nils-herrmann/clean_scirepeval huggingface dataset:
One-Legged Cycle Training for Chronic Obstructive Pulmonary Disease. A Pragmatic Study of Implementation to Pulmonary Rehabilitation.

In patients with chronic obstructive pulmonary disease (COPD), partitioned exercise training using one-legged cycling leads to greater improvements in peak oxygen uptake than conventional two-legged cycling.



We evaluated the feasibility of incorporating one-legged cycling as the principal aerobic training modality for pulmonary rehabilitation in COPD.



Physiotherapists underwent four teaching sessions about the principles and practical implementation of one-legged cycling training. Patients enrolled in a pulmonary rehabilitation program underwent 6-8 weeks of training in which one-legged cycling three times per week was the principal aerobic exercise activity. Participants cycled for 15 minutes with each leg, in each session. An incremental cardiopulmonary exercise test was completed before and after pulmonary rehabilitation along with standard pulmonary rehabilitation outcome measures. Participants and physiotherapists completed a satisfaction survey at the end of the program.



A total of 22 out of 32 participants (14 male; mean [SD] age, 66  years; FEV1% predicted, 32 [17]%; median [interquartile range] Medical Research Council dyspnea scale, 3.5 [3.0-4.3]) completed pulmonary rehabilitation. Peak oxygen uptake increased 1.1 (0.4-1.7) ml·min(-1)·kg(-1) (8%) from baseline (P<0.01). The mean (95% confidence interval) 6-minute-walk test distance improved by 72 (45-98) m (P=0.001). The change in the Chronic Respiratory Questionnaire total score of 1.6 (1.1-2.1; P<0.001) was achieved by improvement in all four domains above the clinically important difference. All the physiotherapists considered one-legged cycling safe and would continue to prescribe it; 75% of participants would recommend it to other patients.



One-legged cycling was successfully implemented into a "real-life" pulmonary rehabilitation program, demonstrating improvements in cardiorespiratory fitness with associated improvement in function for patients with moderate/severe COPD. One-legged cycling should be recommended in professional pulmonary rehabilitation guidelines as an option for exercise training and be available in other pulmonary rehabilitation programs.
Trazodone in late life depressive states: a double-blind multicenter study versus amitriptyline and mianserin

Seventy five elderly depressed in-patients, ages ranging from 60 to 83 years, diagnosed as Major Depression according to DSM III were treated, under double-blind conditions, with 75 mg Amitriptyline (AMI) (26 patients), 60 mg Mianserin (MIA) (24 patients) or 150 mg Trazodone (TRZ) (25 patients) p.o. for 5 weeks. There were no differences in the clinical outcome between the three groups of patients at the end of the trial, with a significant amelioration (P<0.01) at the Hamilton Rating Scale for Depression and Geriatric Depression Scale. TRZ showed a significantly lower incidence of side effects compared to MIA and AMI. Atypical antidepressants, including TRZ, seem more suitable for treating elderly depression than the first generation antidepressants on the basis of risk/benefit ratio considerations.
Colchicine reduces postoperative atrial fibrillation: results of the Colchicine for the Prevention of the Postpericardiotomy Syndrome (COPPS) atrial fibrillation substudy.

Inflammation and pericarditis may be contributing factors for postoperative atrial fibrillation (POAF), and both are potentially affected by antiinflammatory drugs and colchicine, which has been shown to be safe and efficacious for the prevention of pericarditis and the postpericardiotomy syndrome (PPS). The aim of the Colchicine for the Prevention of the Post-Pericardiotomy Syndrome (COPPS) POAF substudy was to test the efficacy and safety of colchicine for the prevention of POAF after cardiac surgery.



The COPPS POAF substudy included 336 patients (mean age, 65.7±12.3 years; 69% male) of the COPPS trial, a multicenter, double-blind, randomized trial. Substudy patients were in sinus rhythm before starting the intervention (placebo/colchicine 1.0 mg twice daily starting on postoperative day 3 followed by a maintenance dose of 0.5 mg twice daily for 1 month in patients ≥70 kg, halved doses for patients <70 kg or intolerant to the highest dose). The substudy primary end point was the incidence of POAF on intervention at 1 month. Despite well-balanced baseline characteristics, patients on colchicine had a reduced incidence of POAF (12.0% versus 22.0%, respectively; P=0.021; relative risk reduction, 45%; number needed to treat, 11) with a shorter in-hospital stay (9.4±3.7 versus 10.3±4.3 days; P=0.040) and rehabilitation stay (12.1±6.1 versus 13.9±6.5 days; P=0.009). Side effects were similar in the study groups.



Colchicine seems safe and efficacious in the reduction of POAF with the potentiality of halving the complication and reducing the hospital stay.
Energy intake and risk of postmenopausal breast cancer: an expanded analysis in the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) cohort.

Although animal experiments have consistently shown a positive relationship between breast cancer and energy intake, evidence from human studies remains inconclusive. In the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial cohort, 29,170 women, ages 55 to 75 years, who successfully completed a food frequency questionnaire (FFQ) at entry (1993-2001), were followed through 2007, and 1,319 incident breast cancers were ascertained (median time from FFQ completion to diagnosis, 4.4 years). Women in the highest quartile of energy intake, relative to the lowest, had modestly, but significantly, increased breast cancer risk [multivariate relative risk (RR), 1.21; 95% confidence interval (95% CI), 1.03-1.42; P(trend) = 0.03]. The inclusion of body mass index and physical activity in the model reduced risk slightly (RR, 1.18; 95% CI, 1.00-1.39; P(trend) = 0.07). However, in similar analyses using energy intake from a FFQ administered approximately five years after entry (27,428 women; 806 incident breast cancers; median time from FFQ completion to diagnosis, 2.7 years), women in the highest and lowest quartiles of energy intake had similar risk. When follow-up time after the first FFQ was divided into three 4-year periods, the multivariate RRs for high versus low energy intake increased from 1.21 to 1.37 to 1.55 with increasing time since dietary assessment. Although the divergent results for the two FFQs could be due to subtle questionnaire differences, our findings suggest a modest positive association between energy intake and postmenopausal breast cancer that strengthens with time since dietary assessment.
Interim analysis of a phase I/IIa trial assessing E39+GM-CSF, a folate binding protein vaccine, to prevent recurrence in ovarian and endometrial cancer patients

Folate binding protein(FBP) is an immunogenic protein over-expressed in endometrial(EC) and ovarian cancer(OC). We are conducting a phase I/IIa trial of E39 (GALE 301)+GM-CSF, an HLA-A2-restricted, FBP-derived peptide vaccine to prevent recurrences in disease-free EC and OC patients. This interim analysis summarizes toxicity, immunologic responses, and clinical outcomes to date.



HLA-A2+ patients were vaccinated(VG), and HLA-A2- or -A2+ patients were followed as controls(CG). Six monthly intradermal inoculations of E39+250mcg GM-CSF were administered to VG. Demographic, safety, immunologic, and recurrence rate(RR) data were collected and evaluated.



This trial enrolled 51 patients; 29 in the VG and 22 in the CG. Fifteen patients received 1000mcg E39, and 14 received <1000mcg. There were no clinicopathologic differences between groups(all p ≥ 0.1). E39 was well-tolerated regardless of dose. DTH increased pre- to post-vaccination (5.7±1.5 mm vs 10.3±3.0 mm, p = 0.06) in the VG, and increased more in the 1000mcg group (3.8±2.0 mm vs 9.5±3.5 mm, p = 0.03). With 12 months median follow-up, the RR was 41% (VG) vs 55% (CG), p = 0.41. Among the 1000mcg patients, the RR was 13.3% vs 55% CG, p = 0.01. Estimated 2-year DFS was 85.7% in the 1000mcg group vs 33.6% in the CG (p = 0.021).



This phase I/IIa trial reveals that E39+GM-CSF is well-tolerated and elicits a strong, dose-dependent in vivo immune response. Early efficacy results are promising in the 1000 mcg dose cohort. This study proves the safety and establishes the dose of E39 for a larger prospective, randomized, controlled trial in HLA-A2+ EC and OC patients to prevent recurrence.
The effects of early aggressive rehabilitation on outcomes after anterior cruciate ligament reconstruction using autologous hamstring tendon: a randomized clinical trial.

Prospective randomized clinical trial.



Thirty-six patients who had a primary anterior cruciate ligament reconstruction (ACL-R) with a semitendinosus-gracilis (STG) autograft from a single orthopedic surgeon were prospectively randomized into 2 groups. Nineteen patients were randomized to the aggressive group (53% male, mean age 30.1 + 10.5 y) and 17 to the nonaggressive group (88% male, mean age 33.1 + 10.9 y). Impairment measures of anteroposterior (A-P) knee laxity, range of motion (ROM), and peak isometric force (PIF) values were obtained 12 wk postoperatively. Subjective response to the International Knee Documentation Committee knee form (IKDC) was collected 1, 12, and 24 wk postoperatively. One-way ANOVA was used to analyze differences between groups at 12 wk for A-P knee laxity, ROM, and PIF. Differences between the groups for the IKDC scores were determined using 1-way ANOVA with repeated measures 1, 12, and 24 wk postoperatively. Bonferroni adjustment was used for multiple comparisons.



There were no differences between the groups for the baseline characteristics (P > .05). There was no difference found between the groups in respect to A-P knee laxity, ROM, or PIF at 12 wk (P > .05). Further analysis also showed no significant differences in the IKDC scores between groups at 12 or 24 wk (P > .05).



No differences were found between early aggressive and nonaggressive rehabilitation after an isolated ACL-R using STG autografts for the primary outcomes of A-P knee laxity and subjective IKDC score. In addition, no differences were observed for secondary outcomes between groups for differences in ROM and PIF values.
Effect of Noninvasive Ventilation on Tracheal Reintubation Among Patients With Hypoxemic Respiratory Failure Following Abdominal Surgery: A Randomized Clinical Trial.

It has not been established whether noninvasive ventilation (NIV) reduces the need for invasive mechanical ventilation in patients who develop hypoxemic acute respiratory failure after abdominal surgery.



To evaluate whether noninvasive ventilation improves outcomes among patients developing hypoxemic acute respiratory failure after abdominal surgery.



Multicenter, randomized, parallel-group clinical trial conducted between May 2013 and September 2014 in 20 French intensive care units among 293 patients who had undergone abdominal surgery and developed hypoxemic respiratory failure (partial oxygen pressure <60 mm Hg or oxygen saturation [SpO2] ≤90% when breathing room air or <80 mm Hg when breathing 15 L/min of oxygen, plus either  a respiratory rate above 30/min or [2] clinical signs suggestive of intense respiratory muscle work and/or labored breathing) if it occurred within 7 days after surgical procedure.



Patients were randomly assigned to receive standard oxygen therapy (up to 15 L/min to maintain SpO2 of 94% or higher) (n = 145) or NIV delivered via facial mask (inspiratory pressure support level, 5-15 cm H2O; positive end-expiratory pressure, 5-10 cm H2O; fraction of inspired oxygen titrated to maintain SpO2 ≥94%) (n = 148).



The primary outcome was tracheal reintubation for any cause within 7 days of randomization. Secondary outcomes were gas exchange, invasive ventilation-free days at day 30, health care-associated infections, and 90-day mortality.



Among the 293 patients (mean age, 63.4 [SD, 13.8] years; n=224 men) included in the intention-to-treat analysis, reintubation occurred in 49 of 148 (33.1%) in the NIV group and in 66 of 145 (45.5%) in the standard oxygen therapy group within+ 7 days after randomization (absolute difference, -12.4%; 95% CI, -23.5% to -1.3%; P = .03). Noninvasive ventilation was associated with significantly more invasive ventilation-free days compared with standard oxygen therapy (25.4 vs 23.2 days; absolute difference, -2.2 days; 95% CI, -0.1 to 4.6 days; P = .04), while fewer patients developed health care-associated infections (43/137 [31.4%] vs 63/128 [49.2%]; absolute difference, -17.8%; 95% CI, -30.2% to -5.4%; P = .003). At 90 days, 22 of 148 patients (14.9%) in the NIV group and 31 of 144 (21.5%) in the standard oxygen therapy group had died (absolute difference, -6.5%; 95% CI, -16.0% to 3.0%; P = .15). There were no significant differences in gas exchange.



Among patients with hypoxemic respiratory failure following abdominal surgery, use of NIV compared with standard oxygen therapy reduced the risk of tracheal reintubation within 7 days. These findings support use of NIV in this setting.
Real-time three-dimensional guided ultrasound targeting system for microwave ablation of liver tumours: a human pilot study.

This study aimed to evaluate a novel three-dimensional ultrasound (US) guidance system for use in hepatic microwave ablation (MWA).



An in vitro assessment was performed in which users with different degrees of experience were evaluated for accuracy in targeting phantom lesions embedded in agar using US alone, or US in conjunction with the InVision™ System (IVS). An eight-patient pilot trial of the IVS was then performed in the setting of open hepatic MWA, in which lesions would otherwise have been targeted with conventional US.



In vitro studies demonstrated that the IVS significantly improved targeting accuracy at all levels of operator experience (novice, beginner and expert). In the human trial, a total of 31 tumours were targeted and all lesions were hit in one pass, as assessed by independent US image observations. There were no adverse operative events; however, there was minor line-of-sight interference with the infra-red tracking mechanism when some lesions high on the dome of the liver were targeted.



The IVS significantly increased the accuracy of complex targeting procedures of phantom lesions and enhanced targeting in an eight-patient clinical pilot study. During the accrual phase of this pilot study, the development of improved non-optical tracking hardware obviated the requirement to maintain a direct line of sight. The trial was then halted prematurely in order to focus on the application of the IVS utilizing this non-optical modality.
Evaluation and optimization of clustering in gene expression data analysis

A measurement of cluster quality is needed to choose potential clusters of genes that contain biologically relevant patterns of gene expression. This is strongly desirable when a large number of gene expression profiles have to be analyzed and proper clusters of genes need to be identified for further analysis, such as the search for meaningful patterns, identification of gene functions or gene response analysis.



We propose a new cluster quality method, called stability, by which unsupervised learning of gene expression data can be performed efficiently. The method takes into account a cluster's stability on partition. We evaluate this method and demonstrate its performance using four independent, real gene expression and three simulated datasets. We demonstrate that our method outperforms other techniques listed in the literature. The method has applications in evaluating clustering validity as well as identifying stable clusters.


AVAILABILITY
Please contact the first author.
Prestroke physical activity is associated with severity and long-term outcome from first-ever stroke.

To determine whether prestroke level of physical activity influenced stroke severity and long-term outcome.



Patients included into the present analyses represent a subset of patients with first-ever stroke enrolled into the ExStroke Pilot Trial. Patients with ischemic stroke were randomized in the ExStroke Pilot Trial to an intervention of repeated instructions and encouragement to increase the level of physical activity or to a control group. Prestroke level of physical activity was assessed retrospectively by interview using the Physical Activity Scale for the Elderly (PASE) questionnaire. The PASE questionnaire quantifies the amount of physical activity done during a 7-day period. In this prospectively collected patient population initial stroke severity was measured using the Scandinavian Stroke Scale and long-term outcome was assessed after 2 years using the modified Rankin Scale. Statistical analyses were done using ordinal logistic regression.



Data from 265 patients were included with a mean (SD) age of 68.2 (12.2) years. Confirming univariable analyses, multivariable analyses showed that patients with physical activity in the top quartile more likely presented with a less severe stroke, OR 2.54 (95% CI 1.30-4.95), and had a decreased likelihood of poor outcome, OR 0.46 (95% CI 0.22-0.96), compared to patients in the lowest quartile.



In the present study physical activity prior to stroke was associated with a less severe stroke and better long-term outcome.
Role of distinct PTSD symptoms in intimate partner reabuse: a prospective study.

This prospective study examines the impact of four posttraumatic stress disorder (PTSD) symptom clusters (hyperarousal, reexperiencing, numbing, and avoidance) on reabuse over 1 year among women exposed to intimate partner violence (IPV). The covariates include severity of IPV, a history of childhood violence, and characteristics of the abusive relationship. Although both hyperarousal and numbing symptoms were higher at baseline among women subsequently reabused, only numbing symptoms increased the odds of reabuse after controlling for the covariates. Greater IPV severity and shorter relationship duration also increased the risk of reabuse. Results indicate that specific symptoms of PTSD, especially numbing, need to be addressed to increase the safety of women seeking services for IPV.
Extracting the haemodynamic response function from fMRI time series using Fourier-wavelet regularised deconvolution with orthogonal spline wavelets

We describe a method to extract the haemodynamic response function (HRF) from functional magnetic resonance imaging (fMRI) time series based on Fourier-wavelet regularised deconvolution (ForWaRD), and introduce a simple model for the HRF. The HRF extraction algorithm extends the ForWaRD algorithm by introducing a more efficient computation in the case of very long wavelet filters. We compute shift-invariant discrete wavelet transforms (SIDWT) in the frequency domain, and apply ForWaRD using orthogonal spline wavelets. Extraction and modelling of subject-specific HRFs is demonstrated, as well as the use of these HRFs in a subsequent brain activation analysis. Temporal responses are predicted by using the extracted HRF coefficients. The resulting activation maps show the effectiveness of the proposed method.
The impact of tiotropium on mortality and exacerbations when added to inhaled corticosteroids and long-acting β-agonist therapy in COPD.

Tiotropium has been shown to improve lung function, quality of life, and exacerbations and reduce mortality when compared with placebo in COPD. It remains unclear whether benefits are seen when tiotropium is used in conjunction with inhaled corticosteroids (ICSs) plus long-acting β-agonists (LABAs).



We performed a retrospective cohort study using a National Health Service database of patients with COPD in Tayside, Scotland, between 2001 and 2010 that is linked with databases regarding hospital admissions, pharmacy prescriptions, and death registries. The impact of the addition of tiotropium (Tio) to ICS + LABA therapy on all-cause mortality, hospital admissions for respiratory disease, and emergency oral corticosteroid bursts was evaluated. Adjusted hazard ratios (HRs) were calculated by Cox regression after inclusion of the following covariates: cardiovascular and respiratory disease, diabetes, smoking, age, sex, and deprivation index.



A total of 1,857 patients were given ICS + LABA + Tio, and 996 were given ICS + LABA. Mean follow-up was 4.65 years. The adjusted HR for all-cause mortality for ICS + LABA + Tio vs ICS + LABA was 0.65 (95% CI, 0.57-0.75; P < .001). Adjusted HRs for hospital admissions and oral corticosteroid bursts were 0.85 (95% CI, 0.73-0.99; P = .04) and 0.71 (95% CI, 0.63-0.80; P < .001), respectively.



The study suggests that the addition of tiotropium to ICSs and LABA therapy may confer benefits in reducing all-cause mortality, hospital admissions, and oral corticosteroid bursts in patients with COPD. Triple therapy is widely used in the real-life management of COPD, with only limited scientific support. The study supports the use of triple therapy in COPD and provides a platform for randomized controlled trials specifically addressing this topic.
Population pharmacokinetics and target attainment analysis of moxifloxacin in patients with diabetic foot infections.

The objective of this study was to provide a pharmacokinetic/pharmacodynamic (PK/PD) analysis of moxifloxacin in patients with diabetic foot infections (DFI). The plasma concentration-time courses were determined in 50 DFI patients on day 1 and 3 after intravenous moxifloxacin 400 mg once-daily. A two-compartment population pharmacokinetic model was developed, identifying as covariates total body weight on central and peripheral volume of distribution (V1, V2) and ideal body weight on clearance (CL), respectively. For a 70 kg patient V1 was 68.1 L (interindividual variability, CV: 27.4%), V2 44.6 L, and CL 12.1 L/h (25.6%). Simulations were performed to calculate the probability of target attainment (PTA) for Gram-positive and Gram-negative pathogens with fAUC/MIC targets of ≥30 and ≥100, respectively. PTA was 0.68-1 for susceptible (MIC ≤0.5 mg/L according to EUCAST) Gram-positive, but <0.25 for Gram-negative pathogens with MIC ≥0.25 mg/L. With the exception of the first 24 hours of therapy, obesity affected PTA only marginally. Pharmacokinetic parameters in DFI patients were similar to those reported for healthy volunteers, indicating the appropriateness of the standard dose of moxifloxacin. Overall clinical efficacy has been shown previously, but PTA is limited in a subpopulation infected with formally susceptible Gram-negative pathogens close to the EUCAST breakpoint.
Noninvasive Positive-Pressure Ventilation in Acute Respiratory Distress Syndrome in Patients With Acute Pancreatitis: A Retrospective Cohort Study.

Noninvasive positive-pressure ventilation (NPPV) in acute respiratory distress syndrome (ARDS) is controversial. We aimed to assess the efficacy of NPPV on ARDS in acute pancreatitis (AP).



In this retrospective, single-center cohort study, demographic data, clinical and biochemical parameters of AP and developed ARDS on admission as well as before and after use of NPPV, and clinical outcomes were retrieved from the medical record database. Degrees of ARDS at presentation were retrospectively classified using the Berlin Definition.



Of 379 patients identified, 127 were eligible for inclusion and had NPPV for more than 24 hours. There were 44 mild, 64 moderate, and 19 severe patients with ARDS at presentation; endotracheal intubation rates were 0% (0/44), 23.4% (15/64), and 47.4% (9/19); and the mortality rates were 0% (0/44), 9.4% (6/64), and 15.8% (3/19), respectively. After NPPV treatment, systolic pressure, heart rate, respiratory rate, and fraction of inspired oxygen decreased, whereas oxygen saturation increased significantly in the NPPV success group compared with the failed group. Similar findings were also observed between survivors and nonsurvivors.



Noninvasive positive-pressure ventilation may be an effective option for the initial treatment of ARDS patients in AP, but the use of NPPV should be applied prudently in the most severe cases.