nils-herrmann/clean_scirepeval huggingface dataset:
Characterisation of composer style using high-level musical features

We describe a preliminary study looking into the characterisation of composer style. The primary motivation of the work is an exploration of methods to automatically extract high level, musicologically valid features. Such features facilitate machine-learning based stylistic classification which, in contrast to previously published results, are more likely to yield musicological insights regarding style characteristics and compositorial techniques. We extract features from scores by Renaissance and Baroque composers, capturing their use of contrapuntal voice leading rules and musical intervals. A composer classification task is performed to test the ability of the feature sets to characterise composer style, yielding an accuracy of 66%. We conclude that although the computation of higher level musical features is challenging, it can give useful insights into characteristics of style which are not revealed by lower level features.
Systematic differences between BNP immunoassays: comparison of methods using standard protocols and quality control materials.

Recent studies suggested that there are marked systematic differences among BNP immunoassays. In this study we compared the BNP data and clinical results obtained with different immunoassays, including a new method (ST-AIA-PACK, TOSOH Corporation).



BNP was measured on plasma-EDTA samples of healthy subjects (HS, n=126) and patients with heart failure (HF, n=31 NYHA I, II; n=46 NYHA III, IV) using the ST-AIA-PACK and the Triage Biosite (Beckman Coulter) methods. Control samples distributed in the CardioOrmoCheck external quality assessment were also measured with TOSOH and the most used BNP immunoassays in Italy.



TOSOH method showed a good correlation (R=0.976; n=327) but a mean bias (-46.9%) compared to Triage Biosite. On the base of the results obtained in 10 samples of the CardioOrmoCheck study, TOSOH method showed a strict agreement with ADVIA Centaur, while it underestimated BNP in comparison with Triage (-52.5%) and ARCHITECT methods (-39.4%). The agreement of ST-AIA-PACK and Triage Biosite methods for classification of HF patients was tested using 100 ng/L of BNP; the positive agreement between methods was 65%, overall agreement was 73%.



Our results confirm that there are marked differences in measured values among commercial methods for BNP assay.
Common genetic variation in the HLA region is associated with late-onset sporadic Parkinson’s disease

Parkinson's disease is a common disorder that leads to motor and cognitive disability. We performed a genome-wide association study of 2,000 individuals with Parkinson's disease (cases) and 1,986 unaffected controls from the NeuroGenetics Research Consortium (NGRC). We confirmed associations with SNCA and MAPT, replicated an association with GAK (using data from the NGRC and a previous study, P = 3.2 × 10−9) and detected a new association with the HLA region (using data from the NGRC only, P = 2.9 × 10−8), which replicated in two datasets (meta-analysis P = 1.9 × 10−10). The HLA association was uniform across all genetic and environmental risk strata and was strong in sporadic (P = 5.5 × 10−10) and late-onset (P = 2.4 × 10−8) disease. The association peak we found was at rs3129882, a noncoding variant in HLA-DRA. Two studies have previously suggested that rs3129882 influences expression of HLA-DR and HLA-DQ. The brains of individuals with Parkinson's disease show upregulation of DR antigens and the presence of DR-positive reactive microglia, and nonsteroidal anti-inflammatory drugs reduce Parkinson's disease risk. The genetic association with HLA supports the involvement of the immune system in Parkinson's disease and offers new targets for drug development.
Dosimetric comparison of doses to organs at risk using 3-D conformal radiotherapy versus intensity modulated radiotherapy in postoperative radiotherapy of periampullary cancers: implications for radiation dose escalation.

Postoperative periampullary cancers with high risk features are managed with adjuvant chemo radiotherapy. Doses of 40-50 Gy have generally been used in conventional radiotherapy. Dose escalation with conventional radiotherapy has been restricted due to surrounding critical organs.



The objective of this dosimetric analysis was to evaluate the dose of radiation received by organs at risk using 3D conformal radiotherapy (3DCRT) and intensity modulated radiotherapy (IMRT).



Ten postoperative patients of periampullary cancers were selected for this dosimetric analysis. Planning CT scans films were taken with slice thickness of 2.5 mm and transferred to Eclipse treatment planning system. The clinical target volume (CTV) included the postoperative tumor bed and draining lymph nodal areas. A 1 cm margin was taken around the CTV to generate the planning target volume (PTV). Critical structures contoured for evaluation included bowel bag, bilateral kidneys, liver, stomach and spinal cord. IMRT plans were generated using seven field coplanar beams and 3DCRT planning was done using one anterior and two lateral fields. A dose of 45 Gy in 25 fractions was prescribed to the PTV.



V45 for bowel bag was 212.3 ± 159.0 cc (mean volume ± standard deviation) versus 80.9 ± 57.4 cc in 3DCRT versus IMRT (P=0.033). The V28 dose analysis for bilateral kidneys showed a value of 32.7±23.5 cc (mean volume ± standard deviation) versus 7.9 ± 7.4 cc for 3DCRT versus IMRT, respectively (P=0.013). The D60 for liver using 3DCRT and IMRT was 28.4 ± 8.6 Gy (mean dose ± standard deviation) and 19.9 ± 3.2 Gy, respectively (P=0.020).



Doses to bowel bag, liver and kidneys was significantly reduced using IMRT leaving ample scope for dose escalation.
Immunoglobulin G Fragment Crystallizable Glycosylation After Hematopoietic Stem Cell Transplantation Is Dissimilar to Donor Profiles

Immunoglobulin G (IgG) fragment crystallizable (Fc) N-glycosylation has a large influence on the affinity of the antibody for binding to Fcγ-receptors (FcγRs) and C1q protein, thereby influencing immune effector functions. IgG Fc glycosylation is known to be partly regulated by genetics and partly by stimuli in the microenvironment of the B cell. Following allogeneic hematopoietic stem cell transplantation (HSCT), and in the presence of (almost) complete donor chimerism, IgG is expected to be produced by, and glycosylated in, B cells of donor origin. We investigated to what extent IgG glycosylation in patients after transplantation is determined by factors of the donor (genetics) or the recipient (environment). Using an IgG subclass-specific liquid chromatography-mass spectrometry method, we analyzed the plasma/serum IgG Fc glycosylation profiles of 34 pediatric patients pre-HSCT and at 6 and 12 months post-HSCT and compared these to the profiles of their donors and age-matched healthy controls. Patients treated for hematological malignancies as well as for non-malignant hematological diseases showed after transplantation a lower Fc galactosylation than their donors. Especially for the patients treated for leukemia, the post-HSCT Fc glycosylation profiles were more similar to the pre-HSCT recipient profiles than to profiles of the donors. Pre-HSCT, the leukemia patient group showed as distinctive feature a decrease in sialylation and in hybrid-type glycans as compared to healthy controls, which both normalized after transplantation. Our data suggest that IgG Fc glycosylation in children after HSCT does not directly mimic the donor profile, but is rather determined by persisting environmental factors of the host.
Eligibility and Safety of Triple Therapy for Hepatitis C: Lessons Learned from the First Experience in a Real World Setting

HCV protease inhibitors (PIs) boceprevir and telaprevir in combination with PEG-Interferon alfa and Ribavirin (P/R) is the new standard of care in the treatment of chronic HCV genotype 1 (GT1) infection. However, not every HCV GT1 infected patient is eligible for P/R/PI therapy. Furthermore phase III studies did not necessarily reflect real world as patients with advanced liver disease or comorbidities were underrepresented. The aim of our study was to analyze the eligibility and safety of P/R/PI treatment in a real world setting of a tertiary referral center.



All consecutive HCV GT1 infected patients who were referred to our hepatitis treatment unit between June and November 2011 were included. Patients were evaluated for P/R/PI according to their individual risk/benefit ratio based on 4 factors: Treatment-associated safety concerns, chance for SVR, treatment urgency and nonmedical patient related reasons. On treatment data were analyzed until week 12.



208 patients were included (F3/F4 64%, mean platelet count 169/nl, 40% treatment-naïve). Treatment was not initiated in 103 patients most frequently due to safety concerns. 19 patients were treated in phase II/III trials or by local centers and a triple therapy concept was initiated at our unit in 86 patients. Hospitalization was required in 16 patients; one patient died due to a gastrointestinal infection possibly related to treatment. A platelet count of <110/nl was associated with hospitalization as well as treatment failure. Overall, 128 patients were either not eligible for therapy or experienced a treatment failure at week 12.



P/R/PI therapies are complex, time-consuming and sometimes dangerous in a real world setting, especially in patients with advanced liver disease. A careful patient selection plays a crucial role to improve safety of PI based therapies. A significant number of patients are not eligible for P/R/PI, emphasizing the need for alternative therapeutic options.
Usefulness of the electrocardiogram in predicting cardiovascular mortality in asymptomatic adults with aortic stenosis (from the Simvastatin and Ezetimibe in Aortic Stenosis Study).

Hypertension and coronary heart disease are common in aortic stenosis (AS) and may impair prognosis for similar AS severity. Different changes in the electrocardiogram may be reflective of the separate impacts of AS, hypertension, and coronary heart disease, which could lead to enhanced risk stratification in AS. The aim of this study was therefore to examine if combining prognostically relevant electrocardiographic (ECG) findings improves prediction of cardiovascular mortality in asymptomatic AS. All patients with baseline electrocardiograms in the SEAS study were included. The primary end point was cardiovascular death. Backward elimination (p >0.01) identified heart rate, Q waves, and Cornell voltage-duration product as independently associated with cardiovascular death. Multivariate logistic and Cox regression models were used to evaluate if these 3 ECG variables improved prediction of cardiovascular death. In 1,473 patients followed for a mean of 4.3 years (6,362 patient-years of follow-up), 70 cardiovascular deaths (5%) occurred. In multivariate analysis, heart rate (hazard ratio [HR] 1.5 per 11.2 minute(-1) [1 SD], 95% confidence interval [CI] 1.2 to 1.8), sum of Q-wave amplitude (HR 1.3 per 2.0 mm [1 SD], 95% CI 1.1 to 1.6), and Cornell voltage-duration product (HR 1.4 per 763 mm × ms [1 SD], 95% CI 1.2 to 1.7) remained independently associated with cardiovascular death. Combining the prognostic information contained in each of the 3 ECG variables improved integrated discrimination for prediction of cardiovascular death by 2.5%, net reclassification by 14.3%, and area under the curve by 0.06 (all p ≤0.04) beyond other important risk factors. ECG findings add incremental predictive information for cardiovascular mortality in asymptomatic patients with AS.
Impact of comorbid conditions in COPD patients on health care resource utilization and costs in a predominantly Medicare population

Patients with chronic obstructive pulmonary disease (COPD) often have multiple underlying comorbidities, which may lead to increased health care resource utilization (HCRU) and costs.



To describe the comorbidity profiles of COPD patients and examine the associations between the presence of comorbidities and HCRU or health care costs.



A retrospective cohort study utilizing data from a large US national health plan with a predominantly Medicare population was conducted. COPD patients aged 40-89 years and continuously enrolled for 12 months prior to and 24 months after the first COPD diagnosis during the period of January 01, 2009, through December 31, 2010, were selected. Eleven comorbidities of interest were identified 12 months prior through 12 months after COPD diagnosis. All-cause and COPD-related hospitalizations and costs were assessed 24 months after diagnosis, and the associations with comorbidities were determined using multivariate statistical models.



Ninety-two percent of 52,643 COPD patients identified had at least one of the 11 comorbidities. Congestive heart failure (CHF), coronary artery disease, and cerebrovascular disease (CVA) had the strongest associations with all-cause hospitalizations (mean ratio: 1.56, 1.32, and 1.30, respectively; P<0.0001); other comorbidities examined had moderate associations. CHF, anxiety, and sleep apnea had the strongest associations with COPD-related hospitalizations (mean ratio: 2.01, 1.32, and 1.21, respectively; P<0.0001); other comorbidities examined (except chronic kidney disease [CKD], obesity, and osteoarthritis) had moderate associations. All comorbidities assessed (except obesity and CKD) were associated with higher all-cause costs (mean ratio range: 1.07-1.54, P<0.0001). CHF, sleep apnea, anxiety, and osteoporosis were associated with higher COPD-related costs (mean ratio range: 1.08-1.67, P<0.0001), while CVA, CKD, obesity, osteoarthritis, and type 2 diabetes were associated with lower COPD-related costs.



This study confirms that specific comorbidities among COPD patients add significant burden with higher HCRU and costs compared to patients without these comorbidities. Payers may use this information to develop tailored therapeutic interventions for improved management of patients with specific comorbidities.
Outcome following tranexamic acid exposure during breastfeeding.

This study evaluated the outcome of infants exposed to tranexamic acid during lactation.



A prospective, controlled observational study design was used. Mothers who contacted the Beilinson Teratology Information Service (BELTIS) regarding use of tranexamic acid while breastfeeding were followed up by phone interview. Data on lactation, neonatal symptoms, and outcomes at the age of 1-3 years were obtained. Mothers' breastfeeding while taking tranexamic acid and their infants were compared with those of a matched control group of breastfeeding mothers using a drug known to be safe during lactation (amoxicillin) and their infants.



Follow-up was obtained for 28 of 32 women who sought advice regarding use of tranexamic acid during breastfeeding. Of the 28 women, six did not take the drug, and one refused to participate. The 21 remaining women (study group) were compared with 42 control women. A decreased amount of breastmilk was reported by one woman in the study group versus two women in the control group (p=1.0). Possible adverse drug effects were reported for one of 21 study group infants (restlessness) and for one of 42 control group infants (gastroesophageal reflux) (p=1.0). Growth below the 3rd percentile was found in one of 21 study group infants versus four of 42 control group infants (p=0.66). Development was normal for all study group infants.



No increase in adverse long-term outcomes was found in infants exposed through breastfeeding to tranexamic acid. Our data in conjunction with previous estimates of very low drug exposure support continuation of breastfeeding in women requiring treatment with tranexamic acid.
A Clinical Laboratory Paradigm for Evaluating Medication Effects on Alcohol Consumption: Naltrexone and Nalmefene

Opiate antagonist medications have been shown to improve alcoholism treatment, but few human laboratory-based studies investigating mechanisms for these effects have been conducted on alcohol dependent persons. The present study was designed to determine the impact of two opiate antagonists on alcohol consumption among nontreatment-seeking alcoholics (n=125) and social drinkers (n=90). Participants were randomly assigned to receive placebo, naltrexone (titrated to 50 mg/day), or nalmefene (titrated to 40 mg/day) for 8 days with an alcohol laboratory session on the final day. Alcohol consumption was monitored in the natural environment during the first 5 medication days, and during a choice consumption paradigm following a standard ‘priming’ alcohol dose in a bar–laboratory setting. Social drinkers consumed less alcohol than alcoholics during the prelab medication period and the laboratory choice consumption paradigm, and they attained lower blood alcohol levels than alcoholics following the priming drink. Both opiate antagonist medications equally reduced drinking amounts and frequency among alcoholics but not social drinkers, relative to placebo, during natural environment and bar–lab alcohol consumption evaluations. Greater medication side effects, mostly mild in nature, were observed in participants taking nalmefene. These findings demonstrate that both naltrexone and nalmefene can lead to reductions in alcohol consumption among alcoholics who are not attempting to reduce drinking. Similar laboratory paradigms may offer substantial advantages for observing these effects during evaluation of other medications as well.
Results in the operative treatment of elderly patients with intracranial meningioma

With life expectancy in the industrial nations increasing during recent years, the number of patients older than 70 years with intracranial tumours and, especially, meningiomas is rising. To evaluate the indications for operative treatment, we reviewed 66 patients older than 70 years who were operated upon for intracranial meningioma in our department between 1991 and 1997. The mean age was 75 years. The oldest patients were 86 years old. Thirteen patients with recurrent meningiomas were operated upon. The mortality rate was 7.6%. Neurological symptoms improved in 38 patients (57.6%), were unchanged in 11 (16.6%), and deteriorated in 12 (18.2%). Patients with recurrent meningiomas seem to have a higher operative risk and their outcome is worse than after a primary operation. In general, there were good postoperative results in patients with few concomitant diseases, small meningiomas, small edema, short time of operation, and accessible location (convexity rather than skull base). Age in general is not a contraindication for operation. In cases of incidental findings of small meningiomas, we recommend observation and MRI follow-up. Symptomatic meningiomas should be removed whenever there is an acceptable risk from an internal or anaesthesiological point of view.
Feasibility and efficacy of high-speed gait training with a voluntary driven exoskeleton robot for gait and balance dysfunction in patients with chronic stroke: nonrandomized pilot study with concurrent control.

The aim of this pilot study was to investigate the feasibility of high-speed gait training with an exoskeleton robot hybrid assistive limb (HAL) in patients with chronic stroke, and to examine the efficacy of eight sessions (8 weeks) of gait training with a HAL compared with conventional physical therapy. Eighteen patients with chronic stroke were included in this study (nine each in the HAL and control groups). The HAL group underwent high-speed gait training with the HAL once a week for 8 weeks (20 min/session). The control group underwent conventional physical therapy for gait disturbance. Outcome measures were walking speed, number of steps, and cadence during a 10 m walking test, a timed up and go test, a functional reach test, and the Berg Balance Scale. Assessments were performed in the absence of the HAL before training and after the fourth and eighth training sessions. All patients in the HAL group completed the high-speed gait training without adverse events. The HAL group improved significantly in walking speed (55.9% increase, P<0.001), number of steps (17.6% decrease, P<0.01), and cadence (32.8% increase, P<0.001) during the 10 m walking test. The patients also exhibited significant improvements in the timed up and go test, the functional reach test, and the Berg Balance Scale after HAL training (P<0.01 in all). No statistical time-dependent changes were observed in any parameter in the control group. For chronic stroke patients, high-speed gait training with a HAL appears to be feasible and effective in improving gait and balance dysfunction despite the limitations of this nonrandomized pilot study.
Interobserver agreement in describing video capsule endoscopy findings: a multicentre prospective study.

Few studies have specifically addressed interobserver agreement in describing lesions identified during capsule endoscopy. The aim of our study is to evaluate interobserver agreement in the description of capsule endoscopy findings.



Consecutive short segments of capsule endoscopy were prospectively observed by 8 investigators. Seventy-five videos were prepared by an external investigator (gold standard). The description of the findings was reported by the investigators using the same validated and standardized capsule endoscopy structured terminology. The agreement was assessed using Cohen's kappa statistic.



As concerns the ability to detect a lesion, the agreement with the gold standard was moderate (kappa 0.48), as well as the agreement relating to the final diagnosis (κ 0.45). The best agreement was observed in identifying the presence of active bleeding (κ 0.72), whereas the poorest agreement concerned the lesion size (κ 0.32). The agreement with the GS was significantly better in endoscopists with higher case/volume of capsule endoscopy per year. Diagnostic concordance was better in the presence of angiectasia than in the presence of polyps or ulcers/erosions.



Correct lesion identification and diagnosis seem more likely to occur in presence of angiectasia, and for readers with more experience in capsule endoscopy reading.