LLukas22/scidocs huggingface dataset:
The IDEAL DVT study, individualised duration elastic compression therapy against long-term duration of therapy for the prevention of post-thrombotic syndrome: protocol of a randomised controlled trial

INTRODUCTION
Post-thrombotic syndrome (PTS) is a serious complication of deep vein thrombosis (DVT) of the leg that affects 20-50% of patients. Once a patient experiences PTS there is no treatment that effectively reduces the debilitating complaints. Two randomised controlled trials showed that elastic compression stocking (ECS) therapy after DVT for 24 months can reduce the incidence of PTS by 50%. However, it is unclear whether all patients benefit to the same extent from ECS therapy or what the optimal duration of therapy for individual patients should be. ECS therapy is costly, inconvenient, demanding and sometimes even debilitating. Tailoring therapy to individual needs could save substantial costs. The objective of the IDEAL DVT study, therefore, is to evaluate whether tailoring the duration of ECS therapy on signs and symptoms of the individual patient is a safe and effective method to prevent PTS, compared with standard ECS therapy.


METHODS AND ANALYSIS
A multicentre, single-blinded, allocation concealed, randomised, non-inferiority trial. A total of 864 consecutive patients with acute objectively documented proximal DVT of the leg are randomised to either standard duration of 24 months or tailored duration of ECS therapy following an initial therapeutic period of 6 months. Signs and symptoms of PTS are recorded at regular clinic visits. Furthermore, quality of life, costs, patient preferences and compliance are measured. The primary outcome is the proportion of patients with PTS at 24 months.


ETHICS AND DISSEMINATION
Based on current knowledge the standard application of ECS therapy is questioned. The IDEAL DVT study will address the central questions that remain unanswered: Which individual patients benefit from ECS therapy and what is the optimal individual treatment duration? Primary ethics approval was received from the Maastricht University Medical Centre.


RESULTS
Results of the study will be disseminated via peer-reviewed publications and presentations at scientific conferences.


TRIAL REGISTRATION NUMBER
NCT01429714 and NTR 2597.
A Systematic Evaluation of the Bag-of-Frames Representation for Music Information Retrieval

There has been an increasing attention on learning feature representations from the complex, high-dimensional audio data applied in various music information retrieval (MIR) problems. Unsupervised feature learning techniques, such as sparse coding and deep belief networks have been utilized to represent music information as a term-document structure comprising of elementary audio codewords. Despite the widespread use of such bag-of-frames (BoF) model, few attempts have been made to systematically compare different component settings. Moreover, whether techniques developed in the text retrieval community are applicable to audio codewords is poorly understood. To further our understanding of the BoF model, we present in this paper a comprehensive evaluation that compares a large number of BoF variants on three different MIR tasks, by considering different ways of low-level feature representation, codebook construction, codeword assignment, segment-level and song-level feature pooling, tf-idf term weighting, power normalization, and dimension reduction. Our evaluations lead to the following findings: 1) modeling music information by two levels of abstraction improves the result for difficult tasks such as predominant instrument recognition, 2) tf-idf weighting and power normalization improve system performance in general, 3) topic modeling methods such as latent Dirichlet allocation does not work for audio codewords.
Gaussian Mixture Model-Based Ensemble Kalman Filtering for State and Parameter Estimation for a PMMA Process

Abstract: Polymer processes often contain state variables whose distributions are multimodal; in addition, the models for these processes are often complex and nonlinear with uncertain parameters. This presents a challenge for Kalman-based state estimators such as the ensemble Kalman filter. We develop an estimator based on a Gaussian mixture model (GMM) coupled with the ensemble Kalman filter (EnKF) specifically for estimation with multimodal state distributions. The expectation maximization algorithm is used for clustering in the Gaussian mixture model. The performance of the GMM-based EnKF is compared to that of the EnKF and the particle filter (PF) through simulations of a polymethyl methacrylate process, and it is seen that it clearly outperforms the other estimators both in state and parameter estimation. While the PF is also able to handle nonlinearity and multimodality, its lack of robustness to model-plant mismatch affects its performance significantly.
Can control of soil erosion mitigate water pollution by sediments?

The detrimental impact of sediment and associated pollutants on water quality is widely acknowledged, with many watercourses in the UK failing to meet the standard of 'good ecological status'. Catchment sediment budgets show that hill slope erosion processes can be significant sources of waterborne sediment, with rates of erosion likely to increase given predicted future weather patterns. However, linking on-site erosion rates with off-site impacts is complicated because of the limited data on soil erosion rates in the UK and the dynamic nature of the source-pathway-receptor continuum over space and time. Even so, soil erosion control measures are designed to reduce sediment production (source) and mobilisation/transport (pathway) on hill slopes, with consequent mitigation of pollution incidents in watercourses (receptors). The purpose of this paper is to review the scientific evidence of the effectiveness of erosion control measures used in the UK to reduce sediment loads of hill slope origin in watercourses. Although over 73 soil erosion mitigation measures have been identified from the literature, empirical data on erosion control effectiveness are limited. Baseline comparisons for the 18 measures where data do exist reveal erosion control effectiveness is highly variable over time and between study locations. Given the limitations of the evidence base in terms of geographical coverage and duration of monitoring, performance of the different measures cannot be extrapolated to other areas. This uncertainty in effectiveness has implications for implementing erosion/sediment risk reduction policies, where quantified targets are stipulated, as is the case in the EU Freshwater Fish and draft Soil Framework Directives. Also, demonstrating technical effectiveness of erosion control measures alone will not encourage uptake by land managers: quantifying the costs and benefits of adopting erosion mitigation is equally important, but these are uncertain and difficult to express in monetary terms.
Minimap2: pairwise alignment for nucleotide sequences

Motivation
Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms.


Results
Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of ≥100 bp in length, ≥1 kb genomic reads at error rate ∼15%, full-length noisy Direct RNA or cDNA reads and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions and introduces new heuristics to reduce spurious alignments. It is 3-4 times as fast as mainstream short-read mappers at comparable accuracy, and is ≥30 times faster than long-read genomic or cDNA mappers at higher accuracy, surpassing most aligners specialized in one type of alignment.


Availability and implementation
https://github.com/lh3/minimap2.


Supplementary information
Supplementary data are available at Bioinformatics online.
Age But Not Sex Is Associated With Efficacy and Adverse Events Following Administration of Intravenous Migraine Medication: An Analysis of a Clinical Trial Database.

BACKGROUND
Migraine prevalence is associated with both sex and age. Differences in efficacy of parenteral migraine medication administration based on the sex and age of the patient have not been explored in the published literature.


OBJECTIVE
The objective was to determine whether sex and age are associated with short-term headache relief, sustained headache freedom, or adverse medication effects in data collected during 3 emergency department (ED)-based acute migraine comparative efficacy trials.


METHODS
Data were combined from 3 studies in which patients who presented to an ED with acute migraine were randomized to one of the following intravenous medication regimens: (1) metoclopramide combined with diphenhydramine; (2) metoclopramide combined with diphenhydramine and dexamethasone; (3) metoclopramide alone; (4) ketorolac; or (5) valproate. In each of these studies, (1) short-term efficacy (patient description of the headache as "mild" or "none" 1 hour after medication administration); (2) sustained efficacy (patient description of the headache as "none" within 2 hours of medication administration and no headache recurrence for 24 hours post ED discharge); and (3) the frequency of any adverse medication effects within 24 hours of medication administration was determined. For each of the medication regimens studied, efficacy and adverse event rates were compared between men vs women and the older vs the younger half of patients. Multivariate logistic regression models were constructed in which sex and age were maintained in the model as well as variables representing each of the medication regimens patients received.


RESULTS
A total of 884 patients were included in this analysis (140 men and 744 women). The median age was 35 years. After controlling for age and medication received, female sex was not associated with short-term efficacy (OR 0.98 [95% confidence interval (CI): 0.66, 1.46]), sustained efficacy (OR 0.72 [95%CI: 0.45, 1.15]), or adverse events (OR 1.14 [95%CI: 0.77, 1.71]). Age >36 years, however, was associated with short-term efficacy (OR 0.66 [95%CI: 0.49, 0.88]), sustained efficacy (OR 0.50 [95%CI: 0.34, 0.73]), and adverse events (OR 1.36 [95%CI: 1.02, 1.82]).


CONCLUSION
Sex was not associated with response to parenteral acute migraine medication. Age was associated with both efficacy and adverse events.
Prolonged survival of patients with breast cancer-related leptomeningeal metastases.

BACKGROUND/AIM
Prolonged overall survival (OS) has been reported for selected patients with leptomeningeal metastases (LM). The management and treatment of such patients is poorly-described. We report our experience on breast cancer (BC)-associated LM and patients with prolonged survival.


PATIENTS AND METHODS
Eleven patients with BC and LM had an OS >12 months in which treatment is described.


RESULTS
Combined intra-cerebro spinal fluid (CSF) and systemic treatment were administered until disease progression or toxicity in all but two patients. Involved-field radiotherapy was administered to two patients. Median OS in this selected cohort following LM diagnosis, was 21.0 (range=13-33.3) months.


CONCLUSION
Prolonged OS but also prolonged responses can be observed in BC with LM. An individualized and multi-disciplinary approach is advised for the management of these patients.
Prevalence and predictors of severe acute pancreatitis in patients with acquired immune deficiency syndrome (AIDS)

OBJECTIVE:Recent case control data suggested that a severe course of acute pancreatitis in HIV+ patients was 1) common (50% of cases), 2) poorly predicted by Ranson's criteria (sensitivity 41%), and 3) accurately predicted by a diagnosis of AIDS (positive predictive value 67%). However, the definition of severity included length of stay in hospital and excluded commonly accepted markers (local complications, systemic complications, and need for surgery). The aim of this study was to determine 1) the prevalence of severity and 2) the value of these predictors with regard to severity, as defined by commonly accepted standardized criteria in patients with AIDS and acute pancreatitis.METHODS:A retrospective review identified 50 patients with AIDS exhibiting clinical, laboratory, and/or radiological features of acute pancreatitis.RESULTS:Only five patients followed a severe course as defined by accepted markers. Of these patients, 29 had values available for at least nine of 11 of Ranson's criteria (sensitivity 80%, specificity 54%). Points were awarded most commonly for decreased serum Ca2+ (n = 14) and elevated serum LDH (n = 7).CONCLUSIONS:In patients with AIDS and acute pancreatitis at our institutions, 1) the prevalence of severity and 2) the sensitivity of Ranson's criteria with regard to severity is comparable to that reported in large historical case series of immunocompetent patients. Pseudohypocalcemia and/or elevation in LDH are frequent, likely due to the catabolic infectious disease state.
'A detective look' at hair biopsies from African-American patients.

BACKGROUND
A patient's ethnicity can be an important clue in the diagnosis of scarring alopecia as some disorders such as traction alopecia (TA) and central centrifugal cicatricial alopecia (CCCA) are more prevalent in or exclusive to African-Americans.


OBJECTIVES
To perform a retrospective review of 60 scalp biopsies from African-American patients including 25 cases of CCCA, 22 cases of TA, five cases of frontal fibrosing alopecia, three cases of discoid lupus erythematosus, three cases of hair breakage and two cases of alopecia areata.


METHODS
Serial horizontal and vertical sections were examined.


RESULTS
Features characteristic of the African-American scalp include: golf club-shaped bulb, elliptical shape of the hair shaft, asymmetrical outer root sheath and paired grouping of hair follicles. Clues to the diagnosis of CCCA include: premature desquamation of the inner root sheath, goggles and naked hair shafts in fibrous streamers. Diagnosis of TA is suggested by preserved sebaceous glands along with follicular miniaturization and drop-out.


CONCLUSIONS
The clues reported here aim to help the dermatopathologists to: recognize at a glance that they are dealing with a scalp biopsy from an African-American patient; make the most probable diagnosis by connecting the clues (even if only vertical sections are present); and understand the morphological basis for the susceptibility of the African hair to damage.
Daily morning running for 3 weeks improved sleep and psychological functioning in healthy adolescents compared with controls.

PURPOSE
To compare sleep electroencephalographic patterns and psychological functioning of healthy adolescents running regularly in the mornings with those of control subjects. Although several studies have shown that regular moderate-to-vigorous exercise is related to favorable sleep and psychological functioning in adolescents, research on the effectiveness of short interventions is more limited.


METHODS
Fifty-one adolescents (mean age = 18.30 years; 27 female [53%]) took part in the study; they were randomly assigned either to a running or to a control group. The running group went running every morning for 30 minutes at moderate intensity during weekdays for 3 consecutive weeks. Sleep electroencephalographic patterns and psychological functioning were assessed in both groups before and after the 3-week period. All participants also kept a sleep log for 3 weeks.


RESULTS
Objective sleep improved (slow-wave sleep increased; sleep onset latency decreased) in the running group compared with the control group. Subjective sleep quality, mood, and concentration during the day improved, whereas sleepiness during the day decreased.


CONCLUSIONS
Thirty minutes of running in the morning during weekdays for 3 consecutive weeks impacted positively on sleep and psychological functioning in healthy adolescents compared with control subjects. Running is inexpensive and easy to implement during school schedules, and as both objective and subjective improvements were observed within 3 weeks, regular physical exercise should be promoted.
Phase I trial of volasertib, a Polo-like kinase inhibitor, in Japanese patients with advanced solid tumors

Purpose This trial evaluated the maximum tolerated dose (MTD), safety, pharmacokinetics, and clinical effects of volasertib, a selective Polo-like kinase inhibitor that induces mitotic arrest and apoptosis, in Japanese patients with advanced solid tumors (NCT01348347; 1230.15). Methods In this phase I, open-label, dose-escalation trial, sequential patient cohorts (3 + 3 dose-escalation design) received volasertib (200–350 mg) as a single dose by intravenous infusion over 2 h on day 1 every 21 days until disease progression or unacceptable toxicity. The primary endpoint was the MTD of volasertib in Japanese patients with an advanced solid tumor; secondary endpoints included safety, pharmacokinetics, and clinical benefit. Results Fifteen patients with an advanced solid tumor were treated. Dose-limiting toxicities of grade 4 neutropenia for ≥7 days and grade 4 thrombocytopenia were both experienced by 2/6 patients in the 350 mg cohort. The MTD of volasertib in Japanese patients was 300 mg. The most common (≥3 patients) drug-related non-hematologic adverse events included fatigue, decreased appetite, and nausea. Exposure to volasertib and its metabolite increased with increasing doses. A partial response in a patient with gastric cancer and stable disease in eleven patients were observed. Conclusions Volasertib had a manageable safety profile up to the MTD determined as 300 mg. Exposure to volasertib and its metabolite increased with increasing doses. The safety profile of volasertib in Japanese patients is comparable with those previously obtained in Caucasian patients. These data support enrollment of Japanese patients in global clinical trials without dose modification.
Trends in vehicle concept and key technology development for hybrid and battery electric vehicles

This paper examines the state-of-the-art and trends in vehicle concept as well as key technology development in the context of electric mobility in a time frame from 2002 until 2012. Thus, an extensive vehicle concept database was designed, covering detailed technical specifications of more than 200 electrified vehicles in 3 different world regions, also considering different stages in vehicle development. By analyzing and comparing over 75 different market- and technology-oriented parameters per vehicle, sophisticated statements for the state-of-the-art and development trends of Hybrid and Battery Electric Vehicles are identified. Results in this paper illustrate trends for Hybrid and Battery Electric Vehicle concept development with a focus on vehicle development stages, vehicle segments and powertrain architectures. On the other hand, state-of-the-art and trends for the development of two electric mobility key technologies are pointed out: Batteries and electric machines. Statements here are made for developments in terms of battery and electric machine technology, installation place, as well as technical parameters like energy capacity and power density. Key results illustrate e.g. a trend towards the use of front and rear axle motors, a more than doubled average electric machine power density with over 1,0kW/kg and an average BEV battery capacity of 19Wh per kg vehicle mass in 2012.
Motor control exercise for symptomatic lumbar disc herniation: protocol for a systematic review and meta-analysis

INTRODUCTION
Lumbar disc herniation (LDH) is a common condition in adults and can impose a heavy burden on both the individual and society. It is defined as displacement of disc components beyond the intervertebral disc space. Various conservative treatments have been recommended for the treatment of LDH and physical therapy plays a major role in the management of patients. Therapeutic exercise is effective for relieving pain and improving function in individuals with symptomatic LDH. The aim of this systematic review is to evaluate the effectiveness of motor control exercise (MCE) for symptomatic LDH.


METHODS AND ANALYSIS
We will include all clinical trial studies with a concurrent control group which evaluated the effect of MCEs in patients with symptomatic LDH. We will search PubMed, SCOPUS, PEDro, SPORTDiscus, CINAHL, CENTRAL and EMBASE with no restriction of language. Primary outcomes of this systematic review are pain intensity and functional disability and secondary outcomes are functional tests, muscle thickness, quality of life, return to work, muscle endurance and adverse events. Study selection and data extraction will be performed by two independent reviewers. The assessment of risk of bias will be implemented using the PEDro scale. Publication bias will be assessed by funnel plots, Begg's and Egger's tests. Heterogeneity will be evaluated using the I2 statistic and the χ2 test. In addition, subgroup analyses will be conducted for population and the secondary outcomes. All meta-analyses will be performed using Stata V.12 software.


ETHICS AND DISSEMINATION
No ethical concerns are predicted. The systematic review findings will be published in a peer-reviewed journal and will also be presented at national/international academic and clinical conferences.


TRIAL REGISTRATION NUMBER
CRD42016038166.
Effects of early pregnancy BMI, mid-gestational weight gain, glucose and lipid levels in pregnancy on offspring’s birth weight and subcutaneous fat: a population-based cohort study

BACKGROUND
Maternal glucose and lipid levels are associated with neonatal anthropometry of the offspring, also independently of maternal body mass index (BMI). Gestational weight gain, however, is often not accounted for. The objective was to explore whether the effects of maternal glucose and lipid levels on offspring's birth weight and subcutaneous fat were independent of early pregnancy BMI and mid-gestational weight gain.


METHODS
In a population-based, multi-ethnic, prospective cohort of 699 women and their offspring, maternal anthropometrics were collected in gestational week 15 and 28. Maternal fasting plasma lipids, fasting and 2-hour glucose post 75 g glucose load, were collected in gestational week 28. Maternal risk factors were standardized using z-scores. Outcomes were neonatal birth weight and sum of skinfolds in four different regions.


RESULTS
Mean (standard deviation) birth weight was 3491 ± 498 g and mean sum of skinfolds was 18.2 ± 3.9 mm. Maternal fasting glucose and HDL-cholesterol were predictors of birth weight, and fasting and 2-hour glucose were predictors of neonatal sum of skinfolds, independently of weight gain as well as early pregnancy BMI, gestational week at inclusion, maternal age, parity, smoking status, ethnic origin, gestational age and offspring's sex. However, weight gain was the strongest independent predictor of both birth weight and neonatal sum of skinfolds, with a 0.21 kg/week increased weight gain giving a 110.7 (95% confidence interval 76.6-144.9) g heavier neonate, and with 0.72 (0.38-1.06) mm larger sum of skinfolds. The effect size of mother's early pregnancy BMI on birth weight was higher in non-Europeans than in Europeans.


CONCLUSIONS
Maternal fasting glucose and HDL-cholesterol were predictors of offspring's birth weight, and fasting and 2-hour glucose were predictors of neonatal sum of skinfolds, independently of weight gain. Mid-gestational weight gain was a stronger predictor of both birth weight and neonatal sum of skinfolds than early pregnancy BMI, maternal glucose and lipid levels.