nils-herrmann/clean_scirepeval huggingface dataset:
A prospective study of the management of non-massive pulmonary embolism in the home.

The objective of this study is to compare the characteristics, outcomes, and clinical complications of patients with pulmonary embolism (PE) who were treated at home as outpatients versus traditional hospitalization.



Prospective study from January 2006 to June 2007. Selected patients diagnosed at the Emergency Department with stable non-massive pulmonary embolism that met standard inclusion criteria of Hospital at Home (HH) were treated at home. Patients that did not meet these criteria were admitted to Conventional Hospitalization (CH). Major and minor bleeding, re-thrombosis, clinical course, unexpected returns to hospital, and need for hospital re-admission in the following 3 months were recorded.



61 patients with PE were included (30 HH and 31 CH). Mean age 66.8 and 66.7 years in HH and CH, respectively. A history of neoplasm was found to be present in 13.3% and 9.7% of HH and CH patients. In the CH group, 19.3% of patients had prior thromboembolic disease. Concomitant DVT was seen in 40% and 29% of HH and CH patient. Pulmonary embolism was bilateral in 30% and 38.7% of HH and CH patients. No major bleeding, re-thrombosis, or death occurred. The home treatment was successfully completed in 100% of the patients. Three patients in the CH group had hospital-acquired infections.



Patients with stable non-massive pulmonary embolism may be safely treated under conditions of home hospitalization.
OnabotulinumtoxinA for chronic migraine: efficacy, safety, and tolerability in patients who received all five treatment cycles in the PREEMPT clinical program

Chronic migraine (CM) is a prevalent and disabling neurological disorder. Phase III REsearch Evaluating Migraine Prophylaxis Therapy (PREEMPT) clinical program assessed efficacy and safety of onabotulinumtoxinA (BOTOX(®)) for prophylaxis of headaches in adults with CM. This secondary analysis assessed patients who received all five treatment cycles and completed the study.



PREEMPT (two phase III studies: 24-week double-blind, placebo-controlled [DBPC], parallel-group phase, followed by 32-week open-label [OL] phase) evaluated the efficacy and safety of onabotulinumtoxinA in CM (≥15 days/month with headache lasting ≥4 h a day). Patients were randomized (1:1) to onabotulinumtoxinA or placebo every 12 weeks for two cycles, followed by onabotulinumtoxinA for three cycles. Multiple headache symptom measures were evaluated. Results for the completer (five cycles) subgroup of patients are reported.



Of 1384 total PREEMPT patients, 1005 received all five treatment cycles (513 received onabotulinumtoxinA only [onabotulinumtoxinA/onabotulinumtoxinA (O/O)] and 492 received two cycles of placebo then three cycles of onabotulinumtoxinA [placebo/onabotulinumtoxinA (P/O)]). Demographics were similar between treatment groups. At Week 56, after all patients were treated with onabotulinumtoxinA, there continued to be significant between-group differences favoring the O/O vs P/O group for the following headache symptom measures: LS mean change from baseline in frequencies of headache days (-12.0 O/O, -11.1 P/O; P = 0.035), migraine days (-11.6 O/O, -10.7 P/O; P = 0.038), and moderate/severe headache days (-11.0 O/O, -10.1 P/O; P = 0.042). For other measures (cumulative hours of headache on headache days, frequency of headache episodes, and percentage with severe Headache Impact Test (HIT)-6 score, and total HIT-6 and Migraine-Specific Quality of Life Questionnaire scores), there were also large mean improvements from baseline. The percent of patients with a ≥50% reduction from baseline in frequency of headache days was significantly greater for the onabotulinumtoxinA-only group at Week 56 (69.6% O/O, 62.8% P/O; P = 0.023). The treatment-related adverse event rate was 28.5% for onabotulinumtoxinA vs 12.4% for placebo in the DBPC phase and 34.8% for patients treated with onabotulinumtoxinA for all five cycles throughout the 56-week trials.



This subgroup analysis demonstrated improvements with onabotulinumtoxinA treatment (five cycles) vs placebo (two cycles)/onabotulinumtoxinA (three cycles) for multiple headache symptom measures and suggests that at Week 56, patients treated earlier with onabotulinumtoxinA had better outcomes. These findings demonstrate the continued need and cumulative benefit over time with continued prophylaxis, an important and clinically pragmatic observation for clinicians and patients.
Coping effectiveness training for men living with HIV: results from a randomized clinical trial testing a group-based intervention.

This randomized clinical trial was designed to compare the effects of a theory-based coping effectiveness training (CET) intervention with an active informational control (HIV-Info) condition and a waiting-list control (WLC) condition on psychological distress and positive mood in HIV-seropositive gay men.



The authors recruited 149 self-identified gay or bisexual men who were 21 to 60 years of age, reported depressed mood, and had CD4 levels of 200 to 700 cells/mm(3). CET and HIV-Info participants attended 10 90-minute group sessions during the 3-month intervention phase and six maintenance sessions over the remainder of the year. Participants were assessed at baseline and at 3, 6, and 12 months. Data were collected 1992 to 1994, before the introduction of HAART. Analyses were based on the 128 participants who completed the 3-month assessment.



After the 3-month intervention phase, when compared with HIV-Info, CET participants showed significantly greater decreases in perceived stress and burnout, and regression analyses indicated that significant increases in coping self-efficacy mediated the improvements in perceived stress and burnout. Compared with WLC, CET participants also showed significantly greater decreases in anxiety, and regression analyses indicated that significant increases in positive states of mind mediated the improvements in anxiety. Significant treatment group differences for positive morale were maintained at 6 and 12 months. In addition, optimism continued to increase in the CET and HIV-Info treatment groups during the maintenance phase.



CET can be an effective strategy for managing psychological distress and improving positive psychological states in patients confronting chronic illness.
Safety of extended-release niacin/laropiprant in patients with dyslipidemia.

To evaluate the safety profile of extended-release niacin/laropiprant (ERN/LRPT), pooling data from studies in the clinical development program.



Data were pooled from three active- or placebo-controlled phase 3 studies and three 1-year extensions of phase 2 studies that ranged from 12 to 52 weeks (N = 4747): ERN/LRPT = 2548; ERN or Niaspan® (ERN-NSP = 1268); or simvastatin or placebo (SIMVA-PBO = 931).



The safety and tolerability profile for ERN/LRPT was similar to that of ERN-NSP, except for fewer flushing-related adverse experiences and discontinuations with ERN/LRPT than ERN-NSP. The incidence of consecutive ≥3× the upper limit of normal increases in alanine aminotransferase and/or aspartate aminotransferase was numerically (but not statistically) greater with ERN/LRPT (1.0%) than ERN-NSP (0.5%) and similar to SIMVA-PBO (0.9%). Elevations were reversible with therapy discontinuation and not associated with clinical hepatotoxicity. There was no evidence that ERN/LRPT administered alone or concurrently with a statin had adverse effects on muscle. ERN/LRPT and ERN-NSP produced small median increases in fasting blood glucose levels (∼4 mg/dL) after 24 weeks of treatment, consistent with known effects of niacin.



The favorable safety and tolerability profile of ERN/LRPT for up to 1 year supports the use of LRPT to achieve improved therapeutic dosing of niacin, an agent with comprehensive lipid-modifying efficacy and shown to reduce cardiovascular risk.
Association of adherence to lifestyle recommendations and risk of colorectal cancer: a prospective Danish cohort study

To evaluate the association between a simple lifestyle index based on the recommendations for five lifestyle factors and the incidence of colorectal cancer, and to estimate the proportion of colorectal cancer cases attributable to lack of adherence to the recommendations.



Prospective cohort study.



General population of Copenhagen and Aarhus, Denmark.



55 487 men and women aged 50-64 years at baseline (1993-7), not previously diagnosed with cancer.



Risk of colorectal cancer in relation to points achieved in the lifestyle index (based on physical activity, waist circumference, smoking, alcohol intake, and diet (dietary fibre, energy percentage from fat, red and processed meat, and fruits and vegetables)) modelled through Cox regression.



During a median follow-up of 9.9 years, 678 men and women had colorectal cancer diagnosed. After adjustment for potential confounders, each additional point achieved on the lifestyle index, corresponding to one additional recommendation that was met, was associated with a lower risk of colorectal cancer (incidence rate ratio 0.89 (95% confidence interval 0.82 to 0.96). In this population an estimated total of 13% (95% CI 4% to 22%) of the colorectal cancer cases were attributable to lack of adherence to merely one additional recommendation among all participants except the healthiest. If all participants had followed the five recommendations 23% (9% to 37%) of the colorectal cancer cases might have been prevented. Results were similar for colon and rectal cancer, but only statistically significant for colon cancer.



Adherence to the recommendations for physical activity, waist circumference, smoking, alcohol intake, and diet may reduce colorectal cancer risk considerably, and in this population 23% of the cases might be attributable to lack of adherence to the five lifestyle recommendations. The simple structure of the lifestyle index facilitates its use in public health practice.
Factors associated with hypertension prevalence, awareness, treatment and control among participants in the International Mobility in Aging Study (IMIAS)

The aim of this study is to assess the factors associated with hypertension prevalence, awareness, treatment, and control, in the elderly populations of the International Mobility in Aging Study (IMIAS). Approximately 200 men and 200 women aged 65–74 years were recruited at each site (n=1995) during IMIAS’ 2012 baseline survey at five cities: Kingston (Canada), Saint-Hyacinthe (Canada), Tirana (Albania), Manizales (Colombia) and Natal (Brazil). Blood pressure and anthropometric measurements were taken at participants’ homes. Hypertension prevalence ranged from 53.4% in Saint-Hyacinthe to 83.5% in Tirana. Diabetes and obesity were identified as risk factors in all cities. More than two-thirds of hypertensive participants were aware of their condition (from 67.3% in Saint-Hyacinthe to 85.4% in Tirana); women were more aware than men. Awareness was positively associated with diabetes in Kingston, Manizales and Natal. Though most of those aware of their hypertensive condition were being treated pharmacologically, associations between awareness and physical activity and refraining from smoking were weak. Control among treated hypertensive participants was low, especially in Tirana and Natal. Diabetes and physical inactivity were associated with poor hypertension control. Hypertension is common in the older populations of IMIAS. Diabetes is strongly associated with hypertension prevalence, awareness and lack of control of hypertension. The fact that awareness is not strongly associated with healthy behaviours suggests that antihypertensive medication is not accompanied by non-pharmacological therapies. Improved health behaviours could strengthen hypertension control. Efforts should be made to increase men’s awareness of hypertension. Hypertension control in diabetic patients is a challenge.
I Know What You Did Last Summer - An Investigation of How Developers Spend Their Time

Developing software is a complex mental activity, requiring extensive technical knowledge and abstraction capabilities. The tangible part of development is the use of tools to read, inspect, edit, and manipulate source code, usually through an IDE (integrated development environment). Common claims about software development include that program comprehension takes up half of the time of a developer, or that certain UI (user interface) paradigms of IDEs offer insufficient support to developers. Such claims are often based on anecdotal evidence, throwing up the question of whether they can be corroborated on more solid grounds.
 We present an in-depth analysis of how developers spend their time, based on a fine-grained IDE interaction dataset consisting of ca. 740 development sessions by 18 developers, amounting to 200 hours of development time and 5 million of IDE events. We propose an inference model of development activities to precisely measure the time spent in editing, navigating and searching for artifacts, interacting with the UI of the IDE, and performing corollary activities, such as inspection and debugging. We report several interesting findings which in part confirm and reinforce some common claims, but also disconfirm other beliefs about software development.
Waterpipe dependence in university students and effect of normative beliefs: a cross-sectional study

The objective of this study was to measure the correlates, including normative beliefs, associated with waterpipe (WP) and cigarette smoking prevalence and dependence.



A cross-sectional study was carried out using a proportionate cluster sample of Lebanese students in 17 public and private universities.



Of the 4900 distributed questionnaires, 3384 (69.1%) were returned to the field worker. All available students during break times were approached, with no exclusion criteria.



sociodemographic variables, detailed active and passive smoking, in addition to items of the tobacco dependence scales were all evaluated.



Correlates to WP smoking were studying in a private university (adjusted OR, aOR=1.50 (1.26 to 1.79); p<0.001) and ever smoking cigarettes (aOR=1.80(1.44 to 2.26); p<0.001); friends' and societal influence were found on smoking behaviour and dependence. Although the role of parents was not visible in decreasing the risk of smoking WP, their protective influence seemed more important on WP dependence (β=-1.09(-1.79 to -0.28); p<0.001), a behaviour that is considered more deleterious for health. Parents' and friends' disagreement with smoking had a protective effect on cigarette smoking and dependence (aOR<1; p<0.01), while thinking that idols and successful people smoke increased the risk of both cigarette smoking and dependence (aOR>1; p<0.01).



In conclusion, WP smoking and dependence are influenced by parents' and friends' opinions, and idols' smoking status. Future research is necessary to further improve our understanding of motives for WP smoking and dependence.
Handover of patient information from the crisis assessment and treatment team to the inpatient psychiatric unit.

Handover, or the communication of patient information between clinicians, is a fundamental component of health care. Psychiatric settings are dynamic environments relying on timely and accurate communication to plan care and manage risk. Crisis assessment and treatment teams are the primary interface between community and mental health services in many Australian and international health services, facilitating access to assessment, treatment, and admission to hospital. No previous research has investigated the handover between crisis assessment and treatment teams and inpatient psychiatric units, despite the importance of handover to care planning. The aim of the present study was to identify the nature and types of information transferred during these handovers, and to explore how these guides initial care planning. An observational, exploratory study design was used. A 20-item handover observation tool was used to observe 19 occasions of handover. A prospective audit was undertaken on clinical documentation arising from the admission. Clinical information, including psychiatric history and mental state, were handed over consistently; however, information about consumer preferences was reported less consistently. The present study identified a lack of attention to consumer preferences at handover, despite the current focus on recovery-oriented models for mental health care, and the centrality of respecting consumer preferences within the recovery paradigm.
Reconstitution of immune cell populations in multiple sclerosis patients after autologous stem cell transplantation.

Multiple sclerosis is an inflammatory T cell-mediated autoimmune disease. In a Phase II clinical trial, high-dose immunosuppressive therapy combined with autologous CD34+ haematopoietic stem cell transplant resulted in 69·2% of subjects remaining disease-free without evidence of relapse, loss of neurological function or new magnetic resonance imaging (MRI) lesions to year 5 post-treatment. A combination of CyTOF mass cytometry and multi-parameter flow cytometry was used to explore the reconstitution kinetics of immune cell subsets in the periphery post-haematopoietic cell transplant (HSCT) and the impact of treatment on the phenotype of circulating T cells in this study population. Repopulation of immune cell subsets progressed similarly for all patients studied 2 years post-therapy, regardless of clinical outcome. At month 2, monocytes and natural killer (NK) cells were proportionally more abundant, while CD4 T cells and B cells were reduced, relative to baseline. In contrast to the changes observed at earlier time-points in the T cell compartment, B cells were proportionally more abundant and expansion in the proportion of naive B cells was observed 1 and 2 years post-therapy. Within the T cell compartment, the proportion of effector memory and late effector subsets of CD4 and CD8 T cells was increased, together with transient increases in proportions of CD45RA-regulatory T cells (Tregs ) and T helper type 1 (Th1 cells) and a decrease in Th17·1 cells. While none of the treatment effects studied correlated with clinical outcome, patients who remained healthy throughout the 5-year study had significantly higher absolute numbers of memory CD4 and CD8 T cells in the periphery prior to stem cell transplantation.
Viral load, CD4 percentage, and delayed-type hypersensitivity in subjects receiving the HIY-1 Immunogen and antiviral drug therapy

Two trials of subjects inoculated with the inactivated, gp120-depleted HIV-1 Immunogen are reported. In one study, in which 19 subjects received ZDV and 8 subjects received ddI, treatment with the HIV-1 Immunogen did not affect the pharmacokinetic parameters of the antiviral drugs. In another study, 65 subjects who were previously immunized with the HIV-1 Immunogen over a mean period of 4.0 years (range, 1.2–5.4 years) received inoculations at 0 and 6 months. At some point during this 48-week study, 72% of the subjects (47/65) were receiving antiviral drug therapy. The HIV-1 DNA load in CD4 cells and CD4 percentage were found to be stable over the 48-week period. Delayed-type hypersensitivity to HIV-1 antigens increased after two inoculations with the HIV-1 Immunogen. In these two trials, no serious treatment-related adverse events were documented in the subjects. The two studies presented herein are the first to suggest that an immune-based therapy such as the HIV-1 Immunogen can be combined safely with antiviral drugs, supporting further study to evaluate the clinical utility of this approach.
Evaluation of disease-mediated therapeutic protein-drug interactions between an anti-interleukin-6 monoclonal antibody (sirukumab) and cytochrome P450 activities in a phase 1 study in patients with rheumatoid arthritis using a cocktail approach.

This therapeutic protein-drug interaction study evaluated the disease-mediated effect of sirukumab (anti-interleukin 6 [anti-IL-6] monoclonal antibody) on the pharmacokinetics of the cytochrome P450 (CYP) probe substrates midazolam (CYP3A), omeprazole (CYP2C19), warfarin (CYP2C9), and caffeine (CYP1A2) in patients with active rheumatoid arthritis (RA). Twelve patients with C-reactive protein (CRP) ≥ 8.0 mg/L at screening received oral administration of a CYP probe cocktail consisting of 0.03 mg/kg midazolam, 10 mg warfarin + 10 mg vitamin K (equivalent to 5 mg S-warfarin), 20 mg omeprazole, and 100 mg caffeine 1 week before and 1, 3, and 6 weeks after a single subcutaneous dose of 300 mg sirukumab. The results showed that the pharmacokinetics of midazolam, omeprazole, and S-warfarin were nonequivalent before and after the administration of a single dose of 300 mg sirukumab. Area under the plasma concentration-time curve (AUC0- ∞ ) for midazolam, omeprazole, and S-warfarin was reduced by 30%-35%, 37%-45%, and 18%-19%, respectively, after sirukumab administration. Caffeine AUC0-∞ was increased by 20%-34% after sirukumab administration. The effect of sirukumab on CYP substrates was sustained for at least 6 weeks. No new adverse drug reactions related to the administration of sirukumab were observed in this study. These results suggest that sirukumab may reverse IL-6-mediated suppression of CYP3A, CYP2C9, and CYP2C19 activities in patients with active RA.
The relationship of palliative transurethral resection of the prostate with disease progression in patients with prostate cancer.

To test, in a prostate-cancer population-based database, the validity of the finding that in single-institution series, palliative transurethral resection of prostate (TURP) is associated with an increased risk of progression.



Using the Surveillance Epidemiology and END Results Registry, we identified men who had a TURP subsequent to their diagnosis of prostate cancer, from 1998 or 1999. The outcome of interest was disease progression, as defined by the initiation of androgen-deprivation therapy or procedures indicating progressive urinary obstruction. Multivariable logistic regression analysis was used to assess the adjusted odds of signal events related to disease progression adjusting for the concurrent effect of the covariates.



There were 29,361 men with prostate cancer and 2742 (9.3%) had a TURP after the diagnosis. These men had a mean age of 75 years and were unlikely to undergo definitive primary treatment. Men receiving TURP were more likely to undergo orchidectomy than men who did not have a TURP (odds ratio 1.64; 95% confidence interval 1.03-2.60) even after adjusting for differences in cancer-directed treatment, tumour stage and grade, prostate-specific antigen level, race, and age at diagnosis. These men were also more likely to have malignant urinary obstruction (ureteric and bladder outlet) than were men who did not have TURP.



The requirement for TURP is an adverse prognostic marker even when this is adjusted for classical tumour characteristics. Although the exact reasons for this finding are unclear, consideration should be given to adjuvant treatment in patients undergoing TURP.