bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vegetarianism, low meat consumption and the risk of colorectal cancer in a population based cohort study
Authors: Gilsing Anne M. J. , Schouten Leo J. , Goldbohm R. Alexandra , Dagnelie Pieter C. , van den Brandt Piet A. , Weijenberg Matty P. 
Published: August 2015

AbstractTo study how a vegetarian or low meat diet influences the risk of colorectal cancer compared to a high meat diet and to assess the explanatory role of factors associated with these diets. In the Netherlands Cohort Study – Meat Investigation Cohort (NLCS-MIC) (cohort of 10,210 individuals including 1040 self-defined vegetarians), subjects completed a baseline questionnaire in 1986, based on which they were classified into vegetarians (n = 635), pescetarians (n = 360), 1 day/week- (n = 1259), 2–5 day/week- (n = 2703) and 6-7 day/week meat consumers (n = 5253). After 20.3 years of follow-up, 437 colorectal cancer cases (307 colon, 92 rectal) were available. A non-significantly decreased risk of CRC for vegetarians, pescetarians and 1 day/week compared to 6-7 day/week meat consumers was observed (age/sex adjusted Hazard Ratios (HR): 0.73(0.47–1.13), 0.80(0.47–1.39) and 0.72(0.52–1.00), respectively). Most of the differences in HR between these groups could be explained by intake of dietary fiber and soy products. Other (non-)dietary factors characteristic for a vegetarian or low meat diet had negligible individual effects, but attenuated the HRs towards the null when combined. Vegetarians, pescetarians and 1 day/week meat eaters showed a non-significantly decreased risk of colorectal cancer compared to 6-7 day/week meat consumers, mainly due to differences in dietary pattern other than meat intake.
Involvement of normalized NMDA receptor and mTOR-related signaling in rapid antidepressant effects of Yueju and ketamine on chronically stressed mice
Authors: Tang Juanjuan , Xue Wenda , Xia Baomei , Ren Li , Tao Weiwei , Chen Chang , Zhang Hailou , Wu Ruyan , Wang Qisheng , Wu Haoxin , Duan Jinao , Chen Gang 
Published: August 2015

AbstractYueju, a Traditional Chinese Medicine formula, exhibited fast-onset antidepressant responses similar to ketamine. This study focused on assessing the rapid and persistent antidepressant efficacy of Yueju and ketamine in chronically stressed mice and its association with alternations in prefrontal N-methyl-D-aspartate (NMDA) receptor and mammalian target of rapamycin (mTOR)-related activity. Chronic mild stress (CMS) led to deficits in sucrose preference test (SPT), forced swim test, tail suspension test and novelty-suppressed feeding test, which were improved differently by acute Yueju or ketamine administration. The improvement in SPT started as soon as 2 hours post Yueju and ketamine but lasted for 6 days only by Yueju. Body weight was regained by Yueju more than ketamine at post-drug administration day (PAD) 6. CMS decreased phosphorylation of the mTOR effectors 4E-BP1 and p70S6K, their upstream regulators ERK and Akt and downstream targets including synaptic protein GluR1. Yueju or ketamine reversed these changes at PAD 2, but only Yueju reversed phosphor-Akt at PAD 6. CMS selectively and lastingly increased NMDA receptor subunit NR1 expression, which was reversed by ketamine or Yueju at PAD 2 but only by Yueju at PAD 6. These findings suggest that NR1 and Akt/mTOR signaling are important therapeutic targets for depression.
Solution structure of the transmembrane domain of the mouse erythropoietin receptor in detergent micelles
Authors: Li Qingxin , Lei Wong Ying , Yueqi Lee Michelle , Li Yan , Kang CongBao 
Published: August 2015

AbstractErythropoiesis is regulated by the erythropoietin receptor (EpoR) binding to its ligand. The transmembrane domain (TMD) and the juxtamembrane (JM) regions of the EpoR are important for signal transduction across the cell membrane. We report a solution NMR study of the mouse erythropoietin receptor (mEpoR) comprising the TMD and the JM regions reconstituted in dodecylphosphocholine (DPC) micelles. The TMD and the C-terminal JM region of the mEpoR are mainly α-helical, adopting a similar structure to those of the human EpoR. Residues from S216 to T219 in mEpoR form a short helix. Relaxation study demonstrates that the TMD of the mEpoR is rigid whilst the N-terminal region preceding the TMD is flexible. Fluorescence spectroscopy and sequence analysis indicate that the C-terminal JM region is exposed to the solvent. Helix wheel result shows that there is hydrophilic patch in the TMD of the mEpoR formed by residues S231, S238 and T242 and these residues might be important for the receptor dimerization.
Hydrogel Walkers with Electro-Driven Motility for Cargo Transport
Authors: Yang Chao , Wang Wei , Yao Chen , Xie Rui , Ju Xiao-Jie , Liu Zhuang , Chu Liang-Yin 
Published: August 2015

AbstractIn this study, soft hydrogel walkers with electro-driven motility for cargo transport have been developed via a facile mould-assisted strategy. The hydrogel walkers consisting of polyanionic poly(2-acrylamido-2-methylpropanesulfonic acid-co-acrylamide) exhibit an arc looper-like shape with two “legs” for walking. The hydrogel walkers can reversibly bend and stretch via repeated “on/off” electro-triggers in electrolyte solution. Based on such bending/stretching behaviors, the hydrogel walkers can move their two “legs” to achieve one-directional walking motion on a rough surface via repeated “on/off” electro-triggering cycles. Moreover, the hydrogel walkers loaded with very heavy cargo also exhibit excellent walking motion for cargo transport. Such hydrogel systems create new opportunities for developing electro-controlled soft systems with simple design/fabrication strategies in the soft robotic field for remote manipulation and transportation.
Low‐quiescent‐current flexible mode buck–boost converter
Authors: Cheng Li‐Ye , Lai Xinquan , Shi Ling‐Feng 
Published: August 2015

In this study, a mode‐flexible buck/boost converter with four operation modes aiming at improving efficiency and extending battery life in portable devices is proposed. When the battery supply decreases or increases, the transition is smooth and the mode can be chosen flexible. High efficiency is obtained because of the introduction of buck–boost mode in pulse‐width modulation and the burst mode under light load. The converter can work in an appropriate mode according to the current sensing block, which is suitable for lithium battery and power bank. Whole chip obtains 35 μA low‐quiescent current in standby mode and 45 μA low‐quiescent current in burst mode. Experimental results show that the peak efficiency is 95% at an output 1 A when the supply voltage is 4.2 V. The peak output ripple is 60 mV in BURST mode and 20 mV in constant current mode.
C5orf30 is a negative regulator of tissue damage in rheumatoid arthritis
Authors: Muthana Munitta , Hawtree Sarah , Wilshaw Adam , Linehan Eimear , Roberts Hannah , Khetan Sachin , Adeleke Gbadebo , Wright Fiona , Akil Mohammed , Fearon Ursula , Veale Douglas , Ciani Barbara , Wilson Anthony G. 
Published: August 2015

SignificanceRecent studies have reported genetic association of chromosome 5 open reading frame 30 (C5orf30) with both rheumatoid arthritis (RA) susceptibility and the severity of radiological damage to joints. The gene is expressed in vertebrate genomes with a high degree of conservation, implying a central function in these organisms. Here, we report that C5orf30 encodes a 206-aa protein that is highly expressed in RA synovial fibroblasts (RASFs), a cell type implicated in causing joint damage. Importantly inhibition of C5orf30 increases the autoaggressive phenotype of RASFs in vitro and increases joint inflammation and damage in murine inflammatory arthritis. Our data reveals C5orf30 to be a negative regulator of tissue breakdown modulating the autoaggressive phenotype that is characteristic of RASFs.
Feeding and Growth of Larval Pacific Lamprey Reared in Captivity
Authors: Jolley Jeffrey C , Uh Christina T , Silver Gregory S , Whitesel Timothy A 
Published: August 2015

Abstract
Pacific Lampreys Entosphenus tridentatus are declining in the Columbia River basin as well as in much of their broader range. To mitigate for reductions in abundance, strategies such as hatchery propagation and captive rearing of lamprey larvae are currently being considered. We conducted a series of experiments using captive larval Pacific Lampreys at Eagle Creek National Fish Hatchery to investigate the effect of different food types and different food concentrations on the growth of larvae. In our first experiment, we evaluated the growth of larvae (TL range, 59–145 mm) given four different food types (algae, leaves, yeast–larval fish food, and salmon carcass analogs) and a control group that was not fed. Assimilation of food types was evaluated by tracking unique stable isotope signatures of δ13C and δ15N within larval tissues. Results from experiment 1 indicated that lampreys fed a diet of salmon carcass analog or algae had positive growth (up to 0.16 mm/d and 42% proportional change in length) over approximately 6 months. Isotopic analyses of larval tissues showed unique signatures that matched those of their specific food treatment. Based on the results of experiment 1, we conducted a second experiment to evaluate the growth of larvae fed four different quantities of salmon carcass analog. Results from this experiment indicated larval growth rate increased with increasing rations of food, but positive growth was observed in all feeding treatments. The highest dose of salmon carcass analog resulted in the highest growth (up to 0.15 mm/d and 36% proportional change in length) over 6 months. We successfully reared larval Pacific Lampreys in captivity with minimal mortality and positive growth, which highlights the potential to use captive rearing and propagation as a conservation tool for this ecologically and culturally important species.
GalPaK3D: A BAYESIAN PARAMETRIC TOOL FOR EXTRACTING MORPHOKINEMATICS OF GALAXIES FROM 3D DATA
Authors: Bouché N. , Carfantan H. , Schroetter I. , Michel-Dansac L. , Contini T. 
Published: August 2015

ABSTRACT
We present a method to constrain galaxy parameters directly from three-dimensional data cubes. The algorithm compares directly the data with a parametric model mapped in

coordinates. It uses the spectral line-spread function and the spatial point-spread function (PSF) to generate a three-dimensional kernel whose characteristics are instrument specific or user generated. The algorithm returns the intrinsic modeled properties along with both an “intrinsic” model data cube and the modeled galaxy convolved with the 3D kernel. The algorithm uses a Markov Chain Monte Carlo approach with a nontraditional proposal distribution in order to efficiently probe the parameter space. We demonstrate the robustness of the algorithm using 1728 mock galaxies and galaxies generated from hydrodynamical simulations in various seeing conditions from 0.″6 to 1.″2. We find that the algorithm can recover the morphological parameters (inclination, position angle) to within 10% and the kinematic parameters (maximum rotation velocity) to within 20%, irrespectively of the PSF in seeing (up to 1.″2) provided that the maximum signal-to-noise ratio (S/N) is greater than ∼3 pixel−1 and that the ratio of galaxy half-light radius to seeing radius is greater than about 1.5. One can use such an algorithm to constrain simultaneously the kinematics and morphological parameters of (nonmerging) galaxies observed in nonoptimal seeing conditions. The algorithm can also be used on adaptive optics data or on high-quality, high-S/N data to look for nonaxisymmetric structures in the residuals.
Fast and accurate approximate inference of transcript expression from RNA-seq data
Authors: Hensman James , Papastamoulis Panagiotis , Glaus Peter , Honkela Antti , Rattray Magnus 
Published: August 2015

Abstract
Motivation: Assigning RNA-seq reads to their transcript of origin is a fundamental task in transcript expression estimation. Where ambiguities in assignments exist due to transcripts sharing sequence, e.g. alternative isoforms or alleles, the problem can be solved through probabilistic inference. Bayesian methods have been shown to provide accurate transcript abundance estimates compared with competing methods. However, exact Bayesian inference is intractable and approximate methods such as Markov chain Monte Carlo and Variational Bayes (VB) are typically used. While providing a high degree of accuracy and modelling flexibility, standard implementations can be prohibitively slow for large datasets and complex transcriptome annotations.
Results: We propose a novel approximate inference scheme based on VB and apply it to an existing model of transcript expression inference from RNA-seq data. Recent advances in VB algorithmics are used to improve the convergence of the algorithm beyond the standard Variational Bayes Expectation Maximization algorithm. We apply our algorithm to simulated and biological datasets, demonstrating a significant increase in speed with only very small loss in accuracy of expression level estimation. We carry out a comparative study against seven popular alternative methods and demonstrate that our new algorithm provides excellent accuracy and inter-replicate consistency while remaining competitive in computation time.
Availability and implementation: The methods were implemented in R and C++, and are available as part of the BitSeq project at github.com/BitSeq. The method is also available through the BitSeq Bioconductor package. The source code to reproduce all simulation results can be accessed via github.com/BitSeq/BitSeqVB_benchmarking.
Contact: james.hensman@sheffield.ac.uk or panagiotis.papastamoulis@manchester.ac.uk or Magnus.Rattray@manchester.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
LIBRA: LIgand Binding site Recognition Application
Authors: Viet Hung Le , Caprari Silvia , Bizai Massimiliano , Toti Daniele , Polticelli Fabio 
Published: August 2015

Abstract
Motivation: In recent years, structural genomics and ab initio molecular modeling activities are leading to the availability of a large number of structural models of proteins whose biochemical function is not known. The aim of this study was the development of a novel software tool that, given a protein’s structural model, predicts the presence and identity of active sites and/or ligand binding sites.
Results: The algorithm implemented by ligand binding site recognition application (LIBRA) is based on a graph theory approach to find the largest subset of similar residues between an input protein and a collection of known functional sites. The algorithm makes use of two predefined databases for active sites and ligand binding sites, respectively, derived from the Catalytic Site Atlas and the Protein Data Bank. Tests indicate that LIBRA is able to identify the correct binding/active site in 90% of the cases analyzed, 90% of which feature the identified site as ranking first. As far as ligand binding site recognition is concerned, LIBRA outperforms other structure-based ligand binding sites detection tools with which it has been compared.
Availability and implementation: The application, developed in Java SE 7 with a Swing GUI embedding a JMol applet, can be run on any OS equipped with a suitable Java Virtual Machine (JVM), and is available at the following URL: http://www.computationalbiology.it/software/LIBRAv1.zip.
Contact: polticel@uniroma3.it
Supplementary information: Supplementary data are available at Bioinformatics online.
InteractiveROSETTA: a graphical user interface for the PyRosetta protein modeling suite
Authors: Schenkelberg Christian D. , Bystroff Christopher 
Published: August 2015

Abstract
Summary: Modern biotechnical research is becoming increasingly reliant on computational structural modeling programs to develop novel solutions to scientific questions. Rosetta is one such protein modeling suite that has already demonstrated wide applicability to a number of diverse research projects. Unfortunately, Rosetta is largely a command-line-driven software package which restricts its use among non-computational researchers. Some graphical interfaces for Rosetta exist, but typically are not as sophisticated as commercial software. Here, we present InteractiveROSETTA, a graphical interface for the PyRosetta framework that presents easy-to-use controls for several of the most widely used Rosetta protocols alongside a sophisticated selection system utilizing PyMOL as a visualizer. InteractiveROSETTA is also capable of interacting with remote Rosetta servers, facilitating sophisticated protocols that are not accessible in PyRosetta or which require greater computational resources.
Availability and implementation: InteractiveROSETTA is freely available at https://github.com/schenc3/InteractiveROSETTA/releases and relies upon a separate download of PyRosetta which is available at http://www.pyrosetta.org after obtaining a license (free for academic use).
Contact: bystrc@rpi.edu
database.bio: a web application for interpreting human variations
Authors: Ou Min , Ma Ricky , Cheung Jeanno , Lo Katie , Yee Patrick , Luo Tewei , Chan T.L. , Au Chun Hang , Kwong Ava , Luo Ruibang , Lam Tak-Wah 
Published: August 2015

Abstract
Summary: Rapid advances of next-generation sequencing technology have led to the integration of genetic information with clinical care. Genetic basis of diseases and response to drugs provide new ways of disease diagnosis and safer drug usage. This integration reveals the urgent need for effective and accurate tools to analyze genetic variants. Due to the number and diversity of sources for annotation, automating variant analysis is a challenging task. Here, we present database.bio, a web application that combines variant annotation, prioritization and visualization so as to support insight into the individual genetic characteristics. It enhances annotation speed by preprocessing data on a supercomputer, and reduces database space via a unified database representation with compressed fields.
Availability and implementation: Freely available at https://database.bio
Contact: rb@l3-bioinfo.com or twlam@cs.hku.hk
Supplementary information: Supplementary data are available at Bioinformatics online.
High-order harmonics in light curves of Kepler planets
Authors: Armstrong Caden , Rein Hanno 
Published: August 2015

Abstract
The Kepler mission was launched in 2009 and has discovered thousands of planet candidates. In a recent paper, Esteves et al. found a periodic signal in the light curves of KOI-13 and HAT-P-7, with a frequency triple the orbital frequency of a transiting planet. We found similar harmonics in many systems with a high occurrence rate. At this time, the origins of the signal are not entirely certain. We look carefully at the possibility of errors being introduced through our data processing routines but conclude that the signal is real. The harmonics on multiples of the orbital frequency are a result of non-sinusoidal periodic signals. We speculate on their origin and generally caution that these harmonics could lead to wrong estimates of planet albedos, beaming mass estimates, and ellipsoidal variations.
Pressure Ulcer-Related Pelvic Osteomyelitis: A Neglected Disease?
Authors: Bodavula Phani , Liang Stephen Y. , Wu Jiami , VanTassell Paige , Marschall Jonas 
Published: August 2015

AbstractBackground.  Decubitus ulcers can become complicated by pelvic osteomyelitis. Little is known about the epidemiology of pressure ulcer-related pelvic osteomyelitis.Methods.  We performed a retrospective cohort study of adult patients with pressure ulcer and pelvic osteomyelitis admitted to an academic center from 2006 to 2011. Data on clinical presentation, diagnostic evaluation, and treatment during the index admission were collected. Outcome measures included length of hospital stay and number of readmissions in the subsequent year.Results.  Two hundred twenty patients were included: 163 (74%) were para/quadriplegic and 148 (67%) were male (148; 67%). Mean age was 50 (±18) years. Pelvic osteomyelitis was the primary admission diagnosis for 117 (53%). Fifty-six (26%) patients had concurrent febrile urinary tract infection. Wound cultures collected for 113 patients (51%) were notable for methicillin-resistant Staphylococcus aureus (37; 33%), Streptococci (19; 17%), and Pseudomonas spp (20; 18%). Plain films were obtained in 89 (40%) patients, computed tomography scans were obtained for 81 (37%) patients, and magnetic resonance images were obtained for 40 (18%) patients. Most patients received osteomyelitis-directed antibiotics (153; 70%), 134 of 153 (88%) of which were scheduled to receive ≥6 weeks of treatment. Fifty-five (25%) patients underwent surgery during the index admission; 48 (22%) patients received a combined medical-surgical approach. One third of patients had ≥2 readmissions during the subsequent year. Patients treated with a combined approach were less likely to be readmitted than those who received antibiotics alone (0 [range, 0–4] vs 1 [0–7] readmissions; P = .04).Conclusions.  This is one of the largest cohort studies of pressure ulcer-related pelvic osteomyelitis to date. Significant variations existed in diagnostic approach. Most patients received antibiotics; those treated with a combined medical-surgical approach had fewer hospital readmissions.
Resurrection of the island rule – human-driven extinctions have obscured a basic evolutionary pattern
Authors: Faurby Søren , Svenning Jens-Christian 
Published: August 2015

AbstractIslands are or have been occupied by unusual species, such as dwarf proboscideans and giant rodents. The discussion of the classical but controversial “island rule,” which states that mammalian body sizes converge on intermediate sizes on islands, has been stimulated by these unusual species. In this paper, we use an unprecedented global data set of the distributions and the body sizes of mammals and a novel analytical method to analyze body size evolution on islands; the analyses produced strong support for the island rule. Islands have suffered massive human-driven losses of species, and we found that the support for the island rule was substantially stronger when the many late-Quaternary extinct species were also considered (particularly, the tendency for dwarfing in large taxa). In this study, the decisive support generated for the island rule confirmed that evolution is markedly different on islands and that human impact may obscure even fundamental evolutionary patterns.