nils-herrmann/clean_scirepeval huggingface dataset:
A randomized trial comparing the efficacy and tolerability of two HAART strategies at two years in antiretroviral naive patients.

The use of HAART combining 2 nucleoside analogues reverse transcriptase inhibitors (NRTIs) plus one protease inhibitor (PI) or 2 NRTIs + 1 non-nucleoside reverse transcriptase inhibitor (NNRTI) has shown comparable efficacy. The study was designed to compare long term (2 years) effectiveness of two antiretroviral (ARV) treatment strategies in patients not previously treated: starting with a nelfinavir based HAART switching to nevirapine in case of failure or side effects or the reverse sequence.



This multicenter, randomized, open label clinical trial enrolled ARV-naïve HIV patients with CD4 counts below 500 cells/mm3. They were randomly assigned to start ddI + d4T + nelfinavir (switching to ZDV + 3TC + NEV in case of failure or toxicity) (PI-NEV arm) or ddI + d4T + nevirapine, switching to ZDV + 3TC + NFV in case of failure or toxicity (NEV-PI arm). The primary study endpoint was the Kaplan-Meier estimates of the time to failure after switching to second regimen if necessary (considering failure as two consecutive plasma HIV-1 RNA determinations above 200 copies/mL, death, a new category C event or toxicity leading to treatment discontinuation of the second regimen) after a minimum follow-up of two years.



A total of 137 patients were evaluable (67 and 70 in the PI-NEV and NEV-PI arms respectively). Baseline characteristics did not differ among groups. Kaplan-Meier estimates of time to failure did not show differences between the two arms neither in the on-treatment (OT) analysis (log rank test, p = 0.81) nor in the intent-to-treat (ITT) analysis (p = 0.58). At 24 months, the estimated proportion of patients free of failure were 72% and 66% respectively in the PI-NEV and NEV-PI arms OT analysis (p = 0.54) and 73% and 64% in the PI-NEV and NEV-PI arms in the ITT analysis (p = 0.49). The difference in the median in CD4+ lymphocyte count at 24 months was not significantly different in the two groups: 393 and 307 CD4 cells/mm3 in the PI-NEV and NEV-PI arms respectively (p = 0.167). The incidence of adverse events (AEs) in the two arms was very similar: 50 (75%) in the PI-NEV and 54 (70%) in the NEV-PI group, as it was for grade 3-4 AEs leading to drug switching.



At two years both treatments strategies (PI-NEV vs NEV-PI) had a high and comparable efficacy and were generally well tolerated.
A protocol and pilot study for managing fibromyalgia with yoga and meditation.

Fibromyalgia is a chronic syndrome characterized by widespread pain, sleep disturbance, stiffness, fatigue, headache, and mood disorders. Recent research has resulted in an improved understanding of fibromyalgia and its possible causes. This article highlights some of the current research, discusses a strategy for using yoga and meditation as a therapy for fibromyalgia sufferers, and presents the results of a preliminary 8-week study using yoga and meditation to help manage fibromyalgia symptoms. The study of 11 participants found significant improvement in the overall health status of the participants and in symptoms of stiffness, anxiety, and depression. Significant improvements were also seen in the reported number of days "felt good" and number of days "missed work" because of fibromyalgia. Nonsignificant improvements were seen in measures of pain, fatigue, and how one felt in the morning. Effect sizes were medium to large for most tested areas. This study supports the benefits of yoga and meditation for individuals with fibromyalgia and encourages further research to explore their use as standard therapies for fibromyalgia.
An untethered shoe with vibratory feedback for improving gait of Parkinson's Patients: The PDShoe

Subjects with Parkinson's disease (PD) often have trouble with ambulation. Some research has shown that auxiliary cueing in the form of vision, audio, or vibration can improve the gait of PD patients. We have developed a new vibratory feedback shoe, known as the PDShoe, which builds on existing research. This device can modulate both frequency and amplitude of feedback for the wearer. It is untethered, and thus can be worn during daily activities. Pressure and tactor status data are transmitted wirelessly over a personal area network to a notebook computer. This computer can also control the tactor actuation and stimulation frequency. This paper describes the details of design and construction of the PDShoe. A preliminary evaluation with four Parkinson's disease subjects and two healthy subjects is included to show the usability of the device.
Gleason score 7 screen-detected prostate cancers initially managed expectantly: outcomes in 50 men.

To assess whether men newly diagnosed with Gleason 7 prostate cancer are eligible for active surveillance (AS) instead of radical treatment. AS is an appropriate initial strategy in selected men who are presently diagnosed with prostate cancer, as many tumours will not progress during a patient's lifetime.  Cancer-specific-, overall and treatment-free survival were analysed retrospectively in men with Gleason score 7 cancer who were initially managed expectantly. All were screen-detected in four centres of the European Randomized Study of Screening for Prostate Cancer.  In 50 men active therapy was initially withheld if they had Gleason 7 disease; 29 of 50 (58%) would otherwise have been suitable for AS, as they had a prostate-specific antigen (PSA) level of < or =10.0 ng/mL, a PSA density of <0.2 ng/mL/mL, stage T1c/T2, and two or fewer positive biopsy-cores; 44 of 50 (88%) had a Gleason score 3 + 4 = 7. The mean (range) age of the men was 69.5 (59.6-76.2) years and the median (interquartile range) follow-up was 2.6 (0.8-5.0) years; the mean American Society of Anesthesiologists score was 1.8. The 6-year cancer-specific survival (nine patients at risk) was 100%, which sharply contrasted with the 68% overall survival. Men alive at the time of analysis had a favourable PSA level and PSA-doubling time. The 6-year treatment-free survival was only 59%, with most patients switching to active therapy, justified on the basis of their PSA level. However, men with otherwise favourable tumour characteristics and a Gleason score of 3 + 4 = 7 remained treatment-free significantly longer than their counterparts with unfavourable other tumour features and a Gleason score of 4 + 3 = 7.  In selected patients with screen-detected Gleason 3 + 4 = 7 prostate cancer, AS might be an option, especially in those with comorbidity and/or a short life-expectancy.
Vitamin D deficiency in community-acquired pneumonia: low levels of 1,25(OH)2 D are associated with disease severity

We aimed to explore the association between vitamin D levels and the severity, mortality and microbiological etiology of community-acquired pneumonia.



Vitamin D levels (both, the reservoir form 25-OH and the activated form 1,25-OH2) of 300 randomly selected patients with community-acquired pneumonia due to pre-specified pathogens included in the German competence network (CAPNETZ) study were measured. Prior to statistical analysis, values of 25-OH and 1,25-OH2 were power-transformed to achieve parametric distribution. All further analyses were performed with seasonally and age adjusted values.



There was only a modest (Spearman Coefficient 0.38) positive correlation between 25-OH and 1,25-OH2. For 1,25-OH2 but not 25-OH, the general linear model revealed a significant inverse correlation between serum concentration and CURB score (p = 0.011). Liver and respiratory co-morbidity were associated with significantly lower 25-OH values and renal co-morbidity with significantly lower 1,25-OH2 values. No significant differences of 1,25-OH2 or 25-OH between different pathogens (influenza virus, Legionella spp., Streptococcus pneumoniae) were detected.



For 1,25-OH2, we found a significant and independent (controlled for age, season and pathogen) negative correlation to pneumonia severity. Therefore, supplementation of non-activated vitamin D to protect from pneumonia may be non-sufficient in patients that have a decreased capacity to hydroxylate 25-OH to 1,25-OH2.
ARM-Seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments

High-throughput RNA sequencing has accelerated discovery of the complex regulatory roles of small RNAs, but RNAs containing modified nucleosides may escape detection when those modifications interfere with reverse transcription during RNA-seq library preparation. Here we describe AlkB-facilitated RNA methylation sequencing (ARM-seq), which uses pretreatment with Escherichia coli AlkB to demethylate N1-methyladenosine (m1A), N3-methylcytidine (m3C) and N1-methylguanosine (m1G), all commonly found in tRNAs. Comparative methylation analysis using ARM-seq provides the first detailed, transcriptome-scale map of these modifications and reveals an abundance of previously undetected, methylated small RNAs derived from tRNAs. ARM-seq demonstrates that tRNA fragments accurately recapitulate the m1A modification state for well-characterized yeast tRNAs and generates new predictions for a large number of human tRNAs, including tRNA precursors and mitochondrial tRNAs. Thus, ARM-seq provides broad utility for identifying previously overlooked methyl-modified RNAs, can efficiently monitor methylation state and may reveal new roles for tRNA fragments as biomarkers or signaling molecules.
Optical coherence tomography assessment of incidence, morphological characteristics, and spontaneous healing course of edge dissections following percutaneous coronary intervention with stent implantation in patients with non-ST segment elevation myocardial infarction.

Stenting-induced edge dissections (ED) can be assessed in detail by optical coherence tomography (OCT). This study sought to investigate the incidence, morphological characteristics, and spontaneous healing course of OCT-identified EDs following drug-eluting stent (DES) implantation in a non-ST segment elevation myocardial infarction (NSTEMI) patient-population.



Acute vessel wall injury at the 5-mm stent adjacent distal and proximal reference segments was assessed by post-procedure OCT and intravascular ultrasound (IVUS) in n=97 NSTEMI-patients (n=97 lesions). Six months OCT follow-up was available in 82 patients (including 35 untreated post-procedure EDs).



The overall incidence of post-procedure OCT-detected ED was 38 per 97 patients (39.2%), and 47 per 182 stent edges (25.8%). None of the EDs were angiographically visualizable, while 10 (21.3%) were visible on concomitant IVUS-analysis. Morphologically, there was a significant difference in plaque type present at ED-edges vs. non-ED-edges when assessed with OCT; (1) lipid-rich and calcified plaques: 80.9% vs. 57.0%, (2) fibrous plaques: 17.0% vs. 26.7%, and (3) normal coronary vessels: 2.1% vs. 16.3%, p<0.01. Plaqueburden, assessed by IVUS, was substantially larger at ED-containing borders: 54.5±10.0% vs. 43.7±11.6%, p=0.01. Three dissections (8.6%) were incompletely healed at 6-month OCT follow-up. None of the EDs caused cardiac events during the 6-month follow-up, however, 1 ED-patient had target lesion revascularization with PCI and DES-implantation in extension of the scheduled OCT-control.



OCT-detected EDs were frequent after stent implantation due to NSTEMI, and the majority of these EDs healed without leading to an adverse prognosis at 6months.
Comparison of everolimus- and sirolimus-eluting stents in patients with long coronary artery lesions: a randomized LONG-DES-III (Percutaneous Treatment of LONG Native Coronary Lesions With Drug-Eluting Stent-III) Trial.

This study compared everolimus-eluting stents (EES) and sirolimus-eluting stents (SES) for long coronary lesions.



Outcomes remain relatively unfavorable for stent-based coronary intervention of lesions with long diseased segments.



This randomized, multicenter, prospective trial compared the use of long EES with SES in 450 patients with long (≥ 25 mm) native coronary lesions. The primary endpoint of the trial was in-segment late luminal loss at 9-month angiographic follow-up.



The EES and SES groups had similar baseline characteristics. Lesion length was 34.0 ± 15.4 mm in the EES group and 34.3 ± 13.5 mm in the SES group (p = 0.85). Nine-month angiographic follow-up was performed in 80% of the EES group and 81% of the SES group (p = 0.69). In-segment late loss as the primary study endpoint was significantly larger in the EES group than in the SES group (0.17 ± 0.41 mm vs. 0.09 ± 0.30 mm, p for noninferiority = 0.96, p for superiority = 0.04). The in-segment binary restenosis rate was also higher in the EES group than in the SES group (7.3% vs. 2.7%, p = 0.046). However, in-stent late loss (0.22 ± 0.43 mm vs. 0.18 ± 0.28 mm, p = 0.29) and in-stent binary restenosis rate (3.9% vs. 2.7%, p = 0.53) were similar among the 2 groups. The incidence of any clinical outcomes (death, myocardial infarction, stent thrombosis, target lesion revascularization, and composite outcomes) was not statistically different between the 2 groups.



For patients with long native coronary artery disease, EES implantation was associated with greater angiographic in-segment late loss and higher rates of in-segment restenosis compared with SES implantation. However, clinical outcomes were both excellent and not statistically different.
The acute hemodynamic response to LV pacing within individual branches of the coronary sinus using a quadripolar lead.

It is not clear whether there is a large difference in acute hemodynamic response (AHR) to left ventricle (LV) pacing in different regions of the same coronary sinus (CS) vein. Using the four electrodes available on a Quartet LV lead, we evaluated the AHR to pacing within individual branches of the CS.



An acute hemodynamic study was attempted in 20 patients. In each patient, we assessed AHR in a number of CS veins and along a significant proportion of each CS branch using three different bipolar configurations. We compared the AHR achieved when pacing using each different vector and also the highest AHR achieved in any position within the same patient with the lowest achieved in that patient.



Sixty-four different CS positions in 19 patients were successfully assessed. No significant difference in AHR was found overall between the three vectors tested. The mean percentage difference in AHR between the CS branch vectors with the lowest and highest dP/dt(max) was +6.5 ± 5.4% (P < 0.001). A much larger difference of +16.9 ± 6.1% (P < 0.001) was seen when comparing the highest and lowest AHR achieved using any vector in any position within the same patient.



A small difference in AHR is seen when pacing within the same branch of the CS compared to pacing in different branches in the same patient. This suggests that although the site of LV lead placement is important, the position within a CS branch is less important than choosing the right vein.
Body composition monitoring and nutrition in maintenance hemodialysis and CAPD patients--a multicenter longitudinal study.

Hydration and nutritional status of end stage renal disease (ESRD) patients are linked to increased morbidity and mortality. Body composition monitoring (BCM) by multi-frequency bioimpedance spectroscopy (MFBS) is considered to be a superior modality of fluid assessment in chronic kidney disease (CKD) dialysis. We did a longitudinal prospective study in South India on maintenance hemodialysis (MHD) and continuous ambulatory peritoneal dialysis (CAPD) patients over 24 months and looked at impact of baseline nutritional parameters and body composition parameters on 24-month mortality. Ninety-nine patients stable on dialysis for at least 3 months were recruited (MHD 85, CAPD 14) at baseline and at 24 months, 41 were alive and 33 had expired, 12 had undergone renal transplant and 13 were lost to follow-up. BCM and nutritional assessment were done at baseline and at follow-up. Baseline overhydration (OH) differed significantly between surviving and dead patients (p < 0.05). Receiver operating characteristic (ROC) curve between OH and mortality showed that the best cut-off point to differentiate between survived and expired patients was 3.15 L. ROC curve for BMI showed lower than cut-off of 22.65 kg/m(2) to predict mortality with sensitivity 41.30% and specificity 81.81%. At follow-up, triceps skin fold thickness (TSF), biceps skin fold thickness (BSF) and mid arm circumference (MAC) increased significantly from baseline (p < 0.001, p = 0.001 and p < 0.001, respectively). Overhydration and BMI are important predictors of mortality in dialysis patients. Improvement in anthropometric markers TSF, BSF and MAC in MHD patients was associated with survival.
Efficacy of a prophylactic epidural blood patch in preventing post dural puncture headache in parturients after inadvertent dural puncture.

Postdural puncture headache (PDPH) occurs in up to 80% of parturients who experience inadvertent dural puncture during epidural catheter placement. The authors performed a randomized double blind study to assess the effect of prophylactic epidural blood patch on the incidence of PDPH and the need for therapeutic epidural blood patch.



Sixty-four parturients who incurred inadvertent dural puncture were randomized to receive a prophylactic epidural blood patch with 20 ml autologous blood (prophylactic epidural blood patch group) or a sham patch (sham group). Subjects were evaluated daily for development of PDPH for a minimum of 5 days after dural puncture. Those who developed a PDPH were followed daily for a minimum of 3 days after resolution of the headache. Subjects with moderate headaches who reported difficulties performing childcare activities and all those with severe headaches were advised to receive a therapeutic epidural blood patch.



Eighteen of 32 subjects in each group (56%) developed PDPH. Therapeutic blood patch was recommended in similar numbers of patients in each group. The groups had similar onset time of PDPH, median peak pain scores, and number of days spent unable to perform childcare activities as a result of postural headache. The median duration of PDPH, however, was shorter in the prophylactic epidural blood patch group.



A decrease in the incidence of PDPH or the need for criteria-directed therapeutic epidural patch was not detected when a prophylactic epidural blood patch was administered to parturients after inadvertent dural puncture. However, prophylactic epidural blood patch did shorten the duration of PDPH symptoms.
Solutions in XML data exchange

The task of XML data exchange is to restructure a document conforming to a source schema under a target schema according to certain mapping rules. The rules are typically expressed as source-to-target dependencies using various kinds of patterns, involving horizontal and vertical navigation, as well as data comparisons. The target schema imposes complex conditions on the structure of solutions, possibly inconsistent with the mapping rules. In consequence, for some source documents there may be no solutions.
 We investigate three problems: deciding if all documents of the source schema can be mapped to a document of the target schema (absolute consistency), deciding if a given document of the source schema can be mapped (solution existence), and constructing a solution for a given source document (solution building).
 We show that the complexity of absolute consistency is rather high in general, but within the polynomial hierarchy for bounded depth schemas. The combined complexity of solution existence and solution building behaves similarly, but the data complexity turns out to be very low.
 In addition to this we show that even for much more expressive mapping rules, based on MSO definable queries, absolute consistency is decidable and data complexity of solution existence is polynomial.
Prospective study on physical activity and risk of in situ breast cancer.

Physical activity has been identified as protective factor for invasive breast cancer risk, whereas comparable studies on in situ carcinoma are rare.



The study included data from 283,827 women of the multinational European Prospective Investigation into C7ancer and Nutrition (EPIC)-cohort study. Detailed information on different types of physical activity conducted during the prior year, such as occupational, recreational, and household activity, as well as on important cofactors, was assessed at baseline. Adjusted HRs for in situ breast cancer were estimated by Cox proportional hazards models.



During a median follow-up period of 11.7 years, 1,059 incidents of breast carcinoma in situ were identified. In crude and adjusted multivariable models, no associations were found for occupational, household, and recreational physical activity. Furthermore, total physical activity was not associated with risk of in situ breast cancer. Comparing moderately inactive, moderately active, and active participants with inactive study participants resulted in adjusted HRs of 0.99 [95% confidence interval (CI), 0.83-1.19], 0.99 (95% CI, 0.82-1.20), and 1.07 (95% CI, 0.81-1.40), respectively (P value of trend test: 0.788). No inverse associations were found in any substrata defined by age at diagnosis or body mass index (BMI) status.



In this large prospective study, we did not find any evidence of an association between physical activity and in situ breast cancer risk. If not by chance, the contrast between our results for carcinoma in situ and the recognized inverse association for invasive breast cancer suggests that physical activity may have stronger effects on proliferation and late stage carcinogenesis.
Neutralizing and binding antibodies to interferon beta in patients with multiple sclerosis: a comparison of assay results from three italian centres.

Interferon (IFN) beta therapy for multiple sclerosis (MS) is associated with the development of binding antibodies (BAbs) and neutralizing antibodies (NAbs) in a percentage of patients. This study investigated the reproducibility of results of two different antibody detection techniques using serum from 100 patients with MS who were receiving IFN beta therapy. Fifty samples were analysed using a commercially available kit-based BAb assay and a further 50 different samples were analysed using a widely used NAb cytopathic effect assay, at three different laboratories. All three centres agreed on the BAb status of all serum samples. However, only 84% agreement was reached on serum NAb status, and there was significant inter-laboratory variation in NAb titre values. Further analysis of these data revealed a correlation between the mean NAb titre and the coefficient of variation of serum samples, indicating greater discordance with higher NAb titres. A significant interlaboratory variation in NAb titres does exist; thus, caution is required when comparing titres from different centres. It is clear that validated detection assays are needed to accurately quantify NAb titres.