nils-herrmann/clean_scirepeval huggingface dataset:
Pramipexole and levodopa in early parkinson’s disease

In chronic disease, treatment effects and costs accumulate over time; hence, the choice of time horizon in cost-effectiveness analysis can be particularly important. In this article we analyse the dynamic changes in cumulative costs, effects and incremental cost effectiveness of two competing drug strategies in patients with early Parkinson’s disease (PD).  Three hundred and one subjects with PD were randomised to initial pramipexole or levodopa and followed every 3 months over a 4-year period. Healthcare resource use was recorded in patient diaries and valued using a variety of sources at year 2002 $US values. Health-related quality of life (HRQoL) was measured using the EuroQoL EQ-5D. The study was conducted from a US societal perspective. Missing data were imputed using a multivariate fixed-effects model. Additional quality adjusted life years (QALY) gained by using pramipexole compared with levodopa were estimated as the area between the normalised treatment HRQoL profiles. The QALYs and costs for each treatment arm were calculated for various study horizons. The incremental cost-effectiveness ratio (ICER) and the net monetary benefit (NB) [using $US50 000, $US100 000 and $US150 000 as the value of a QALY] were estimated, and were bootstrapped to calculate the standard errors. Cost-effectiveness acceptability curves (CEAC) were built to estimate the probability that pramipexole was cost effective given different societal values of QALY, for various study horizons. We conducted sensitivity analyses on the ICER and the NB to test their robustness to various assumptions about missing data, for various subpopulations and under changes in the drug prices.  Under the base-case assumptions, the ICER for pramipexole was $US42 989 per QALY. Using the CEAC approach, the probability that pramipexole was cost effective relative to levodopa over the first 4 years was 0.57, 0.77 and 0.82 when a QALY was valued at $US50 000, $US100 000, and $US150 000, respectively. Over time, the ICER for pramipexole improved and uncertainty around the ICER decreased. If, after treatment withdrawal, HRQoL improved in pramipexole subjects and declined in levodopa subjects (best-case scenario for pramipexole), the probability of pramipexole being cost effective increased to 0.88, 0.96 and 0.98, respectively. Factors that improved the ICER of pramipexole were a decrease in the relative price of pramipexole and having low HRQoL or depression at baseline.  The cost effectiveness of pramipexole compared with levodopa in the treatment of early PD increased as the time horizon of the clinical trial extended from 2 to 4 years. Our results suggest that pramipexole is more cost effective for patients with depression and low baseline HRQoL than in other patient subgroups.
An Online Health Prevention Intervention for Youth with Addicted or Mentally Ill Parents: Experiences and Perspectives of Participants and Providers from a Randomized Controlled Trial

Mental illnesses affect many people around the world, either directly or indirectly. Families of persons suffering from mental illness or addiction suffer too, especially their children. In the Netherlands, 864,000 parents meet the diagnostic criteria for a mental illness or addiction. Evidence shows that offspring of mentally ill or addicted parents are at risk for developing mental disorders or illnesses themselves. The Kopstoring course is an online 8-week group course with supervision by 2 trained psychologists or social workers, aimed to prevent behavioral and psychological problems for children (aged 16 to 25 years) of parents with mental health problems or addictions. The course addresses themes such as roles in the family and mastery skills. An online randomized controlled trial (RCT) was conducted to assess the effectiveness of the Kopstoring course.



The aim was to gain knowledge about expectations, experiences, and perspectives of participants and providers of the online Kopstoring course.



A process evaluation was performed to evaluate the online delivery of Kopstoring and the experiences and perspectives of participants and providers of Kopstoring. Interviews were performed with members from both groups. Participants were drawn from a sample from the Kopstoring RCT.



Thirteen participants and 4 providers were interviewed. Five main themes emerged from these interviews: background, the requirements for the intervention, experience with the intervention, technical aspects, and research aspects. Overall, participants and providers found the intervention to be valuable because it was online; therefore, protecting their anonymity was considered a key component. Most barriers existed in the technical sphere. Additional barriers existed with conducting the RCT, namely gathering informed consent and gathering parental consent in the case of minors.



This study provides valuable insight into participants' and providers' experiences and expectations with the online preventive intervention Kopstoring. It also sheds light on the process of the online provision of Kopstoring and the accompanying RCT. The findings of this study may partly explain dropout rates when delivering online interventions. The change in the (financial) structure of the youth mental health care system in the Netherlands has financial implications for the delivery of prevention programs for youth. Lastly, there are few RCTs that assess the effectiveness and cost-effectiveness of online prevention programs in the field of (youth) mental health care and not many process evaluations of these programs exist. This hampers a good comparison between online interventions and the expectations and experiences of the participants and providers.
Independent validation of the prolonged length of stay score.

The prolonged length of stay (PLOS) score has recently been derived and validated in 2 independent national cohorts of acute stroke patients in Israel. The present study aimed to determine the performance of the PLOS score in an independent population-based cohort of stroke patients in a health care system considerably different from that in which the score was derived.



The study was performed on all 434 patients with ischemic stroke or intracerebral hemorrhage hospitalized during the first 5 years of the population-based Oxford Vascular Study (OXVASC) in Oxfordshire, UK. Median (interquartile range) length of stay (LOS) and rates of LOS ≥7 days and LOS ≥30 days by the PLOS score were calculated. Model discrimination was assessed by the c-statistic and goodness of fit was evaluated with the Hosmer-Lemeshow test.



Median LOS and rates of LOS ≥7 days increased with the increase in PLOS score among all inpatients and hospital survivors. In the analysis of LOS ≥7 days, the PLOS c-statistic (95% CI) was 0.676 (0.618-0.734) for all inpatients and 0.722 (0.664-0.779) for hospital survivors. Findings were similar for LOS ≥30 days. The Hosmer-Lemeshow showed good calibration.



The PLOS score successfully predicted PLOS in the OXVASC population of acute stroke patients. Although the score was originally derived for the prediction of prolonged acute hospitalization, it successfully predicted prolonged total LOS.
Single nucleotide polymorphism in the RAD18 gene and risk of colorectal cancer in the Japanese population.

The RAD18 gene, located on the human chromosome 3p24-p25, plays a crucial role in post-replication repair (PRR) in various organisms from yeast to humans. In the human RAD18 gene, one coding single nucleotide polymorphism (SNP) at codon 302, encoding either arginine (Arg, CGA) or glutamine (Gln, CAA), was reported. Although the molecular function of the RAD18 protein came to be elucidated, the association between the RAD18 Arg302Gln polymorphism and the risk of human cancer development was not examined. Therefore, we investigated the relationship between the polymorphism and the development of human primary colorectal cancer (CRC). The Arg302Gln polymorphism in 100 patients with CRC and 200 healthy controls were genotyped by the polymerase chain reaction with confronting two-pair primer (PCR-CTPP) assay. The Gln/Gln genotype was significantly more frequent in CRC (18.0%) than in the healthy controls (11.5%) (p=0.046). The increased risk was detected in CRC patients with the Gln/Gln genotype (Odds ratio [OR], 2.10; 95% confidence interval [CI], 1.00 to 4.40). When the relationship of the SNP with clinicopathological parameters of CRC was investigated, particularly in the well-differentiated grade and in the lymph node metastasis (N1) CRC patients, significantly higher risks were detected (OR, 7.00; 95% CI, 1.19-41.1 and OR, 3.71; 95% CI, 1.30-10.6, respectively). These results suggested that the RAD18 Arg302Gln polymorphism is associated with the risk of CRC. This report provides evidence for an association between the RAD18 Arg302Gln polymorphism and human CRC risk.
Decreased intraperitoneal disease recurrence in epithelial ovarian cancer patients receiving intraperitoneal consolidation treatment with yttrium-90-labeled murine HMFG1 without improvement in overall survival.

This study analyzes the site of disease recurrence in ovarian cancer patients to assess the influence of a single intraperitoneal (IP) administration of yttrium-90-labeled murine monoclonal antibody HMFG1 ((90)Y-muHMFG1) on the pattern of disease recurrence. In a large phase III trial ovarian cancer patients in complete clinical remission with FIGO stage Ic-IV were randomized between standard treatment plus a single IP (90)Y-labeled muHMFG1 versus standard treatment alone after negative second-look laparoscopy. Case report forms of all patients with disease recurrence were reviewed to determine site and date of recurrent disease. In total 447 patients were included in the study with a median follow-up of 3.5 years. Relapse was seen in 104/224 in the active and 98/223 in the control arm. Significantly fewer IP (p < 0.05) and more extraperitoneal (p < 0.05) relapses occurred in the active treatment arm. Time to IP recurrence was significantly longer (p = 0.0019) and time to extraperitoneal recurrence was significantly shorter for the active treatment arm (p < 0.001). The impact of IP radioimmunotherapy on IP relapse-free survival could only be seen in the subgroup of patients with residual disease after primary surgery (HR, 0.31; 95% CI, 0.18 to 0.53; p = 0.002). Although, there is no survival benefit for IP radioimmunotherapy as consolidation treatment for epithelial ovarian cancer, we found an improved control of IP disease, that was offset by increased extraperitoneal recurrences.
Use of an activity monitor to detect response to treatment in dogs with osteoarthritis.

To determine whether an activity monitor (AM) could be used to detect changes in activity in dogs with osteoarthritis treated with carprofen or a placebo.



Randomized controlled trial.



70 dogs with no clinically important abnormalities other than osteoarthritis for which they were not currently being treated.


PROCEDURES
Dogs wore an AM continuously for 21 days. On days 8 through 21, the dogs were treated with carprofen (n = 35) or a placebo (35). Total activity counts for days 1 through 7 (baseline) were compared with total activity counts for days 15 through 21 (endpoint). The change in total activity count from baseline to endpoint was assessed within each treatment group as well as between groups. Linear regression analysis was performed to test for an association between treatment and percentage change in activity counts while controlling for other variables.



For placebo-treated dogs, median baseline total activity count was not significantly different from median endpoint total activity count (1,378,408 vs 1,310,112, respectively). For dogs receiving carprofen, there was a significant increase in median activity count from baseline to endpoint (1,276,427 vs 1,374,133). When age and baseline activity counts were controlled for, dogs in the carpofen-treated group had a 20% increase in activity counts, compared with placebo-treated dogs (95% confidence interval, 10% to 26%).



Results suggested that the AM used in the present study may be a valid outcome assessment tool for documenting improved activity associated with treatment in dogs with osteoarthritis.
The validity and precision of the leicester cough questionnaire in COPD patients with chronic cough

A validated instrument to assess the effects of chronic cough on health status in patients with chronic obstructive pulmonary disease (COPD) is currently not available. The Leicester Cough Questionnaire (LCQ) is a cough-specific health status questionnaire which is originally validated for a population of general patients presenting with chronic cough. We examined the psychometric performance of the LCQ in patients with COPD and chronic productive cough.



Concurrent validity, internal consistency, reproducibility and responsiveness were determined. The St. George's Respiratory Questionnaire (SGRQ) and the Short Form-36 (SF-36) were used as external criteria. Questionnaires were completed at the start of the study. After 2 and 12 weeks the LCQ was repeated, together with a global rating of change.



In total 54 patients were included. Concurrent validity analysis showed significant correlations between corresponding domains of the LCQ and the SGRQ (r(s) -0.31 to -0.60). Corresponding domains of the LCQ and the SF-36 showed weaker correlations (r(s) 0.04 to 0.41). Internal consistency was adequate for two of the three domains (Cronbach's α 0.74 - 0.86). Test-retest reliability in stable patients was high (intraclass correlation coefficients 0.79 - 0.93). The mean difference after two weeks was 0.73 (± 1.75). Responsiveness analysis indicated that the LCQ was able to detect changes after 12 weeks.



The LCQ is a valid, reliable, responsive instrument to measure health status in COPD patients with chronic productive cough.
Impact of acute kidney injury on coagulation in adult minimal change nephropathy

A hypercoagulable state exists in patients with nephrotic syndrome (NS), which more easily leads to venous thromboembolism (VTE). However, whether acute kidney injury (AKI), a common complication of NS, affects the hypercoagulable state and VTE has rarely been elucidated. In this study, we aimed to explore coagulation changes and analyze relevant influencing factors in NS-AKI patients.A total of 269 consecutive NS patients with minimal change disease (MCD) between 2011 and 2016 were included in this observational study. Ninety-one cases were in the AKI group and 178 cases in the non-AKI group. The 1:1 propensity score matching (PSM) method was applied to match the baseline information. The coagulation biomarkers were compared, and the thrombosis events were recorded. Linear correlation was performed to detect any relation between D-dimer and clinical data.The PSM method gave matched pairs of 88 MCD patients with AKI and non-AKI patients, resulting in no differences in baseline information. The D-dimer, fibrinogen, and thromboelastography parameters maximum amplitude (MA), G values of the MCD-AKI patients were significantly higher than the levels of the MCD patients without AKI (D-dimer: 1.8 [1.0, 3.3] vs 1.1 [0.6, 1.7] mg/L, P < 0.001; fibrinogen: 7.0±2.0 vs 6.5 ± 1.4 g/L, P = 0.036; MA: 74.6 ± 5.0 vs 70.5 ± 5.3 mm, P = 0.020; G: 15.7 ± 5.3 vs 12.5 ± 3.3, P = 0.034). For the MCD patients, the serum creatinine, white blood cell count, and interleukin-6 levels in the patients with D-dimers >1 mg/L were significantly higher than those of patients with D-dimers ≤1 mg/L. The correlation analysis showed that the D-dimer level was correlated with serum creatinine, white blood cell count, and interleukin-6 (r = 0.410, P =  < 0.001; r = 0.248, P =  < 0.001; r = 0.306, P =  < 0.001, respectively). Five deep vein thrombosis events occurred in the AKI group and 1 pulmonary embolism event occurred in the non-AKI group after adjusting the propensity score value. AKI appeared to have an association with higher incidence of VTE, but the difference was not statistically significant (RR: 4.9, 95% CI: 0.6-42.7, P = 0.154).The MCD-NS patients complicated with AKI had a more severe hypercoagulable state, which might be associated with the active inflammation of AKI that mediated activation of the coagulation system.
Influenza vaccination is safe and effective in patients suffering from fibromyalgia syndrome.

The fibromyalgia syndrome (FMS) is considered to result from the exposure of a genetically susceptible individual to various triggers, such as physical trauma, stress, viral infections etc. A possible role of vaccination in FMS etiology has been suspected. Our objective was to evaluate the efficacy and safety of influenza vaccination in FMS patients. Nineteen FMS patients underwent physical and dolorimetric examinations and answered the fibromyalgia impact questionnaire (FIQ), the widespread pain index (WPI) checklist and the symptoms severity scale (SSS), which are part of the 2010 diagnostic criteria. Thirty-eight healthy subjects were recruited as controls. All participants were vaccinated with the inactivated split virion influenza vaccine. Serum was collected for antibody titration. Six weeks after vaccination, sera were tested by hemagglutination (HI) against A/California (H1N1), A/Perth (H3N2) and B/Brisbane. Humoral response was defined as either a fourfold or greater increase in titer, or an increase from a non-protective baseline level of <1/40 to a level of 1/40. No severe vaccination reactions were observed. No significant change was observed between WPI, SSS and FIQ values before and after vaccination, indicating no worsening of FMS symptoms. Vaccine immunogenicity: Six weeks after vaccination, FMS patients showed a significant increase in geometric mean titers of HI antibody. The rates of sero-protection increased from 22.9% for H1N1 to 89.5% post-vaccination. A significant increase in HI antibody titers was also demonstrated among healthy controls. Influenza vaccination was both safe and effective in FMS patients. In view of these results, FMS patients should be encouraged to undergo influenza vaccination according to the standard WHO recommendations.
Scalable clone detection using description logic

The semantic web is slowly transforming the web as we know it into a machine understandable pool of information that can be consumed and reasoned about by various clients. Source-code is no exception to this trend and various communities have proposed standards to share code as linked data. With the availability of large amounts of open source code published in publically accessible repositories and the introduction of massively horizontally scaling frameworks and cloud computing infrastructure, a new era of software mining across information silos is reshaping the software engineering landscape. The so far unreachable goal of analyzing code at a global level, and therefore detecting global software clones, has become manageable. Description logic and semantic web reasoners have so far only plaid a minor role in this transformation and are mainly used to model source code data. In this paper, we introduce a clone detection algorithm that uses a semantic web reasoner and is based on the Hadoop map-reduce framework that can scale horizontally to a large amount of data. We also define a novel and compact clone model that only considers control-blocks and used data types while still yielding similar clone detection results than more complex representations. In order to validate our approach we have compared our algorithm to some of the leading clone detection tools (CCFinder, JCD and Simian) and show differences in performance and detection precision.
Clinical profile of homozygous JAK2 617V>F mutation in patients with polycythemia vera or essential thrombocythemia.

JAK2 617V>F mutation occurs in a homozygous state in 25% to 30% of patients with polycythemia vera (PV) and 2% to 4% with essential thrombocythemia (ET). Whether homozygosity associates with distinct clinical phenotypes is still under debate. This retrospective multicenter study considered 118 JAK2 617V>F homozygous patients (104 PV, 14 ET) whose clinical characteristics were compared with those of 587 heterozygous and 257 wild-type patients. Irrespective of their clinical diagnosis, homozygous patients were older, displayed a higher leukocyte count and hematocrit value at diagnosis, and presented larger spleen volume. Aquagenic pruritus was significantly more common among homozygous PV patients. JAK2 617V>F homozygosity associated with more frequent evolution into secondary myelofibrosis in both PV and ET. After adjustment for sex, age, leukocyte count, and previous thrombosis in a multivariate analysis, homozygous ET patients displayed a significantly higher risk of cardiovascular events (hazard ratio [HR] 3.97, 95% confidence interval [CI] 1.34-11.7; P = .013) than wild-type (HR = 1.0) or heterozygous patients (HR = 1.49). No significant association of JAK2 617V>F homozygosity with thrombosis risk was observed in PV. Finally, JAK2 617V>F homozygous patients were more likely to receive chemotherapy for control of disease. We conclude that JAK2 617V>F homozygosity identifies PV or ET patients with a more symptomatic myeloproliferative disorder and is associated with a higher risk of major cardiovascular events in patients with ET.
Enhancing limb salvage by non-mobilized peripheral blood angiogenic cell precursors therapy in patients with critical limb ischemia.

Stem cell therapy has been proposed to enhance the salvage of critically ischemic limbs.



Assess the efficacy and safety of the implantation of non-mobilized peripheral blood angiogenic cell precursors (NMPB-ACPs) in patients with critical limb ischemia (CLI) who were poor candidates for standard revascularization treatment options.



Six patients with CLI due to the infrapopliteal artery occlusive disease were included in the present study. Intramuscular injections of NMPB-ACPs were administered in the ischemic limbs. The efficacy was evaluated by clinical outcomes, ankle brachial index, toe brachial index, and computerized tomographic angiography.



There was no evidence of local or systemic complication related to the procedure. Five patients (83.3%) had clinically significant improvement of adequate circulation at the distal limb for the complete healing. Four of them had complete healing of ischemic ulcers and stumps of toe amputation. However one patient with adequate granulation tissue at the stump of the left first toe amputation subsequently suffered from severe foot infection originating from the other toes and eventually underwent below knee amputation. There was no improvement of circulation at the distal limb after the administration of NMPB-ACPs in one patient (16.7%) who eventually underwent major amputation.



The preliminary result of NMPB-ACPs therapy may be safe and provide benefits in the improvement of circulation in patients with CLI. A larger controlled trial is required to ascertain these preliminary results.