nils-herrmann/clean_scirepeval huggingface dataset:
Age and National Institutes of Health Stroke Scale Score within 6 hours after onset are accurate predictors of outcome after cerebral ischemia: development and external validation of prognostic models.

To date, no validated, comprehensive, and practicable model exists to predict functional recovery within the first hours of cerebral ischemic symptoms. The purpose of this study was to externally validate 2 prognostic models predicting functional outcome and survival at 100 days within the first 6 hours after onset of acute cerebral ischemia.



On admission to a participating hospital, patients were registered prospectively and included according to defined criteria. Follow-up was performed 100 days after the event. With the use of prospectively collected data, 2 prognostic models were developed and internally calibrated in 1079 patients and externally validated in 1307 patients. By means of age and National Institutes of Health Stroke Scale (NIHSS) score as independent variables, model I predicts incomplete functional recovery (Barthel Index <95) versus complete functional recovery, and model II predicts mortality versus survival.



In the validation data set, model I correctly predicted 62.9% of the patients who were incompletely restituted or had died and 83.2% of the completely restituted patients, and model II correctly predicted 57.9% of the patients who had died and 91.5% of the surviving patients. Both models performed better than the treating physicians' predictions made within 6 hours after admission.



The resulting prognostic models are useful to correctly stratify treatment groups in clinical trials and should guide inclusion criteria in clinical trials, which in turn increases the power to detect clinically relevant differences.
A multicenter pilot study of a bronchial valve for the treatment of severe emphysema.

Chronic obstructive pulmonary disease (COPD) affects millions of people and has limited treatment options. Surgical treatments for severe COPD with emphysema are effective for highly selected patients. A minimally invasive method for treating emphysema could decrease morbidity and increase acceptance by patients.



To study the safety and effectiveness of the IBV(R) Valve for the treatment of severe emphysema.



A multicenter study treated 91 patients with severe obstruction, hyperinflation and upper lobe (UL)-predominant emphysema with 609 bronchial valves placed bilaterally into ULs.



Valves were placed in desired airways with 99.7% technical success and no migration or erosion. There were no procedure-related deaths and 30-day morbidity and mortality were 5.5 and 1.1%, respectively. Pneumothorax was the most frequent serious device-related complication and primarily occurred when all segments of a lobe, especially the left UL, were occluded. Highly significant health-related quality of life (HRQL) improvement (-8.2 +/- 16.2, mean +/- SD change at 6 months) was observed. HRQL improvement was associated with a decreased volume (mean -294 +/- 427 ml, p = 0.007) in the treated lobes without visible atelectasis. FEV(1), exercise tests, and total lung volume were not changed but there was a proportional shift, a redirection of inspired volume to the untreated lobes. Combined with perfusion scan changes, this suggests that there is improved ventilation and perfusion matching in non-UL lung parenchyma.



Bronchial valve treatment of emphysema has multiple mechanisms of action and acceptable safety, and significantly improves quality of life for the majority of patients.
Evolution of an international collaborative student project

International collaborative student projects are inherently difficult for everyone concerned -- the students working on the projects, the faculty guiding the students, and the clients submitting the projects. With more and more schools recommending, or even requiring, that their students have some form of international experience in their degree programs, these projects will become more prevalent in helping to educate computing students in the 21st century. Understanding cultural differences between countries helps students have a better appreciation for the global aspects of computing and the issues faced in making soft ware work in an environment they are not used to. This paper discusses the evolution over four years of collaborative projects between computing students at two schools, one in Sweden and one in the United States. The projects are based in courses at both schools that deal with computing in society. We discuss what the faculty teaching the courses and guiding the projects have learned and how they have improved the experience, what the students learn through these projects, and how the clients interact with the students and faculty. Suggestions for further development of these projects are also made.
Hcm1 integrates signals from Cdk1 and calcineurin to control cell proliferation

Cyclin-dependent kinase (Cdk1) orchestrates progression through the cell cycle by coordinating the activities of cell-cycle regulators. Although phosphatases that oppose Cdk1 are likely to be necessary to establish dynamic phosphorylation, specific phosphatases that target most Cdk1 substrates have not been identified. In budding yeast, the transcription factor Hcm1 activates expression of genes that regulate chromosome segregation and is critical for maintaining genome stability. Previously we found that Hcm1 activity and degradation are stimulated by Cdk1 phosphorylation of distinct clusters of sites. Here we show that, upon exposure to environmental stress, the phosphatase calcineurin inhibits Hcm1 by specifically removing activating phosphorylations and that this regulation is important for cells to delay proliferation when they encounter stress. Our work identifies a mechanism by which proliferative signals from Cdk1 are removed in response to stress and suggests that Hcm1 functions as a rheostat that integrates stimulatory and inhibitory signals to control cell proliferation.
Creatinine-or cystatin C-based equations to estimate glomerular filtration in the general population: impact on the epidemiology of chronic kidney disease

Chronic kidney disease (CKD) is a major issue in public health. Its prevalence has been calculated using estimation of glomerular filtration rate (GFR) by the creatinine-based equations developed in the Modified Diet in Renal Disease (MDRD) and Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) study. Recently, new equations based either on cystatin C (CKD-EPI Cys) or both cystatin and creatinine (CKD-EPI mix) have been proposed by the CKD-EPI consortium. The aim of this study was to measure the difference in the prevalence of stage 3 CKD, defined as an estimated GFR less than 60 mL/min/1.73 m2, in a population using these four equations.



CKD screening was performed in the Province of Liège, Belgium. On a voluntary basis, people aged over 50 years have been screened. GFR was estimated by the four equations. Stage 3 CKD was defined as a GFR less than 60 mL/min/1.73 m2.



The population screened consisted of 4189 people (47% were men, mean age 63 ± 7y). Their mean serum creatinine and plasma cystatin C levels were 0.88 ± 0.21 mg/dL and 0.85 ± 0.17 mg/L, respectively. The prevalence of CKD in this population using the MDRD, the CKD-EPI, the CKD-EPI Cys and the CKD-EPI mix equations was 13%, 9.8%, 4.7% and 5%, respectively. The prevalence of CKD was significantly higher with the creatinine-based (MDRD and the CKD-EPI) equations compared to the new cystatin C-based equations.



Prevalence of CKD varies strongly depending on the method used to estimate GFR. Such discrepancies are of importance and must be confirmed and explained by additional studies, notably by studies using GFR measured with a reference method.
The magnitude of the association between smoking and the risk of developing cancer in Brazil: a multicenter study

To estimate the magnitude of association and identify the aetiological fraction (AF) attributable to smoking in the development of different types of cancers in Brazil.



We conducted a case-control study, including 231 102 patients registered in the Cancer Hospital Registries (CHR) in the period from 1998 to 2011.



A total of 204 131 cancer cases relating to 30 topographies were compared with 26 971 cases of non-melanoma skin cancer.



Smoking exposure was considered at the time of hospital registration. We calculated OR, unadjusted and adjusted for gender, age and alcohol consumption, with 95% CIs.



After adjustment, the risk of developing cancer associated with smoking was very high (piriform sinus, bronchi and lung, larynx, hypopharynx, oropharynx and oral cavity), high (oesophagus and bladder), moderate (anus and anal canal stomach, nasal cavity, middle ear and paranasal sinuses, pancreas, nasopharynx, other parts of the biliary tract and kidney and low (liver, gall)). There was no association between smoking and cancers of the central nervous system and myeloid leukaemia. For thyroid cancer there was a decreased risk of developing the disease. The AF was higher than 50% for hypopharynx, larynx, bronchi and lung, oropharynx, oral cavity and oesophagus cancers.



This study confirms a high risk of developing cancer of the hypopharynx, bronchi and lung, larynx, oropharynx and oral cavity, oesophagus and bladder cancer among smokers and establishes the AF attributable to smoking in the development of different types of cancer in Brazil.
Vernakalant hydrochloride for rapid conversion of atrial fibrillation: a phase 3, randomized, placebo-controlled trial.

The present study assessed the efficacy and safety of vernakalant hydrochloride (RSD1235), a novel compound, for the conversion of atrial fibrillation (AF).



Patients were randomized in a 2:1 ratio to receive vernakalant or placebo and were stratified by AF duration of 3 hours to 7 days (short duration) and 8 to 45 days (long duration). A first infusion of placebo or vernakalant (3 mg/kg) was given for 10 minutes, followed by a second infusion of placebo or vernakalant (2 mg/kg) 15 minutes later if AF was not terminated. The primary end point was conversion of AF to sinus rhythm for at least 1 minute within 90 minutes of the start of drug infusion in the short-duration AF group. A total of 336 patients were randomized and received treatment (short duration, n=220; long duration, n=116). Of the 145 vernakalant patients, 75 (51.7%) in the short-duration AF group converted to sinus rhythm (median time, 11 minutes) compared with 3 of the 75 placebo patients (4.0%; P<0.001). Overall, in the short- and long-duration AF groups, 83 of the 221 vernakalant patients (37.6%) experienced termination of AF compared with 3 of the 115 placebo patients (2.6%; P<0.001). Transient dysgeusia and sneezing were the most common side effects in vernakalant-treated patients. Four vernakalant-related serious adverse events (hypotension [2 events], complete atrioventricular block, and cardiogenic shock) occurred in 3 patients.



Vernakalant demonstrated rapid conversion of short-duration AF and was well tolerated.
A phase I and pharmacokinetic study of paclitaxel poliglumex and cisplatin in patients with advanced solid tumors

Determine the toxicity, maximum tolerated dose (MTD), and pharmacokinetics of paclitaxel poliglumex (PPX; CT-2103) in combination with cisplatin administered every 3 weeks. Forty-three patients with advanced solid tumors were treated at escalating doses of PPX with a fixed dose of cisplatin at 75 mg/m2. Conjugated and unconjugated paclitaxel were measured in plasma and urine. Cisplatin, as total platinum content in urine, was also assayed. Dose-limiting toxicities included neutropenia and neuropathy with a cycle 1 MTD of 210 mg/m2. Conjugated taxanes had a prolonged half-life of >100 h. Nine patients had partial responses, and 19 had stable disease. PPX is a water-soluble paclitaxel-polymer conjugate with a prolonged half-life and a limited volume of distribution. PPX/cisplatin showed good activity in a refractory patient population; however, cumulative neuropathy was a significant issue at high doses, suggesting that a lower dose may be appropriate for prolonged therapy.
Sorafenib and irinotecan (NEXIRI) as second- or later-line treatment for patients with metastatic colorectal cancer and KRAS-mutated tumours: a multicentre Phase I/II trial

This trial evaluated the feasibility and efficacy of combined sorafenib and irinotecan (NEXIRI) as second- or later-line treatment of patients with KRAS-mutated metastatic colorectal cancer (mCRC), who had progressed after irinotecan-based chemotherapy.In Phase I, in a 3+3 dose escalation schedule, patients received irinotecan (125, 150 or 180 mg m−2 every 2 weeks), in combination with 400 mg sorafenib b.d. The primary end point was the maximum-tolerated dose of irinotecan. In Phase II, the primary end point was disease control rate (DCR). Secondary end points were progression-free survival (PFS), overall survival (OS) and toxicity.Phase I included 10 patients (median age 63 (49–73)); no dose-limiting toxicity was seen. In Phase II, 54 patients (median age 60 (43–80) years) received irinotecan 180 mg m−2 every 2 weeks with sorafenib 400 mg b.d. Nine patients (17%) remained on full-dose sorafenib. The DCR was 64.9% (95% CI, 51–77). Median PFS and OS were 3.7 (95% CI, 3.2–4.7) and 8.0 (95% CI, ) months, respectively. Toxicities included Grade 3 diarrhoea (37%), neutropenia (18%), hand-foot syndrome (13%) and Grade 4 neutropenia (17%).Conclusion:The NEXIRI regimen showed promising activity as second- or later-line treatment in this heavily pretreated mCRC population (ClinicalTrials.gov NCT00989469).
Osteoarthritis of the hip: agreement between joint space width measurements on standing and supine conventional radiographs.

To assess the effect of standing position on joint space width (JSW) measurements of the hips with and without osteoarthritis (OA) on pelvic radiographs.



Adult patients aged 18 or more had pelvic anteroposterior conventional radiographs standing and supine performed by a single radiologist in the same radiology unit according to standardised guidelines. JSW measurements in mm were made by a single reader blind to patients' identity and type of view, using a 0.1 mm graduated magnifying glass directly laid over the radiograph, at the narrowest point for OA hips or at the vertical joint space for non-OA hips. Agreement of JSW between both views was assessed using the Bland and Altman graphical analysis.



JSW was greater on standing than supine radiographs, for example, 7.1% for OA hips. Mean (SD) differences and limits of agreement (mm) between both views were 0.08 (0.27) and -0.46 to 0.62 for the 70 non-OA hips, 0.02 (0.31) and -0.60 to 0.64 for the 46 OA hips. Corresponding 95% confidence intervals of mean difference were 0.02, -0.14 mm and -0.07, -0.11 mm.



Measurements of JSW of the hip on pelvic standing and supine radiographs are concordant. Changes less than or equal to 0.64 mm between the two views are similar or inferior to radiological progression of OA.
Idiomatic design

Here we use idiomatic differently than the way the programming community uses the similar word idiom. The American Heritage Dictionary gives its primary definition of idiomatic as “peculiar to or characteristic of a given language” and defines idiom as “a speech form or expression peculiar to itself grammatically, or one that cannot be understood from the individual meanings of its elements.” Programmers have come to treat as primary the secondary definition of idiom: “a specialized vocabulary or jargon used by a group of people.
A phase II study of cladribine treatment for fludarabine refractory B cell chronic lymphocytic leukemia: results from CALGB Study 9211

Cladribine has been reported to have little activity in fludarabine- refractory chronic lymphocytic leukemia (CLL). We sought to determine whether resistance to therapy with cladribine in fludarabine-refractory CLL patients represented primary drug resistance or the inability to tolerate the myelosuppression associated with this therapy. Patients with fludarabine refractory CLL patients without severe thrombocytopenia (platelets ≥50 × 109/l) or granulocytopenia (neutrophils >1.5 × 109/l) were enrolled. All patients received cladribine (0.14 mg/kg) as a 2-h intravenous infusion daily for 5 days, repeated every 4 weeks. Patients received up to six cycles of therapy. Twenty-eight patients enrolled; 13 had intermediate (Rai stage I or II) and 15 high (Rai stage III and IV) risk stages. No patient had a complete remission, but nine (32%; 95% confidence interval, 15–49%) attained a partial remission when assessed using the modified NCI criteria (1996). The median time to relapse for responders was 12 months, while median progression-free survival for the entire group was 9 months (95% confidence interval, 4–14 months). The median overall survival was 2.2 years (95% confidence interval, 0.8–3.1 years). Response was predicted by pre-treatment Rai status with seven of 13 (54%) intermediate risk vs two of 15 (13%) high-risk patients responding (P = 0.04). Toxicity was myelosuppression and infections (grade 3–5: neutropenia 75%, thrombocytopenia 68%, and infections 43%). Cladribine has modest clinical activity and considerable toxicity in a very selected group of patients with fludarabine-refractory CLL lacking pre-treatment neutropenia and thrombocytopenia.
Effect of essential fatty acids on circulating T cell subsets in patients with colorectal cancer

The effect of essential fatty acids (EFA), given orally as dietary supplements, on the responsiveness in vitro of peripheral blood lymphocytes (PBL), to the mitogen concanavalin A have been studied in 10 patients with localized and 14 patients with advanced colorectal cancer. The degree of lymphocyte activation was assessed by measuring the amount of tritiated [3H]thymidine incorporated into newly synthesised lymphocyte DNA. The results were expressed as stimulation indices. T cell responses to concanavalin A stimulation showed a significant reduction of stimulation indices following EFA supplementation, in both the localized (P=0.026) and advanced (P=0.016) tumour groups, when compared with pretreatment activity in vitro. Mixing experiments, using EFA-supplemented and non-EFA-supplemented lymphocytes with concanavalin A, suggest no enhancement of T suppressor cell activity. Cell surface marker analysis (fluorescence-activated cell sorting for CD phenotyping) revealed a reduction of absolute numbers of CD4+ and CD8+ lymphocytes following EFA supplementation. The stimulation indices returned to presupplementation values 3 months following cessation of EFA intake. There was no significant change of these indices in the control (no EFA supplementation) advanced tumour group tested. This study suggests that EFA supplementation in patients with colorectal cancer selectively reduces circulating PBL. and T cell subset (including suppressor cells) numbers and/or activity. Such effects may have an important outcome in patients with malignant disease.
Intermittent ischaemic arrest and cardioplegia in coronary artery surgery: coming full circle?

To compare the cardioprotective efficacy of cold crystalloid cardioplegia and intermittent ischaemic arrest in patients undergoing elective coronary artery surgery.



Prospective randomised trial.



London teaching hospital.



20 patients with at least moderately good left ventricular function undergoing elective coronary artery surgery by one experienced surgeon and needing at least two bypass grafts.



Patients were randomised to cold crystalloid cardioplegia or intermittent ischaemic arrest.



The primary determinant of the efficacy of myocardial protection was serial measurement (before and at 1, 6, 24, and 72 hours after the end of cardiopulmonary bypass) of cardiac troponin T (cTnT), a highly sensitive and specific marker of myocardial damage.



There was no significant difference in age, ejection fraction, number of grafts, bypass times, or cross clamp times between the two groups. One patient in the cardioplegia group had a perioperative infarct and was excluded from further study. In both groups there was a significant increase in cTnT, with peak concentrations being reached 6 hours after the end of cardiopulmonary bypass and remaining significantly high at 72 hours. At 6 hours the median (75% interquartile range) concentrations of cTnT were similar in both groups (1.8 (1.0-3.6) micrograms/l for cardioplegia v 1.9 (1.0-3.5) micrograms/l for intermittent ischaemic arrest).



This trial shows that intermittent ischaemic arrest, even without systemic cooling or venting of the left ventricle, provides a similar level of myocardial protection to cardioplegia in patients with moderate left ventricular function and short ischaemic times.
HIV-1-driven regulatory T-cell accumulation in lymphoid tissues is associated with disease progression in HIV/AIDS.

Regulatory T (Treg) cells accumulate in the lymphoid tissues of human immunodeficiency virus (HIV)-infected individuals, contributing to the inability of the immune system to control virus replication. We investigate here Treg-cell numbers and functional markers (FOXP3, CTLA-4, IDO, and TGF-beta1) in lymphoid tissues from untreated infected hosts with progressive or nonprogressive disease (HIV-infected humans and simian immunodeficiency virus [SIV]-infected macaques). We found that increased numbers of FOXP3(+) T cells as well as increased expression of Treg-cell-associated functional markers were detected only during progressive disease. Such increases were not correlated with immune activation. Of importance, a high-perforin/FOXP3 ratio was associated with nonprogressive disease, suggesting that the immune control of virus replication represents a balance between cell-mediated immune responses and Treg-cell-mediated counter regulation of such responses. Furthermore, using an in vitro model of Treg-cell-HIV interactions, we showed that exposure of Treg cells to HIV selectively promoted their survival via a CD4-gp120-dependent pathway, thus providing an underlying mechanism for the accumulation of Treg cells in infected hosts with active viral replication. Considered together, our findings imply that therapeutic manipulation of Treg-cell number and/or function could improve immune control of HIV infection.
Prevention of COPD exacerbation by lysozyme: a double-blind, randomized, placebo-controlled study

Lysozyme (mucopeptide N-acetyl-muramyl hydrolase) is widely used as a mucolytic and anti-inflammatory agent in Japan. We evaluated the effects of long-term lysozyme administration on COPD exacerbation.



In a 1-year, randomized, double-blind, placebo-controlled, parallel trial, patients with moderate-to-severe COPD and one or more episodes of COPD exacerbation in the previous year before enrollment were selected. Lysozyme (270 mg) or placebo was administered orally for 52 weeks as an add-on to the standard therapies such as bronchodilators. COPD exacerbation, pulmonary function, and COPD assessment test scores were analyzed. An exacerbation was defined as worsening of more than one symptom of COPD (cough, sputum volume, purulent sputum, or breathlessness) leading to a change in medication. The primary endpoint was exacerbation rate.



A total of 408 patients were randomly assigned to the lysozyme and placebo groups. The baseline characteristics were similar between the two groups. The exacerbation rate was not significantly different between the two groups (1.4 vs 1.2; P=0.292, Poisson regression). However, a subgroup analysis showed that lysozyme might reduce exacerbation rate in patients with airway-dominant phenotype (1.2 vs 1.6). Moreover, the median time to first exacerbation was longer in patients with airway-dominant phenotype in the lysozyme group than that in the placebo group. The levels of improvement in forced expiratory volume in 1 second and COPD assessment test scores were not statistically different between the groups, but were always greater in the lysozyme group than in the placebo group over the 52 weeks of the study.



The effects of using lysozyme as an add-on to standard COPD therapy were not significantly different compared with placebo and were insufficient to prevent COPD exacerbation.