bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanoscale distribution of Bi atoms in InP1−xBix
Authors: Zhang Liyao , Wu Mingjian , Chen Xiren , Wu Xiaoyan , Spiecker Erdmann , Song Yuxin , Pan Wenwu , Li Yaoyao , Yue Li , Shao Jun , Wang Shumin 
Published: September 2017

AbstractThe nanoscale distribution of Bi in InPBi is determined by atom probe tomography and transmission electron microscopy. The distribution of Bi atoms is not uniform both along the growth direction and within the film plane. A statistically high Bi-content region is observed at the bottom of the InPBi layer close to the InPBi/InP interface. Bi-rich V-shaped walls on the (−111) and (1–11) planes close to the InPBi/InP interface and quasi-periodic Bi-rich nanowalls in the (1–10) plane with a periodicity of about 100 nm are observed. A growth model is proposed to explain the formation of these unique Bi-related nanoscale features. These features can significantly affect the deep levels of the InPBi epilayer. The regions in the InPBi layer with or without these Bi-related nanostructures exhibit different optical properties.
The effect of sleep restriction on empathy for pain: An fMRI study in younger and older adults
Authors: Tamm Sandra , Nilsonne Gustav , Schwarz Johanna , Lamm Claus , Kecklund Göran , Petrovic Predrag , Fischer Håkan , Åkerstedt Torbjörn , Lekander Mats 
Published: September 2017

AbstractAge and sleep both affect emotional functioning. Since sleep patterns change over the lifespan, we investigated the effects of short sleep and age on empathic responses. In a randomized cross-over experimental design, healthy young and older volunteers (n = 47 aged 20–30 years and n = 39 aged 65–75 years) underwent functional magnetic resonance imaging (fMRI) after normal sleep or night sleep restricted to 3 hours. During fMRI, participants viewed pictures of needles pricking a hand (pain) or Q-tips touching a hand (control), a well-established paradigm to investigate empathy for pain. There was no main effect of sleep restriction on empathy. However, age and sleep interacted so that sleep restriction caused increased unpleasantness in older but not in young participants. Irrespective of sleep condition, older participants showed increased activity in angular gyrus, superior temporal sulcus and temporo-parietal junction compared to young. Speculatively, this could indicate that the older individuals adopted a more cognitive approach in response to others’ pain. Our findings suggest that caution in generalizability across age groups is needed in further studies of sleep on social cognition and emotion.
Melt layer erosion during ELM-like heat loading on molybdenum as an alternative plasma-facing material
Authors: Sinclair G. , Tripathi J. K. , Diwakar P. K. , Hassanein A. 
Published: September 2017

AbstractTransient events that occur during plasma instabilities in fusion reactors impart large heat fluxes onto the surrounding plasma-facing components (PFCs). Erosion and splashing of PFCs can contaminate the plasma and shorten material lifetime. Although tungsten is currently considered the most promising candidate material for future PFCs, concerns over the thermal shock performance during type-I ELMs (transient events expected in fusion devices) necessitate the study of other comparable materials. ELM-like heat loading was applied via a pulsed Nd:YAG millisecond laser on a pristine molybdenum (Mo) surface to measure surface melting and mass loss. One potential advantage of Mo is its higher specific heat of vaporization, which could lead to reduced particle emission. Imaging of the surface after loading revealed that complete surface melting began at 1.0 MJ m−2 (heat load parameter of 31.62 MJ m−2 s−1/2). Photon excitation also increased significantly above 1.0 MJ m−2, indicating possible phase change. At 1.4 MJ m−2 (44.27 MJ m−2 s−1/2), in situ mass loss measurements found an exponential increase in particle emission, indicating the presence of droplet formation and boiling. Direct comparisons of erosion during pulsed heat loading between PFC candidate materials will ensure that future fusion devices design components with optimal thermal strength.
Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle
Authors: Thomas Milton , Webb Megan , Ghimire Sudeep , Blair Amanda , Olson Kenneth , Fenske Gavin John , Fonder Alex Thomas , Christopher-Hennings Jane , Brake Derek , Scaria Joy 
Published: September 2017

AbstractIn North America, antibiotic feed additives such as monensin and tylosin are added to the finishing diets of feedlot cattle to counter the ill-effects of feeding diets with rapidly digestible carbohydrates. While these feed additives have been proven to improve feed efficiency and reduce liver abscess incidence, how these products impact the gastrointestinal microbiota is not completely understood. In this study, we analyzed the impact of providing antibiotic feed additives to feedlot cattle using metagenome sequencing of treated and control animals. Our results indicate that use of antibiotic feed additives does not produce discernable changes at the phylum level. However, treated cattle had reduced abundance of gram-positive bacteria at the genus level. The abundance of Ruminococcus, Erysipelotrichaceae and Lachnospiraceae in the gut of treated steers was reduced. Functional analysis of the data indicates that there was only minimal impact due to the treatment in the rumen. Genes involved in detoxification were significantly increased in the rumen of AB steers. But the relative abundance of these genes was < 0.3%. However, our results did not show any correlation between the presence of antimicrobial resistance genes in the gut microbiota and the administration of antibiotic feed additives.
Resveratrol Increases Hepatic SHBG Expression through Human Constitutive Androstane Receptor: a new Contribution to the French Paradox
Authors: Saez-Lopez Cristina , Brianso-Llort Laura , Torres-Torronteras J. , Simó Rafael , Hammond Geoffrey L. , Selva David M. 
Published: September 2017

AbstractSex hormone-binding globulin (SHBG) carries sex steroids in blood regulating their bioavailability. Red wine consumption increases plasma SHBG levels, and we have discovered that resveratrol, a polyphenol enriched in red wine, acts specifically through the human constitutive androstane receptor (CAR), a drug/xenobiotic detoxification gene regulator, to increase hepatic SHBG production. Chromatin immunoprecipitation and luciferase reporter gene assays show that human CAR binds to a typical direct repeat 1 nuclear hormone receptor-binding element in the human SHBG proximal promoter. Resveratrol also increased hepatic SHBG production in humanized SHBG/CAR transgenic mice. Moreover, SHBG expression correlated significantly with CAR mRNA levels in human liver biopsies. We conclude that the beneficial effects of red wine on the metabolic syndrome and it associated co-morbidities, including cardiovascular disease and type 2 diabetes, may be mediated in part by resveratrol acting via CAR to increase plasma SHBG levels.
Transcriptomic analysis of the role of RasGEF1B circular RNA in the TLR4/LPS pathway
Authors: Ng Wei Lun , Marinov Georgi K. , Chin Yoon-Ming , Lim Yat-Yuen , Ea Chee-Kwee 
Published: September 2017

AbstractCircular RNAs (circRNAs) have recently emerged as a large class of novel non-coding RNA species. However, the detailed functional significance of the vast majority of them remains to be elucidated. Most functional characterization studies targeting circRNAs have been limited to resting cells, leaving their role in dynamic cellular responses to stimuli largely unexplored. In this study, we focus on the LPS-induced cytoplasmic circRNA, mcircRasGEF1B, and combine targeted mcircRasGEF1B depletion with high-throughput transcriptomic analysis to gain insight into its function during the cellular response to LPS stimulation. We show that knockdown of mcircRasGEF1B results in altered expression of a wide array of genes. Pathway analysis revealed an overall enrichment of genes involved in cell cycle progression, mitotic division, active metabolism, and of particular interest, NF-κB, LPS signaling pathways, and macrophage activation. These findings expand the set of functionally characterized circRNAs and support the regulatory role of mcircRasGEF1B in immune response during macrophage activation and protection against microbial infections.
A multiscale imaging and modelling dataset of the human inner ear
Authors: Gerber Nicolas , Reyes Mauricio , Barazzetti Livia , Kjer Hans Martin , Vera Sergio , Stauber Martin , Mistrik Pavel , Ceresa Mario , Mangado Nerea , Wimmer Wilhelm , Stark Thomas , Paulsen Rasmus R. , Weber Stefan , Caversaccio Marco , Ballester Miguel A. González 
Published: September 2017

AbstractUnderstanding the human inner ear anatomy and its internal structures is paramount to advance hearing implant technology. While the emergence of imaging devices allowed researchers to improve understanding of intracochlear structures, the difficulties to collect appropriate data has resulted in studies conducted with few samples. To assist the cochlear research community, a large collection of human temporal bone images is being made available. This data descriptor, therefore, describes a rich set of image volumes acquired using cone beam computed tomography and micro-CT modalities, accompanied by manual delineations of the cochlea and sub-compartments, a statistical shape model encoding its anatomical variability, and data for electrode insertion and electrical simulations. This data makes an important asset for future studies in need of high-resolution data and related statistical data objects of the cochlea used to leverage scientific hypotheses. It is of relevance to anatomists, audiologists, computer scientists in the different domains of image analysis, computer simulations, imaging formation, and for biomedical engineers designing new strategies for cochlear implantations, electrode design, and others.
The BDNF Val66Met polymorphism regulates glucocorticoid-induced corticohippocampal remodeling and behavioral despair
Authors: Notaras M , Du X , Gogos J , van den Buuse M , Hill R A 
Published: September 2017

AbstractThe BDNF Val66Met polymorphism has been associated with sensitivity to stress and affective disorders. We therefore sought to model the inter-causality of these relationships under controlled laboratory conditions. We subjected humanized BDNF Val66Met (hBDNFVal66Met) transgenic mice to a history of stress, modeled by chronic late-adolescent corticosterone (CORT) exposure, before evaluating affective-related behavior using the forced-swim test (FST) in adulthood. While hBDNFMet/Met mice had a depression-like phenotype in the FST irrespective of CORT, hBDNFVal/Val wildtype mice had a resilient phenotype but developed an equally robust depressive-like phenotype following CORT. A range of stress-sensitive molecules were studied across the corticohippocampal axis, and where genotype differences occurred following CORT they tended to inversely coincide with the behavior of the hBDNFVal/Val group. Notably, tyrosine hydroxylase was markedly down-regulated in the mPFC of hBDNFVal/Val mice as a result of CORT treatment, which mimicked expression levels of hBDNFMet/Met mice and the FST behavior of both groups. The expression of calretinin, PSD-95, and truncated TrkB were also concomitantly reduced in the mPFC of hBDNFVal/Val mice by CORT. This work establishes BDNFVal66Met genotype as a regulator of behavioral despair, and identifies new biological targets of BDNF genetic variation relevant to stress-inducible disorders such as depression.
Diabetes-Associated Biobanking: More Topical Than Ever?
Authors: Lydia Kynast Katharina , Volk Nadine , Fleming Thomas , Herpel Esther 
Published: September 2017

AbstractThe increasing prevalence of diabetes and its accompanying long-term complications, as well as the associated economic burden, calls for a rapid clinical translation of biomedical research to better valid the physiological relevance of the findings from basic research. To meet this condition, the Collaborative Research Center (CRC) 1118 has established the first nationwide diabetes-specific Biomaterialbank (BMB) that permanently preserves solid and liquid specimen retro- and prospectively at the Institute of Pathology and Department of Endocrinology of the University Hospital Heidelberg. The main purpose of this BMB is to collect, preserve, characterize and provide human diabetic specimen to researchers investigating the role of reactive metabolites (RM) as cause of diabetic late complications. In this review we discuss the urgent need to support translational and clinical research projects by making use of diabetic solid and liquid specimen and provide an insight into the organization and general conditions of biobanking procedures which are pivotal to guaranteeing high-quality human biomaterial. In light of diabetes-tailored biobanking, we describe our newly initiated activities and introduce the diverse technology platforms that can be used for the investigation of promising molecular targets pertinent for diabetes. With this article we demonstrate that the preservation of rare specimen is also particularly relevant in the non-neoplastic field and contributes to basic investigation, promotes comprehensive scientific data and fortifies the sustainability for diabetes research. In addition, the increased understanding of how metabolic imbalance triggers diabetes onset and progression and favors diabetic late symptoms might hold some promise for future innovative diagnostic and/ or therapeutic applications, eventually adding to the improvement of patient care.
Cardiovascular Responses to Resistance Exercise Performed with Large and Small Muscle Mass
Authors: Matos-Santos Lenifran , Farinatti Paulo , P. Borges Juliana , Massaferri Renato , Monteiro Walace 
Published: September 2017

AbstractPrior research about the effects of the amount of exercised muscle mass upon cardiovascular responses (CVR) has neglected a potential bias related to total exercise and concentric/eccentric duration. Autonomic responses and perceived exertion (RPE) were compared in resistance exercises performed with larger and smaller muscle mass and matched for total exercise and concentric/eccentric duration. Twelve men performed 4 sets of 12 repetitions of unilateral (UNI) and bilateral (BIL) knee extensions at 70% of 12RM. Increases in CVR were always greater at the last set of BIL over UNI, as were SBP (35% vs. 23%), DBP (36% vs. 23%), HR (40% vs. 26%), RRP (90% vs 53%) and CO (55% vs 39%). No difference between protocols was found for autonomic modulation before and after exercise, but BIL induced significantly greater changes than UNI from baseline for R-R intervals (−13% vs. −7%), SDNN (−38% vs. −17%) and rMSSD (−41% vs. −21%). The rate of perceived exertion in the last set was higher in BIL than UNI (7.6±0.5 vs. 6.6±1.4 OMNI-RES; P<0.05) and did not correlate with any CVR. Thus, CVR were greater in resistance exercise performed with larger than smaller muscle mass. This information is relevant for patients with high cardiovascular risk.
A Comparison of the Efficacy of Once-Daily Fluticasone Furoate/Vilanterole with Twice-Daily Fluticasone Propionate/Salmeterol in Elderly Asthmatics
Authors: Ishiura Yoshihisa , Fujimura Masaki , Shiba Yasutaka , Ohkura Noriyuki , Hara Johsuke , Abo Miki , Kasahara Kazuo 
Published: September 2017

Abstract
Background Asthma in the elderly population has been focused because it affects quality of life and results in a higher hospitalization rate and mortality. Fluticasone furoate (FF)/vilanterole (VI) is a novel inhaled corticosteroids (ICS)/long-acting β2 agonist (LABA) combination being developed for once-daily administration for asthma with greater anti-inflammatory activity and longer duration of bronchidilation. The ElliptaTM dry powder inhaler (DPI) has also been available as a new device with high levels of satisfaction and preference.
Methods A 12-week, randomized, open-label cross-over, pilot study was conducted in 18 elderly patients with bronchial asthma to compare the effectiveness of once-daily FF/VI 200/25 µg via the ElliptaTM DPI vs. twice-daily fluticasone propionate (FP)/salmeterol (SAL) 500/50 µg via the DiskusTM DPI. The study period included a 4-week run-in, the first 4-week treatment, and the second 4-week treatment. Respiratory functions, fractional exhaled nitric oxide (FeNO) and asthma control test (ACT) scores were measured 0, 4, and 8 weeks after randomization. Preferences for their device were also assessed using a self-completed questionnaire.
Results Spirometric paramters, FeNO levels and ACT scores were not significantly different during the run-in period, the FP/SAL treatment period, and the FF/VI treatment period. FF/VI treatment via the ElliptaTM DPI was preferred to the FP/SAL treatment via the DiskusTM DPI (p<0.01).
Conclusions These data indicate that FF/VI treatment via the ElliptaTM DPI is preferred in elderly patients with asthma based on its ease-of-use, suggesting the potential to improve patient adherence and, as a result, overall disease management.
A relational (re)view of the UK’s social care crisis
Authors: Harding Rosie 
Published: September 2017

AbstractIt has become commonplace to say that there is a crisis in adult social care in the United Kingdom. This comment reflects on empirical and conceptual work on care, and feminist perspectives on re-valuing care, to make the case for a fundamental re-appraisal of how we resource and regulate adult social care. The problems generated by the uneven implementation of contemporary legal frameworks and the chronic underfunding of social care are explored, to demonstrate how regulatory, governmental and policy choices shape the everyday experience of delivering and receiving formal care services. Once these relational connections between regulation and everyday life are exposed, the need for a different, fairer and more just approach to care regulation becomes clear.
A big city perspective oncome/camevariation
Authors: Levey Stephen , Fox Susan , Kastronic Laura 
Published: September 2017

AbstractThis study examines the alternation between non-standard preteritecomeand its standard counterpartcamein London English. A major component of the investigation centers on the comparison ofcome/camevariation in the speech of Anglo (British-heritage) and non-Anglo (migrant-heritage) youth. Rates of preteritecomevary markedly across different age cohorts and minority ethnic groups, foregrounding the importance of social factors as key determinants of variant use. By contrast, the internal conditioning of variant selection is not robust, as inferred from the paucity of significant linguistic effects. Similarities in variable patterning in elderly and adolescent Anglo speaker groups nevertheless suggest that shared structural affinities may be due to historical transmission. Conversely, comparison of Anglo and non-Anglo adolescents’ use ofcome/camevariation reveals fewer correspondences in the grammar underlying variable use. The results demonstrate that data from non-Anglo groups contribute to a fuller understanding ofcome/camevariation in an ethnically diverse metropolis.
Protein–protein interaction specificity is captured by contact preferences and interface composition
Authors: Nadalin Francesca , Carbone Alessandra 
Published: September 2017

Abstract

Motivation
Large-scale computational docking will be increasingly used in future years to discriminate protein–protein interactions at the residue resolution. Complete cross-docking experiments make in silico reconstruction of protein–protein interaction networks a feasible goal. They ask for efficient and accurate screening of the millions structural conformations issued by the calculations.

Results
We propose CIPS (Combined Interface Propensity for decoy Scoring), a new pair potential combining interface composition with residue–residue contact preference. CIPS outperforms several other methods on screening docking solutions obtained either with all-atom or with coarse-grain rigid docking. Further testing on 28 CAPRI targets corroborates CIPS predictive power over existing methods. By combining CIPS with atomic potentials, discrimination of correct conformations in all-atom structures reaches optimal accuracy. The drastic reduction of candidate solutions produced by thousands of proteins docked against each other makes large-scale docking accessible to analysis.

Availability and implementation
CIPS source code is freely available at http://www.lcqb.upmc.fr/CIPS.

Supplementary information
Supplementary data are available at Bioinformatics online.
graphkernels: R and Python packages for graph comparison
Authors: Sugiyama Mahito , Ghisu M Elisabetta , Llinares-López Felipe , Borgwardt Karsten 
Published: September 2017

Abstract

Summary
Measuring the similarity of graphs is a fundamental step in the analysis of graph-structured data, which is omnipresent in computational biology. Graph kernels have been proposed as a powerful and efficient approach to this problem of graph comparison. Here we provide graphkernels, the first R and Python graph kernel libraries including baseline kernels such as label histogram based kernels, classic graph kernels such as random walk based kernels, and the state-of-the-art Weisfeiler-Lehman graph kernel. The core of all graph kernels is implemented in C ++ for efficiency. Using the kernel matrices computed by the package, we can easily perform tasks such as classification, regression and clustering on graph-structured samples.

Availability and implementation
The R and Python packages including source code are available at https://CRAN.R-project.org/package=graphkernels and https://pypi.python.org/pypi/graphkernels.

Supplementary information
Supplementary data are available online at Bioinformatics.
Universality laws for randomized dimension reduction, with applications
Authors: Oymak Samet , Tropp Joel A 
Published: September 2017

AbstractDimension reduction is the process of embedding high-dimensional data into a lower dimensional space to facilitate its analysis. In the Euclidean setting, one fundamental technique for dimension reduction is to apply a random linear map to the data. This dimension reduction procedure succeeds when it preserves certain geometric features of the set. The question is how large the embedding dimension must be to ensure that randomized dimension reduction succeeds with high probability. This article studies a natural family of randomized dimension reduction maps and a large class of data sets. It proves that there is a phase transition in the success probability of the dimension reduction map as the embedding dimension increases. For a given data set, the location of the phase transition is the same for all maps in this family. Furthermore, each map has the same stability properties, as quantified through the minimum RSV. These results can be viewed as new universality laws in high-dimensional stochastic geometry. Universality laws for randomized dimension reduction have many applications in applied mathematics, signal processing and statistics. They yield design principles for numerical linear algebra algorithms, for compressed sensing measurement ensembles and for random linear codes. Furthermore, these results have implications for the performance of statistical estimation methods under a large class of random experimental designs.