bluuebunny/crossref_metadata_2025_split huggingface dataset:
Free‐weight resistance exercise on pulse wave reflection and arterial stiffness between sexes in young, resistance‐trained adults
Authors: Kingsley J. Derek , Tai Yu Lun , Mayo Xian , Glasgow Alaina , Marshall Erica 
Published: July 2017

AbstractWe sought to determine the sex‐specific effects of an acute bout of free‐weight resistance exercise (RE) on pulse wave reflection (aortic blood pressures, augmentation index (AIx), AIx at 75 bpm (AIx@75), augmentation pressure (AP), time of the reflected wave (Tr), subendocardial viability ratio (SEVR)), and aortic arterial stiffness in resistance‐trained individuals. Resistance‐trained men (n = 14) and women (n = 12) volunteered to participate in the study. Measurements were taken in the supine position at rest, and 10 minutes after 3 sets of 10 repetitions at 75% 1‐repetition maximum on the squat, bench press, and deadlift. A 2 × 2 × 2 ANOVA was used to analyse the effects of sex (men, women) across condition (RE, control) and time (rest, recovery). There were no differences between sexes across conditions and time. There was no effect of the RE on brachial or aortic blood pressures. There were significant condition × time interactions for AIx (rest: 12.1 ± 7.9%; recovery: 19.9 ± 10.5%, p = .003), AIx@75 (rest: 5.3 ± 7.9%; recovery: 24.5 ± 14.3%, p = .0001), AP (rest: 4.9 ± 2.8 mmHg; recovery: 8.3 ± 6.0 mmHg, p = .004), and aortic arterial stiffness (rest: 5.3 ± 0.6 ms; recovery: 5.9 ± 0.7 ms, p = .02) with significant increases during recovery from the acute RE. There was also a significant condition × time for time of the reflected wave (rest: 150 ± 7 ms; recovery: 147 ± 9 ms, p = .02) and SEVR (rest: 147 ± 17%; recovery: 83 ± 24%, p = .0001) such that they were reduced during recovery from the acute RE compared to the control. These data suggest that an acute bout of RE increases AIx, AIx@75, and aortic arterial stiffness similarly between men and women without significantly altering aortic blood pressures.
TITINdb—a computational tool to assess titin’s role as a disease gene
Authors: Laddach Anna , Gautel Mathias , Fraternali Franca 
Published: July 2017

Abstract

Summary
Large numbers of rare and unique titin missense variants have been discovered in both healthy and disease cohorts, thus the correct classification of variants as pathogenic or non-pathogenic has become imperative. Due to titin’s large size (363 coding exons), current web applications are unable to map titin variants to domain structures. Here, we present a web application, TITINdb, which integrates titin structure, variant, sequence and isoform information, along with pre-computed predictions of the impact of non-synonymous single nucleotide variants, to facilitate the correct classification of titin variants.

Availability and implementation
TITINdb can be freely accessed at http://fraternalilab.kcl.ac.uk/TITINdb

Supplementary information
Supplementary data are available at Bioinformatics online.
DeepLoc: prediction of protein subcellular localization using deep learning
Authors: Almagro Armenteros José Juan , Sønderby Casper Kaae , Sønderby Søren Kaae , Nielsen Henrik , Winther Ole 
Published: July 2017

Abstract

Motivation
The prediction of eukaryotic protein subcellular localization is a well-studied topic in bioinformatics due to its relevance in proteomics research. Many machine learning methods have been successfully applied in this task, but in most of them, predictions rely on annotation of homologues from knowledge databases. For novel proteins where no annotated homologues exist, and for predicting the effects of sequence variants, it is desirable to have methods for predicting protein properties from sequence information only.

Results
Here, we present a prediction algorithm using deep neural networks to predict protein subcellular localization relying only on sequence information. At its core, the prediction model uses a recurrent neural network that processes the entire protein sequence and an attention mechanism identifying protein regions important for the subcellular localization. The model was trained and tested on a protein dataset extracted from one of the latest UniProt releases, in which experimentally annotated proteins follow more stringent criteria than previously. We demonstrate that our model achieves a good accuracy (78% for 10 categories; 92% for membrane-bound or soluble), outperforming current state-of-the-art algorithms, including those relying on homology information.

Availability and implementation
The method is available as a web server at http://www.cbs.dtu.dk/services/DeepLoc. Example code is available at https://github.com/JJAlmagro/subcellular_localization. The dataset is available at http://www.cbs.dtu.dk/services/DeepLoc/data.php.
Gravitational wave sources from Pop III stars are preferentially located within the cores of their host Galaxies
Authors: Pacucci Fabio , Loeb Abraham , Salvadori Stefania 
Published: July 2017

Abstract
The detection of gravitational waves (GWs) generated by merging black holes has recently opened up a new observational window into the Universe. The mass of the black holes in the first and third Laser Interferometer Gravitational Wave Observatory (LIGO) detections (36–29 M⊙ and 32–19 M⊙) suggests low-metallicity stars as their most likely progenitors. Based on high-resolution N-body simulations, coupled with state-of-the-art metal enrichment models, we find that the remnants of Pop III stars are preferentially located within the cores of galaxies. The probability of a GW signal to be generated by Pop III stars reaches ∼90 per cent at ∼0.5 kpc from the galaxy centre, compared to a benchmark value of ∼5 per cent outside the core. The predicted merger rates inside bulges is ∼60 × βIII Gpc−3 yr−1 (βIII is the Pop III binarity fraction). To match the 90 per cent credible range of LIGO merger rates, we obtain: 0.03 &lt; βIII &lt; 0.88. Future advances in GW observatories and the discovery of possible electromagnetic counterparts could allow the localization of such sources within their host galaxies. The preferential concentration of GW events within the bulge of galaxies would then provide an indirect proof for the existence of Pop III stars.
Spinal Fusion for Pediatric Spondylolisthesis: National Trends, Complications, and Short-Term Outcomes
Authors: Rumalla Kavelin , Yarbrough Chester K , Pugely Andrew J , Dorward Ian G 
Published: July 2017

Abstract

BACKGROUND
Current surgical management guidelines for pediatric spondylolisthesis (PS) are reliant on data from single-center cohorts.

OBJECTIVE
To analyze national trends and predictors of short-term outcomes in spinal fusion surgery for PS by performing a retrospective cross-sectional analysis of the Kids’ Inpatient Database (KID).

METHODS
The KID (sampled every 3 yr) was queried from 2003 to 2012 to identify all cases (age 5-17) of spinal fusion for PS (n = 2646). We analyzed trends in patient characteristics, surgical management, and short-term outcomes. Both univariate and multivariable analyses were utilized.

RESULTS
The 2646 spinal fusions for PS included posterior-only fusions (86.8%, PSF), anterior lumbar interbody fusions (4.8%, ALIF), and combined anterior and posterior fusions (8.4%, APLF) procedures. The utilization of APLF decreased over time (9.9%-6.4%, P = .023), whereas the number of total spinal fusions and the proportion of PSF and ALIF procedures have not changed significantly. Uptrends in Medicaid insured individuals (1.2%-18.9%), recombinant human bone morphogenetic protein-2 insertion (8.8%-16.6%), decompression (34.7%-42.8%), and mean inflation-adjusted hospital costs ($21 855-$32 085) were identified (all P < .001). In multivariable analysis, Medicaid status (odds ratio [OR] = 1.93, P = .004), teaching hospitals (OR = 1.94, P = .01), decompression (OR = 1.78, P = .004), and the APLF procedure (OR = 2.47, P = .001) increased the likelihood of complication occurrence (all P < .001).

CONCLUSION
The addition of decompression during fusion and the APLF procedure were associated with more in-hospital complications, though this may have been indicative of greater surgical complexity. The utilization of the APLF procedure has decreased significantly, while costs associated with the treatment of PS have increased over time.
Cerebral Ischemic Reperfusion Injury Following Recanalization of Large Vessel Occlusions
Authors: Al-Mufti Fawaz , Amuluru Krishna , Roth William , Nuoman Rolla , El-Ghanem Mohammad , Meyers Philip M 
Published: July 2017

Abstract
Although stroke has recently dropped to become the nation's fifth leading cause of mortality, it remains the top leading cause of morbidity and disability in the US. Recent advances in stroke treatment, including intravenous fibrinolysis and mechanical thromboembolectomy, allow treatment of a greater proportion of stroke patients than ever before. While intra-arterial fibrinolysis with recombinant tissue plasminogen is an effective for treatment of a broad range of acute ischemic strokes, endovascular mechanical thromboembolectomy procedures treat severe strokes due to large artery occlusions, often resistant to intravenous drug. Together, these procedures result in a greater proportion of revascularized stroke patients than ever before, up to 88% in 1 recent trial (EXTEND-IA). Subsequently, there is a growing need for neurointensivists to develop more effective strategies to manage stroke patients following successful reperfusion. Cerebral ischemic reperfusion injury (CIRI) is defined as deterioration of brain tissue suffered from ischemia that concomitantly reverses the benefits of re-establishing cerebral blood flow following mechanical or chemical therapies for acute ischemic stroke. Herein, we examine the pathophysiology of CIRI, imaging modalities, and potential neuroprotective strategies. Additionally, we sought to lay down a potential treatment approach for patients with CIRI following emergent endovascular recanalization for acute ischemic stroke.
Systematics of the Culex coronator complex (Diptera: Culicidae): morphological and molecular assessment
Authors: Laurito Magdalena , Briscoe Andrew G , Almirón Walter R , Harbach Ralph E 
Published: July 2017

AbstractThe Culex coronator complex of the mosquito subgenus Culex includes five currently recognized species: Cx. camposi, Cx. coronator, Cx. ousqua, Cx. usquatissimus and Cx. usquatus. Because of the confusing taxonomic history of the complex, we aimed to clarify the specific status of these nominal forms based on an examination of holotypes and lectotypes and molecular data from other specimens. Critical assessment of published descriptions and study of type specimens revealed that the known distributions of the five species overlap considerably and exhibit biotic sympatry in some areas. Sequences from the COI barcode region and complete mitochondrial genomes were used to assess the relationships and degree of genetic divergence of the species and two newly discovered morphological forms, Cx. coronator Forms 1 and 2. Genetic distances in the COI dataset varied from 0.00 to 2.67%, with the largest relative divergence being 4.41 between specimens of Cx. coronator and Cx. coronator Form 1. Bayesian Poisson tree process analysis of the COI barcode region also failed to provide support for the nominal species. Evidence from the morphological and molecular data thus leads us to conclude (at least provisionally) that the Cx. coronator complex is a single polymorphic species. The forms constitute a monophyletic group but there is no support for the specific status of the five nominal forms.
Energy metabolites mediated cross-protection to heat, drought and starvation induced plastic responses in tropicalD.ananassaeof wet-dry seasons
Authors: Lambhod Chanderkala , Pathak Ankita , Munjal Ashok K , Parkash Ravi 
Published: July 2017

AbstractCross-tolerance effects for cold and drought stressors are well known for temperate and polar ectothermic organisms. However, less attention has been paid to plastic changes induced by wet-dry conditions for the tropical insect taxa.Drosophila ananassaeis abundant in wet habitats but its desiccation sensitivity is likely to make it vulnerable under expected drought conditions due to climate change. We tested plastic effects of heat hardening, acclimation to drought or starvation; and changes in trehalose, proline and body lipids inD. ananassaeflies reared under wet or dry season specific conditions. Wet season flies showed significant increase in heat knockdown, starvation resistance and body lipids after heat hardening. However, accumulation of proline was observed only after desiccation acclimation of dry season flies while wet season flies elicited no proline but trehalose only. Thus, drought induced proline can be a marker metabolite for dry season flies. Further, partial utilization of proline and trehalose under heat hardening reflects their possible thermoprotective effects. Heat hardening elicited cross-protection to starvation stress. Stressor specific accumulation or utilization as well as rates of metabolic change for each energy metabolite were significantly higher in wet season flies than dry season flies. Energy budget changes due to inter-related stressors (heat vs desiccation or starvation) resulted in possible maintenance of energetic homeostasis in wet or dry season flies. Thus, low or high humidity induced plastic changes in energy metabolites can provide cross-protection to seasonally varying climatic stressors.Summary statementIn the tropicalDrosophila ananassae, low or high humidity induced plastic changes in energy metabolites provide cross-protection to seasonally varying climatic stressors
Repeat associated mechanisms of genome evolution and function revealed by theMus caroliandMus paharigenomes
Authors: Thybert David , Roller Maša , Navarro Fábio C.P. , Fiddes Ian , Streeter Ian , Feig Christine , Martin-Galvez David , Kolmogorov Mikhail , Janoušek Václav , Akanni Wasiu , Aken Bronwen , Aldridge Sarah , Chakrapani Varshith , Chow William , Clarke Laura , Cummins Carla , Doran Anthony , Dunn Matthew , Goodstadt Leo , Howe Kerstin , Howell Matthew , Josselin Ambre-Aurore , Karn Robert C. , Laukaitis Christina M. , Jingtao Lilue , Martin Fergal , Muffato Matthieu , Quail Michael A. , Sisu Cristina , Stanke Mario , Stefflova Klara , Oosterhout Cock Van , Veyrunes Frederic , Ward Ben , Yang Fengtang , Yazdanifar Golbahar , Zadissa Amonida , Adams David , Brazma Alvis , Gerstein Mark , Paten Benedict , Pham Son , Keane Thomas , Odom Duncan T , Flicek Paul 
Published: July 2017

ABSTRACTUnderstanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of theMus caroliandMus paharigenomes. Together with theMus musculusandRattus norvegicusgenomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype ofMus musculusandMus carolibetween 3 to 6 MYA, but that are absent in the Hominidae. In fact, Hominidae show between four-and seven-fold lower rates of nucleotide change and feature turnover in both neutral and functional sequences suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. For example, recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically inMus caroli. This process resulted in thousands of novel, species-specific CTCF binding sites. Our results demonstrate that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.
Linking Normative Models of Natural Tasks to Descriptive Models of Neural Response
Authors: Jaini Priyank , Burge Johannes 
Published: July 2017

AbstractUnderstanding how nervous systems exploit task relevant properties of sensory stimuli to perform natural tasks is fundamental to the study of perceptual systems. However, there are few formal methods for determining which stimulus properties are most useful for a given task. As a consequence, it is difficult to develop principled models for how to compute task-relevant latent variables from natural signals, and it is difficult to evaluate descriptive models fit to neural response. Accuracy Maxmization Analysis (AMA) is a recently developed Bayesian method for finding the optimal task-specific filters (receptive fields). Here, we introduce AMA-Gauss, a new faster form of AMA that incorporates the assumption that the class-conditional filter responses are Gaussian distributed. Next, we use AMA-Gauss to show that its assumptions are justified for two fundamental visual tasks: retinal speed estimation and binocular disparity estimation. Then, we show that AMA-Gauss has striking formal similarities to popular quadratic models of neural response: the energy model and the Generalized Quadratic Model (GQM). Together, these developments deepen our understanding of why the energy model of neural response have proven useful, improve our ability to evaluate results from subunit model fits to neural data, and should help accelerate psychophysics and neuroscience research with natural stimuli.
Receptor-Based Mechanism of Cell Memory and Relative Sensing in Mammalian Signaling Networks
Authors: Lyashenko Eugenia , Niepel Mario , Dixit Purushottam D. , Lim Sang Kyun , Sorger Peter K. , Vitkup Dennis 
Published: July 2017

AbstractDetecting relative rather than absolute changes in external signals enables cells to make decisions in fluctuating environments and diverse biological contexts. However, how mammalian signaling networks store the memories of past stimuli and use them to compute relative signals is not well understood. Using the growth factor-activated PI3K-Akt signaling pathway, we develop computational and analytical models, and experimentally validate a novel mechanism of relative sensing in mammalian cells. This non-transcriptional mechanism relies on a new form of cellular memory, where cells effectively encode past stimulation levels in the abundance of cognate receptors on the cell surface. We show the robustness and specificity of the relative sensing for two physiologically important ligands, epidermal growth factor (EGF) and hepatocyte growth factor (HGF), and across wide ranges of background stimuli. The described memory and sensing mechanism could play a role in multiple other sensory cascades where stimulation leads to a proportional reduction in the abundance of cell surface receptors.
A tale of two universities: graduates perceived value of entrepreneurship education
Authors: Jones Paul , Pickernell David , Fisher Rebecca , Netana Celia 
Published: July 2017

Purpose
The purpose of this paper is to evaluate career impact of entrepreneurship education (EE) considering evidence drawn from a quantitative study of alumni within two UK higher education institutions (HEIs) from a retrospective perspective. The findings inform the value of the EE experience and its impact on both self-employability and wider employability career choices. This study will be of relevance to both enterprise support agencies and government policy makers.

Design/methodology/approach
This research study considers evidence drawn from an online quantitative survey of EE within two UK HEIs. The survey evaluated a range of issues including course design, programme satisfaction, impact, career outcomes and respondents demographics. Over 80 respondents completed the survey in full which was analysed using a range of bivariate techniques.

Findings
The evidence suggested here indicates that EE programmes provide value both in terms of helping to enable business start-ups and also in supporting other career paths, through the enterprising knowledge and skill sets graduates acquire during their specialised studies. This study contributes to the literature by recognising and measuring these contributions. For example, this study enables discernment between different EE course components and their value for different career outcomes.

Research limitations/implications
The study recognises the limitations of this survey data in terms of the size of the sample, number of HEIs evaluated and its point in time design.

Practical implications
The HEI sector must evaluate its practices and measure the effectiveness of its graduates in terms of achieving sustainable business start-up. In course design, the evidence suggested that students value both the enterprising and entrepreneurial skills and knowledge components and discern value between them in their later careers. The findings suggest that EE graduates typically experience portfolio careers with multiple occupations in different sectors and roles within both employment and self-employment. Thus it is important that EE programme design includes both enterprising and entrepreneurial components to meet the future requirements of their graduates postgraduation.

Originality/value
This study contributes new evidence regarding the value of EE in UK HEIs. This evidence should inform course design and policy makers regarding the value of EE in creating self-employment and creating enterprising employees.
Undergraduate perceptions of social media proficiency and graduate employability
Authors: Sutherland Karen , Ho Susie 
Published: July 2017

Purpose
The purpose of this paper is to explore undergraduate student attitudes towards the inclusion of social media training within higher education pedagogy, student perceptions of social media proficiency as professional expertise and its impact on graduate employability.

Design/methodology/approach
In all, 81 undergraduate students studying medicine, law, science and arts volunteered to complete an online survey. Questions examined student attitudes towards the delivery of social media pedagogy at university and the perceived benefits of social media proficiency.

Findings
Participants stated that social media skills should be taught in optional classes (85 per cent) covering generic competencies (56 per cent). The majority (91 per cent) of respondents reported that social media skills and training were valuable for employability.

Research limitations/implications
This was a pilot study and was therefore limited by the self-selection of participants, sample size and geographic location.

Practical implications
This study identifies that undergraduates across a range of disciplines are receptive to developing professionally relevant social media skills within higher education pedagogy and identify a link between social media proficiency and graduate employability.

Originality/value
Despite the increasing necessity for social media skills in professional environments, few studies have examined the teaching of social media skills as a core competency in higher education. Instead, social media is largely examined in relation to curriculum delivery and student engagement. This study explores attitudes towards the delivery of social media pedagogy at university and the perceived benefits of social media proficiency exclusively from the viewpoint of undergraduate students, to provide an alternative insight rarely explored in the literature.