartate aminotransferase increase [26 % (11/42) patients each]. Grade ≥3 AEs occurred in 19 and 52 % of patients in cycles 0 and 1, respectively. Cardiac dose-limiting toxicities occurred in two patients (both AZD7762 monotherapy): grade 3 troponin I increase (32 mg) and grade 3 myocardial ischemia with chest pain, electrocardiogram changes, decreased left ventricular ejection fraction, and increased troponin I (40 mg). AZD7762 exposure increased linearly. Gemcitabine did not affect AZD7762 pharmacokinetics. Two non-small-cell lung cancer patients achieved partial tumor responses (AZD7762 6 mg/gemcitabine 750 mg/m2 and AZD7762 9 mg cohort). The maximum-tolerated dose of AZD7762 in combination with gemcitabine 1,000 mg/m2 was 30 mg. Although development of AZD7762 is not going forward owing to unpredictable cardiac toxicity, Chk1 remains an important therapeutic target.
Validity of the Common Cold Questionnaire (CCQ) in Asthma Exacerbations

The common cold questionnaire (CCQ) is used to discriminate those with and without a viral infection. Its usefulness in people with acute asthma is unknown. Our aim was to assess the ability of the CCQ to detect viral infection and to monitor recovery during a viral induced asthma exacerbation and confirmed by virological testing.



We studied subjects (> or =7 yrs) admitted to hospital with acute asthma and diagnosed as positive (n = 63), or negative to viral infection (n = 27) according to molecular and virological testing from respiratory samples. CCQ, asthma history and asthma control questionnaires were completed and repeated 4-6 weeks later. Sensitivity, specificity, and response to change of the CCQ were assessed by receiver operator curve (ROC) analysis and effect size calculation respectively. The CCQ did not discriminate between viral and non-viral infection for subjects with asthma (sensitivity = 76.2%; specificity = 29.6%). ROC analysis could not differentiate between positive or negative virus in subjects with asthma. The CCQ had a large response to change following recovery (effect size = 1.01). 39% of subjects recovering from viral exacerbation remained positive to virological testing at follow-up despite improvement in clinical symptoms. The CCQ reflected clinical improvement in these subjects, thus providing additional information to complement virological testing.



The CCQ is a useful instrument for monitoring response to viral infection in people with asthma. Reliable differentiation between viral and non-viral asthma exacerbations was not achieved with the CCQ and requires specific virological testing. When combined with virological testing, the CCQ should be a useful outcome measure for evaluating therapies in viral-induced asthma.