LLukas22/scidocs huggingface dataset:
Agarose Gel Size Selection for DNA Sequencing Libraries.

Agarose gel electrophoresis may be used to purify fragmented genomic DNA after ligation of adaptors. After electrophoresis, the region of the gel containing the desired size range of DNA is excised, and the DNA is subsequently extracted from the gel and purified by passage through a spin column.
Source Separation of Convolutive and Noisy Mixtures Using Audio-Visual Dictionary Learning and Probabilistic Time-Frequency Masking

In existing audio-visual blind source separation (AV-BSS) algorithms, the AV coherence is usually established through statistical modelling, using e.g., Gaussian mixture models (GMMs). These methods often operate in a low-dimensional feature space, rendering an effective global representation of the data. The local information, which is important in capturing the temporal structure of the data, however, has not been explicitly exploited. In this paper, we propose a new method for capturing such local information, based on audio-visual dictionary learning (AVDL). We address several challenges associated with AVDL, including cross-modality differences in size, dimension and sampling rate, as well as the issues of scalability and computational complexity. Following a commonly employed bootstrap coding-learning process, we have developed a new AVDL algorithm which features, a bimodality balanced and scalable matching criterion, a size and dimension adaptive dictionary, a fast search index for efficient coding, and cross-modality diverse sparsity. We also show how the proposed AVDL can be incorporated into a BSS algorithm. As an example, we consider binaural mixtures, mimicking aspects of human binaural hearing, and derive a new noise-robust AV-BSS algorithm by combining the proposed AVDL algorithm with Mandel's BSS method, which is a state-of-the-art audio-domain method using time-frequency masking. We have systematically evaluated the proposed AVDL and AV-BSS algorithms, and show their advantages over the corresponding baseline methods, using both synthetic data and visual speech data from the multimodal LILiR Twotalk corpus.
Code Switch Point Detection in Arabic

This paper introduces a dual-mode stochastic system to automatically identify linguistic code switch points in Arabic. The first of these modes determines the most likely word tag (i.e. dialect or modern standard Arabic) by choosing the sequence of Arabic word tags with maximum marginal probability via lattice search and 5-gram probability estimation. When words are out of vocabulary, the system switches to the second mode which uses a dialectal Arabic (DA) and modern standard Arabic (MSA) morphological analyzer. If the OOV word is analyzable using the DA morphological analyzer only, it is tagged as “DA”, if it is analyzable using the “MSA” morphological analyzer only, it is tagged as MSA, otherwise if analyzable using both of them, then it is tagged as “both”. The system yields an Fβ=1 score of 76.9% on the development dataset and 76.5% on the held-out test dataset, both judged against human-annotated Egyptian forum data.
Quaternary dynamics of the SecA motor drive translocase catalysis.

Most secretory preproteins exit bacterial cells through the protein translocase, comprising the SecYEG channel and the dimeric peripheral ATPase motor SecA. Energetic coupling to work remains elusive. We now demonstrate that translocation is driven by unusually dynamic quaternary changes in SecA. The dimer occupies several successive states with distinct protomer arrangements. SecA docks on SecYEG as a dimer and becomes functionally asymmetric. Docking occurs via only one protomer. The second protomer allosterically regulates downstream steps. Binding of one preprotein signal peptide to the SecYEG-docked SecA protomer elongates the SecA dimer and triggers the translocase holoenzyme to obtain a lower activation energy conformation. ATP hydrolysis monomerizes the triggered SecA dimer, causing mature chain trapping and processive translocation. This is a unique example of one protein exploiting quaternary dynamics to become a substrate receptor, a "loading clamp," and a "processive motor." This mechanism has widespread implications on protein translocases, chaperones, and motors.
Composition operators on Hardy-Orlicz spaces

We investigate composition operators on Hardy-Orlicz spaces when the Orlicz function Ψ grows rapidly: compactness, weak compactness, to be psumming, order bounded, . . . , and show how these notions behave according to the growth of Ψ. We introduce an adapted version of Carleson measure. We construct various examples showing that our results are essentially sharp. In the last part, we study the case of Bergman-Orlicz spaces. Mathematics Subject Classification. Primary: 47 B 33 – 46 E 30; Secondary: Key-words. Bergman-Orlicz space – Carleson measure – composition operator – Hardy-Orlicz space
Is oxaliplatin combined with weekly bolus 5-fluorouracil and leucovorin an option for stage II and III colon cancer?

BACKGROUND The Multicenter International Study of Oxaliplatin/5-Fluorouracil, Leucovorin in the Adjuvant Treatment of Colon Cancer (MOSAIC) study reported that the addition of oxaliplatin to a regimen of bolus and continuous-infusion 5-fluorouracil (5-FU) combined with leucovorin (LV)—the FOLFOX4 regimen—improved 3-year disease-free survival (DFS) in comparison with FULV (5-FU and LV administered alone).
Modeling and Control of a Grid-connected Wind/PV Hybrid Generation System

This paper deals with power control of a wind and solar hybrid generation system for interconnection operation with electric distribution system. The proposed system consists of a variable-speed direct-drive wind generator, wind-side converter, solar array, dc-dc converter and grid interface inverter. Power control strategy is to extract the maximum energy available from varying condition of wind speed and solar irradiance while maintaining power quality at a satisfactory level. In order to capture the maximum power, variable speed control is employed for wind turbine and maximum power point tracking is applied for photovoltaic system. The grid interface inverter transfers the energy drawn from the wind turbine and PV array into the grid by keeping common dc voltage constant. Modeling and simulation study on the entire control scheme is carried out using a power system transient analysis tool, PSCAD/EMTDC. The simulation results show the control performance and dynamic behavior of the wind/PV system
Anisotropic analysis of multi-component T2 and T1ρ relaxations in achilles tendon by NMR spectroscopy and microscopic MRI.

PURPOSE
To study the anisotropic characteristics of both multi-component T2 and T1ρ relaxation times in tendon.


MATERIALS AND METHODS
T2 and T1ρ were measured in tendon by NMR spectroscopy at different orientations and by microscopic MRI at the magic angle. Several experimental issues in the multi-component relaxation measurements were investigated, including the effects of echo spacing, the resolution of MRI experiments, the influence of the specimen orientations, and the strengths of different spin-lock frequencies in T1ρ experiments.


RESULTS
Both the values and fractions of T2 in tendon showed significant orientational dependence. The values and fractions of T1ρ strongly depended on both the specimen orientation and the spin-lock strength. The imaging resolution (35-280 μm) had little influence in the T2 experiments. Both the echo spacings (0.6-3.0 ms) in the T2 experiment and the spin-lock strengths (0.5-5 kHz) in the T1ρ experiment affected the quantification of the multi-component relaxation. Up to three T2 and T1ρ components were resolved in tendon.


CONCLUSION
Multi-component relaxations could be attributed to different populations of water in the tissue. The transitions between a mono-component and multi-component result call for the caution in interpreting the relaxation results.
Empirical evaluation of the revised end user computing acceptance model

This paper proposed a revised technology acceptance model for measuring end user computing (EUC) acceptance. An empirical study was conducted to collect data. This data was empirically used to test the proposed research model. The structural equation modeling technique was used to evaluate the causal model and confirmatory factor analysis was performed to examine the reliability and validity of the measurement model. The results demonstrate that the model explains 56% of the variance. This finding contributes to an expanded understanding of the factors that promote EUC acceptance. The implication of this work to both researchers and practitioners is discussed. 2004 Elsevier Ltd. All rights reserved.
Teachers' participation in research programs improves their students' achievement in science.

Research experience programs engage teachers in the hands-on practice of science. Program advocates assert that program participation enhances teachers' skills in communicating science to students. We measured the impact of New York City public high-school science teachers' participation in Columbia University's Summer Research Program on their students' academic performance in science. In the year before program entry, students of participating and nonparticipating teachers passed a New York State Regents science examination at the same rate. In years three and four after program entry, participating teachers' students passed Regents science exams at a rate that was 10.1% higher (P = 0.049) than that of nonparticipating teachers' students. Other program benefits include decreased teacher attrition from classroom teaching and school cost savings of U.S. $1.14 per $1 invested in the program.
Treatment response to a second or third TNF-inhibitor in RA: results from the South Swedish Arthritis Treatment Group Register.

OBJECTIVES
To study treatment response rates of RA patients undergoing second- and third-line anti-TNF therapy and to identify baseline predictors of response to second-line treatment.


METHODS
RA patients monitored in a prospective, observational study, having switched anti-TNF therapy once (first-time switchers, n = 337) or twice (second-time switchers, n = 36)--i.e. following failures with one antibody- and one receptor-type agent--between March 1999 and December 2006, were studied. Treatment responses at 3 months were assessed by the ACR and European League Against Rheumatism (EULAR) response criteria. Predictive potentials for response to second-line treatment of demographics, baseline disease activity measures, disease and treatment characteristics were analysed using logistic regression.


RESULTS
ACR20 response was met by 51% of first-time and 35% of second-time switchers. Corresponding ACR50 rates were 27 and 18%; EULAR overall rates (EULAR good or moderate response) 71 and 58%; EULAR good rates 25 and 9% and 28-joint disease activity score (DAS28) remission rates 16 and 6%. Identified baseline predictors of response to second-line treatment were lower age and HAQ scores, elevated DAS28 values and having ceased the former anti-TNF treatment due to adverse events rather than inefficacy. No variable was predictive for all examined response criteria.


CONCLUSIONS
Response rates of first-time anti-TNF switchers are somewhat below those of anti-TNF naïve RA patients, while the markedly inferior response rates of second-time switchers suggest other therapeutic options to be considered in this situation. Identified baseline predictors of response may be useful indicators to second-line anti-TNF therapy, but vary depending on the response criteria set studied.
Effect of weight loss on markers of triglyceride-rich lipoprotein metabolism in the metabolic syndrome.

BACKGROUND
Hypertriglyceridaemia, a consistent feature of dyslipidaemia in the metabolic syndrome (MetS), is related to the extent of abdominal fat mass and altered adipocytokine secretion. We determined the effect of weight loss by dietary restriction on markers of triglyceride-rich lipoprotein (TRL) metabolism and plasma adipocytokines.


DESIGN
Thirty-five men with MetS participated in a 16 week randomized controlled dietary intervention study. Apolipoprotein (apo) C-III, apoB-48, remnant-like particle (RLP)-cholesterol, total adiponectin, high-molecular weight (HMW) adiponectin, and retinol-binding protein-4 (RBP-4) concentrations were measured using immunoassays.


RESULTS
Compared with weight maintenance (n = 15), weight loss (n = 20) significantly decreased body weight, plasma insulin, triglycerides, total cholesterol, low-density lipoprotein (LDL)-cholesterol and lathosterol (P < 0.05). Weight loss also decreased plasma concentrations of apoC-III (-33%), apoB-48 (-37%), very low-density lipoprotein (VLDL)-apoB (-43%), RLP-cholesterol (-48%), and RBP-4 (-20%), and significantly increased plasma total (+20%) and HMW-adiponectin (+19%) concentrations. In the weight loss group, reduction in plasma apoC-III was associated (P < 0.05) with reduction in plasma apoB-48, VLDL-apoB, RLP-cholesterol and triglycerides. Increase in total adiponectin was associated (P < 0.05) with the reduction in plasma VLDL-apoB and triglycerides. The changes in HMW-adiponectin and RBP-4 were not associated with changes in plasma apoB-48, apoC-III, VLDL-apoB, RLP-cholesterol or triglycerides. In multiple regression analysis including changes in visceral fat, insulin and total adiponectin concentrations, the fall in plasma apoC-III concentration was an independent predictor of the reductions in plasma apoB-48, VLDL-apoB, RLP-cholesterol and triglycerides concentrations.


CONCLUSIONS
In men with MetS, weight loss decreases the plasma concentrations of apoB-48, VLDL-apoB, RLP-cholesterol and triglycerides. This effect could partly relate to concomitant changes in plasma apoC-III and adiponectin concentrations that accelerate the catabolism of TRLs.
Use of sodium thiosulphate in a multi-interventional setting for the treatment of calciphylaxis in dialysis patients.

BACKGROUND
Calciphylaxis is a life-threatening complication in patients with end-stage renal disease (ESRD). No established therapy exists so far. The aim of the present study was to determine the therapeutic response to a multi-interventional treatment regimen with consistent use of sodium thiosulphate (STS) in an Austrian cohort of calciphylaxis patients.


METHODS
We retrospectively collected demographic, clinical and laboratory data on 27 calciphylaxis patients treated with STS at seven Austrian dialysis centres between June 2004 and November 2010.


RESULTS
Twenty-seven dialysis patients (68 ± 12 years) were treated with STS for a median (25th, 75th percentile) of 96 (54, 133) days. Seven patients (26%) suffered from proximal-type, and 20 patients (74%) from distal-type calciphylaxis. Fourteen patients (52%) showed a complete remission, five patients (19%) a partial remission and eight patients (30%) progression that resulted in amputation in four patients. During a median follow-up of 101 (79, 273) days, 14 patients died (52%). Non-survivors were older (P = 0.04), showed higher CRP values (P = 0.04), presented more frequently with proximal-type calciphylaxis (P = 0.03), had a higher disease severity score at diagnosis (P = 0.01), were treated more often with antibiotics (P = 0.01) and cinacalcet (P = 0.03) and had a lower remission rate during treatment (P = 0.004) than did survivors. The use of antibiotics and cinacalcet, disease severity at diagnosis and remission rates were found to be significant survival predictors in logistic regression analysis.


CONCLUSIONS
Calciphylaxis remains a serious complication with high mortality. Early and consistent therapy including STS may help to improve the disease outcome.
How human perceptions of Mura affect LCD market values

Liquid crystal displays (LCDs) hold a large share of the flat-panel display market because LCDs offer advantages such as low power consumption, low radiation, and good image quality. However, image defects, such as spotlight, uniformity, and Mura defects, can impair the quality of an LCD. This research examined human perceptions of region-Mura and used Response Time and subjective markdown price to indicate the various severity levels of region-Mura that appeared at different display locations. The results indicate that, within a specific Mura Level range, the Mura’s location has a considerable impact on perceived quality (p < 0.001). Mura on the centers of LCDs have more impact than Mura on the corners of LCDs. Not all peripheral Mura were considered to be equal; participants chose different price markdown prices for LCDs with Mura in lower corners than they chose for LCDs with Mura in upper corners. These findings suggest that a manufacturer should establish a scraping threshold for LCDs based on information regarding Mura location to avoid the production waste from scrapping those LCDs, and should rotate the panel to position the most severe Mura in the lower part of the display to obtain a better perceived quality. 2011 Elsevier B.V. All rights reserved.
MEAD - A Platform for Multidocument Multilingual Text Summarization

Abstract This paper describes the functionality of MEAD, a comprehensive, public domain, open source, multidocument multilingual summarization environment that has been thus far downloaded by more than 500 organizations. MEAD has been used in a variety of summarization applications ranging from summarization for mobile devices to Web page summarization within a search engine and to novelty detection.
Treatment of venous thromboembolism with the oral thrombin inhibitor, ximelagatran.

BACKGROUND
Venous thromboembolic diseases are treated initially with low molecular weight heparin followed by oral coumarins.


OBJECTIVES
To investigate an orally available direct thrombin inhibitor for the acute treatment of venous thromboembolism as well as for prophylaxis of recurrent events.


METHODS
The direct thrombin inhibitor ximelagatran was compared with subcutaneous LMW heparins followed by oral warfarin in a double-blind randomized prospective multicenter trial in patients with acute VTE. A pharmacokinetic study was performed in the VTE patients. For assessing the prevention of recurrent VTE, double-blind prospective randomized studies were conducted as follows: a) ximelagatran compared to warfarin for 6 months, and b) prolonged anticoagulation of ximelagatran vs. placebo for 18 months after termination of 6 months coumarin therapy.


RESULTS
Two dose-finding studies and the pharmacokinetic analysis of ximelagatran in acute VTE were completed. About 2,500 patients were randomized to investigate 2 x 36 mg ximelagatran versus 2 x 1 mg/kg body weight enoxaparin followed by warfarin. The study hypothesized that the efficacy was equal in both treatment regimens for recurrent VTE documented by objective methods. The second study, with 1,234 patients, aimed to demonstrate a reduced incidence of recurrent thromboembolic events documented by objective methods after 18 months of treatment with 2 x 24 mg ximelagatran daily compared to placebo.


CONCLUSION
These large-scale clinical trials will soon yield the results of the comparison between oral ximelagatran and subcutaneous LMW heparin for treatment of acute VTE, and of warfarin for prophylaxis of recurrent events for 6 months and for a prolonged prophylaxis for another 18 months.
Risk factors related to the presence and severity of hot flushes in mid-aged Ecuadorian women.

BACKGROUND
Several studies drawn from the Ecuadorian population have previously reported that more than half of mid-aged women present hot flushes, which can impair their quality of life. However up-to-date risk factors for their presence and severity have not been assessed.


OBJECTIVE
To assess hot flush frequency and intensity and related risk factors among middle-aged Ecuadorian women.


METHODS
In this cross-sectional study, 1154 healthy women aged 40-59 years, visiting healthcare centers of eight main cities of Ecuador with more than 100,000 inhabitants, were assessed with the first item of the Menopause Rating Scale (MRS) and a questionnaire containing female and partner socio-demographic data.


RESULTS
Mean age of the entire sample was 48.8+/-5.6 years (median 48), a 48.7% had 12 or less years of schooling, 52.8% were postmenopausal, 43.6% lived at high altitude, 56.8% were married and 10% were on hormonal therapy (HT). Hot flushes accounted for 56% (n=646) of the whole sample, of which 29.1% and 9.1% were respectively graded as severe and very severe. Logistic regression determined that female sedentarism (OR: 2.42, CI 95% [1.63-3.59]), accessing a free healthcare system (OR: 1.96, CI 95% [1.30-2.96]), living at high altitude (OR: 1.82, CI 95% [1.14-2.90]) and having a partner abusing alcohol (OR: 1.92, CI 95% [1.09-3.35]) were significant risk factors related to the presence of hot flushes. The regression model also determined that among women with hot flushes (n=646), sedentarism (OR: 1.73, CI 95% [1.14-2.62]) and having a partner with erectile dysfunction (OR: 2.57, CI 95% [1.44-4.59]) were significant risk factors related to severe/very severe hot flushes whereas married status (OR: 0.53, CI 95% [0.32-0.86]), living at high altitude (OR: 0.46, CI 95% [0.26-0.78]) and partner healthiness (OR: 0.59, CI 95% [0.36-0.95]) were not.


CONCLUSION
To the best of our knowledge this is the first and largest study assessing hot flushes in a mid-aged Ecuadorian population. We found that the presence and severity were not significantly related to age and hormonal status yet to other individual female/male characteristics and the demography of the studied population.
Early tumor necrosis factor α antagonist therapy in everyday practice for inflammatory back pain suggesting axial spondyloarthritis: results from a prospective multicenter french cohort.

OBJECTIVE
To determine the frequency of and factors associated with early tumor necrosis factor α (TNFα) antagonist therapy in everyday clinical practice in patients with suspected axial spondyloarthropathy (SpA).


METHODS
We used data from the prospective observational study in the French Devenir des Spondylarthropathies Indifférenciées Récentes (DESIR; Outcome of Recent Undifferentiated Spondylarthropathies) cohort of 708 patients with recent-onset (<3 years) inflammatory back pain (IBP) suggesting axial SpA. TNFα antagonist use was recorded at months 6 and 12 and factors independently associated with TNFα antagonist therapy were identified by multivariate logistic regression.


RESULTS
Among the 708 patients (mean age 33.8 years, 46.2% men), 166 (23.4%) patients received TNFα antagonist therapy by month 12, including 120 (73.6%) patients who fulfilled Assessment of SpondyloArthritis international Society (ASAS) axial criteria and 157 (94.6%) who fulfilled at least 1 SpA criteria set; 109 (65.6%) had no sacroiliitis. Factors independently associated with early TNFα antagonist therapy were high Ankylosing Spondylitis Disease Activity Score using the C-reactive protein level (odds ratio [OR]1-point increase 1.60, 95% confidence interval [95% CI] 1.25-2.03, P < 0.001), high physician's global disease activity score (OR 1.37, 95% CI 1.21-1.54, P < 0.001), ASAS nonsteroidal antiinflammatory drug score >50 (OR 1.88, 95% CI 1.24-2.87, P = 0.003), current or past disease-modifying antirheumatic drug use (OR 2.09, 95% CI 1.22-3.59, P = 0.008), systemic corticosteroid use (OR 2.48, 95% CI 1.43-4.34, P = 0.002), and mild to severe radiographic hip abnormalities (OR 9.43, 95% CI 2.11-42.09, P = 0.003). After adjustment on these factors, Achilles enthesis hypervascularization by power Doppler and number of work days missed were associated with TNFα antagonist therapy.


CONCLUSION
In the DESIR cohort, approximately one-fourth of patients with recent IBP suggestive of axial SpA were under anti-TNFα therapy after 1 year of followup. All factors associated with this early initiation reflected higher disease activity, refractoriness, or severity, which suggests compliance of French rheumatologists with current treatment guidelines.