bluuebunny/crossref_metadata_2025_split huggingface dataset:
Caffeine use in a Super Rugby game and its relationship to post‐game sleep
Authors: Dunican Ian C. , Higgins Charles C. , Jones Maddison J. , Clarke Michael W. , Murray Kevin , Dawson Brian , Caldwell John A. , Halson Shona L. , Eastwood Peter R. 
Published: February 2018

AbstractObjective: To examine the relationship between regular game‐related caffeine consumption on sleep after an evening Super Rugby game. Methods: Twenty elite rugby union players wore a wrist‐activity monitor to measure sleep for three days before, three days after and on the night of an evening Super Rugby game (19:00–21:00). Players ingested caffeine as they would normally (i.e. before and sometimes during a game) and saliva samples were collected before (17:00) and after (21:30) the game for caffeine concentration. Results: Compared to the nights leading up to the game, on the night of the game, players went to bed 3 h later (23:08 ± 66 min vs 02:11 ± 114 min; p < .001) and had 1:30 hh:mm less sleep (5:54 ± 2:59 vs 8:02 ± 1:24 hh:mm; p < .05) and four players did not sleep after the game. Post‐game caffeine saliva concentrations were greater than pre‐game levels in 17 players (Pre‐game 0.40 µg/mL vs Post‐game 2.77 µg/mL; p < .001). The increase in caffeine saliva concentrations was moderately associated with an increase in sleep latency (p < .05), a decrease in sleep efficiency (p < .05), and a trend for a decrease in sleep duration (p = .06) on game night. Conclusion: Caffeine consumption before a Super Rugby game markedly increases post‐game saliva caffeine levels. This may contribute to the observed 3.5 h delay in time at sleep onset and the 1.5 h reduction in sleep duration on the night of the game. This study highlights the need for a strategic approach to the use of caffeine within a Super Rugby team considering the potential effect on post‐game sleep.
Effect of movement velocity during resistance training on muscle‐specific hypertrophy: A systematic review
Authors: Hackett Daniel A. , Davies Timothy B. , Orr Rhonda , Kuang Kenny , Halaki Mark 
Published: February 2018

AbstractCurrently, it is unclear whether manipulation of movement velocity during resistance exercise has an effect on hypertrophy of specific muscles. The purpose of this systematic review of literature was to investigate the effect of movement velocity during resistance training on muscle hypertrophy. Five electronic databases were searched using terms related to movement velocity and resistance training. Inclusion criteria were randomised and non‐randomised comparative studies; published in English; included healthy adults; used dynamic resistance exercise interventions directly comparing fast training to slower movement velocity training; matched in prescribed intensity and volume; duration ≥4 weeks; and measured muscle hypertrophy. A total of six studies were included involving 119 untrained participants. Hypertrophy of the quadriceps was examined in five studies and of the biceps brachii in two studies. Three studies found significantly greater increases in hypertrophy of the quadriceps for moderate‐slow compared to fast training. For the remaining studies examining the quadriceps, significant within‐group increase in hypertrophy was found for only moderate‐slow training in one study and for only fast training in the other study. The two studies that examined hypertrophy of the biceps brachii found greater increases for fast compared to moderate‐slow training. Caution is required when interpreting the findings from this review due to the low number of studies, hence insufficient data. Future longitudinal randomised controlled studies in cohorts of healthy adults are required to confirm and extend our findings.
Biofortification, Crop Adoption and Health Information: Impact Pathways in Mozambique and Uganda
Authors: de Brauw Alan , Eozenou Patrick , Gilligan Daniel O. , Hotz Christine , Kumar Neha , Meenakshi J.V. 
Published: February 2018

AbstractBiofortification is a promising strategy to combat micronutrient malnutrition by promoting the adoption of staple food crops bred to be dense sources of specific micronutrients. Research on biofortified orange‐fleshed sweet potato (OFSP) has shown that the crop improves the vitamin A status of children who consume as little as 100 grams per day, and intensive promotion strategies improve dietary intakes of vitamin A in field experiments. However, little is known about OFSP adoption behavior, or about the role that nutrition information plays in promoting adoption and changing diet. We report evidence from similar randomized field experiments conducted in Mozambique and Uganda to promote OFSP. We further use causal mediation analysis to study impact pathways for adoption and dietary intakes. Despite different agronomic conditions and sweet potato cropping patterns across the two countries, the project had similar impacts, leading to adoption by 61% to 68% of farmers exposed to the project, and doubling vitamin A intakes in children. In both countries, two intervention models that differed in training intensity and cost had comparable impacts relative to the control group. The project increased the knowledge of key nutrition messages; however, added knowledge of nutrition messages appears to have minimally affected adoption, conditional on assumptions required for causal mediation analysis. Increased vitamin A intakes were largely explained by adoption and not by nutrition knowledge gained, though in Uganda a large share of impacts on vitamin A intakes cannot be explained by mediating variables. Similar impacts could likely have been achieved by reducing the scope of nutrition trainings.
pBRIT: gene prioritization by correlating functional and phenotypic annotations through integrative data fusion
Authors: Kumar Ajay Anand , Van Laer Lut , Alaerts Maaike , Ardeshirdavani Amin , Moreau Yves , Laukens Kris , Loeys Bart , Vandeweyer Geert 
Published: February 2018

Abstract

Motivation
Computational gene prioritization can aid in disease gene identification. Here, we propose pBRIT (prioritization using Bayesian Ridge regression and Information Theoretic model), a novel adaptive and scalable prioritization tool, integrating Pubmed abstracts, Gene Ontology, Sequence similarities, Mammalian and Human Phenotype Ontology, Pathway, Interactions, Disease Ontology, Gene Association database and Human Genome Epidemiology database, into the prediction model. We explore and address effects of sparsity and inter-feature dependencies within annotation sources, and the impact of bias towards specific annotations.

Results
pBRIT models feature dependencies and sparsity by an Information-Theoretic (data driven) approach and applies intermediate integration based data fusion. Following the hypothesis that genes underlying similar diseases will share functional and phenotype characteristics, it incorporates Bayesian Ridge regression to learn a linear mapping between functional and phenotype annotations. Genes are prioritized on phenotypic concordance to the training genes. We evaluated pBRIT against nine existing methods, and on over 2000 HPO-gene associations retrieved after construction of pBRIT data sources. We achieve maximum AUC scores ranging from 0.92 to 0.96 against benchmark datasets and of 0.80 against the time-stamped HPO entries, indicating good performance with high sensitivity and specificity. Our model shows stable performance with regard to changes in the underlying annotation data, is fast and scalable for implementation in routine pipelines.

Availability and implementation
http://biomina.be/apps/pbrit/; https://bitbucket.org/medgenua/pbrit.

Supplementary information
Supplementary data are available at Bioinformatics online.
Clinical pathways for primary care: current use, interest and perceived usability
Authors: Toy Jennifer M , Drechsler Adam , Waters Richard C 
Published: February 2018

Abstract

Objective
Translating clinical evidence to daily practice remains a challenge and may improve with clinical pathways. We assessed interest in and usability of clinical pathways by primary care professionals.

Methods
An online survey was created. Interest in pathways for patient care and learning was assessed at start and finish. Participants completed baseline questions then pathway-associated question sets related to management of 2 chronic diseases. Perceived pathway usability was assessed using the system usability scale. Accuracy and confidence of answers was compared for baseline and pathway-assisted questions.

Results
Of 115 participants, 17.4% had used clinical pathways, the lowest of decision support tool types surveyed. Accuracy and confidence in answers significantly improved for all pathways. Interest in using pathways daily or weekly was above 75% for the respondents.

Conclusion
There is low utilization of, but high interest in, clinical pathways by primary care clinicians. Pathways improve accuracy and confidence in answering written clinical questions.
NeuroForm Atlas Stent-Assisted Coiling: Preliminary Results
Authors: ten Brinck Michelle F M , de Vries Joost , Bartels Ronald H M A , Grotenhuis J André , Boogaarts Hieronymus D 
Published: February 2018

Abstract

BACKGROUND
Stent-assisted coiling (SAC) is increasingly being performed as intervention for wide-neck intracranial aneurysms. The NeuroForm Atlas Stent (CE-marked; Stryker, Kalamazoo, Michigan) is relatively new.

OBJECTIVE
To evaluate the effectiveness and safety of NeuroForm Atlas SAC for intracranial aneurysms in the first such study.

METHODS
We retrospectively analyzed data from all patients treated with the NeuroForm Atlas SAC of an intracranial aneurysm, both ruptured and unruptured, between June 2015 and December 2016. Primary end-points were favorable clinical outcomes (modified Rankin scale score 0-2) and successful aneurysm occlusion (Raymond-Roy class I/II), both at 6-mo follow-up. Secondary end-points were the occurrence of intervention-related complications leading to permanent neurological deficit, the occurrence of intervention-related stroke and neurological death, immediate aneurysm occlusion, rupture (or rerupture) of the aneurysm, and recanalization.

RESULTS
Twenty-seven consecutive patients, 10 with ruptured saccular wide-neck aneurysms, were treated with NeuroForm Atlas SAC. At 6-mo follow-up, 18/26 (69.2%) survivors had successful aneurysm occlusion and 22/26 (84.6%) had favorable clinical outcome. One patient had died of a cause unrelated to treatment. No intervention-related complications leading to permanent neurological deficit occurred. However, intraprocedural thromboembolic complications occurred in 4/27 patients (14.8%), and ischemic stroke related to treatment occurred in 4/26 (15.4%). No hemorrhagic complications were observed.

CONCLUSION
NeuroForm Atlas SAC is a feasible way to treat ruptured and unruptured wide-neck aneurysms that are not amenable to conventional coiling or clipping. Aneurysm occlusion and favorable clinical outcome are consistent with previously reported rates for SAC of wide-neck aneurysms with other devices.
Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees
Authors: Hu Zhirui , Sackton Timothy B. , Edwards Scott V. , Liu Jun S. 
Published: February 2018

AbstractConservation of DNA sequence over evolutionary time is a strong indicator of function, and gain or loss of sequence conservation can be used to infer changes in function across a phylogeny. Changes in evolutionary rates on particular lineages in a phylogeny can indicate shared functional shifts, and thus can be used to detect genomic correlates of phenotypic convergence. However, existing methods do not allow easy detection of patterns of rate variation, which causes challenges for detecting convergent rate shifts or other complex evolutionary scenarios. Here we introduce PhyloAcc, a new Bayesian method to model substitution rate changes in conserved elements across a phylogeny. The method assumes several categories of substitution rate for each branch on the phylogenetic tree, estimates substitution rates per category, and detects changes of substitution rate as the posterior probability of a category switch. Simulations show that PhyloAcc can detect genomic regions with rate shifts in multiple target species better than previous methods and has a higher accuracy of reconstructing complex patterns of substitution rate changes than prevalent Bayesian relaxed clock models. We demonstrate the utility of PhyloAcc in two classic examples of convergent phenotypes: loss of flight in birds and the transition to marine life in mammals. In each case, our approach reveals numerous examples of conserved non-exonic elements with accelerations specific to the phenotypically convergent lineages. Our method is widely applicable to any set of conserved elements where multiple rate changes are expected on a phylogeny.
Single day construction of multi-gene circuits with 3G assembly
Authors: Halleran Andrew D. , Swaminathan Anandh , Murray Richard M. 
Published: February 2018

AbstractThe ability to rapidly design, build, and test prototypes is of key importance to every engineering discipline. DNA assembly often serves as a rate limiting step of the prototyping cycle for synthetic biology. Recently developed DNA assembly methods such as isothermal assembly and type IIS restriction enzyme systems take different approaches to accelerate DNA construction. We introduce a hybrid method, Golden Gate-Gibson (3G), that takes advantage of modular part libraries introduced by type IIS restriction enzyme systems and isothermal assembly‘s ability to build large DNA constructs in single pot reactions. Our method is highly efficient and rapid, facilitating construction of entire multi-gene circuits in a single day. Additionally, 3G allows generation of variant libraries enabling efficient screening of different possible circuit constructions. We characterize the efficiency and accuracy of 3G assembly for various construct sizes, and demonstrate 3G by characterizing variants of an inducible cell-lysis circuit.
Learning of goal-relevant and irrelevant complex visual sequences in human V1
Authors: Rosenthal Clive R. , Mallik Indira , Caballero-Gaudes Cesar , Sereno Martin I. , Soto David 
Published: February 2018

AbstractLearning and memory are supported by a network involving the medial temporal lobe and linked neocortical regions. Emerging evidence indicates that primary visual cortex (i.e., V1) may contribute to recognition memory, but this has been tested only with a single visuospatial sequence as the target memorandum. The present study used functional magnetic resonance imaging to investigate whether human V1 can support the learning of multiple, concurrent, and complex visual sequences involving discontinous (second-order) associations. Two peripheral, goal-irrelevant but structured sequences of orientated gratings appeared simultaneously in fixed locations of the right and left visual fields alongside a central, goal-relevant sequence that was in the focus of spatial attention. Pseudorandom sequences were introduced at multiple intervals during the presentation of the three structured visual sequences to provide an online measure of sequence-specific knowledge at each retinotopic location. We found that a network involving the precuneus and V1 was involved in learning the structured sequence presented at central fixation, whereas right V1 was modulated by repeated exposure to the concurrent structured sequence presented in the left visual field. The same result was not found in left V1. These results indicate for the first time that human V1 can support the learning of multiple concurrent sequences involving complex discontinuous inter-item associations, even peripheral sequences that are goal-irrelevant.
The relationship between brain atrophy and cognitive-behavioral symptoms in retired Canadian football players with multiple concussions
Authors: Misquitta Karen , Dadar Mahsa , Tarazi Apameh , Hussain MW , Alatwi MK , Ebraheem Ahmed , Multani Namita , Khodadadi Mozhgan , Goswami Ruma , Wennberg Richard , Tator Charles , Green Robin , Colella Brenda , Davis Karen , Mikulis David , Grinberg Mark , Sato Christine , Rogaeva Ekaterina , Collins D. Louis , Tartaglia Maria Carmela 
Published: February 2018

AbstractMultiple concussions, particularly in contact sports, have been associated with cognitive deficits, psychiatric impairment and neurodegenerative diseases like chronic traumatic encephalopathy. We used volumetric and deformation-based morphometric analyses to test the hypothesis that repeated concussions may be associated with smaller regional brain volumes, poorer cognitive performance and behavioural symptoms among former professional football players compared to healthy controls. This study included fifty-three retired Canadian Football League players, 25 age- and education-matched healthy controls, and controls from the Cambridge Centre for Aging and Neuroscience database for validation. Volumetric analyses revealed greater hippocampal atrophy than expected for age in former athletes with multiple concussions than controls and smaller left hippocampal volume was associated with poorer verbal memory performance. Deformation-based morphometric confirmed smaller bilateral hippocampal volume that were associated with poorer verbal memory performance in athletes. Repeated concussions may lead to greater regional atrophy than expected for age.
Generating genomic platforms to studyCandida albicanspathogenesis
Authors: Legrand Mélanie , Bachellier-Bassi Sophie , Lee Keunsook K. , Chaudhari Yogesh , Tournu Hélène , Arbogast Laurence , Boyer Hélène , Chauvel Murielle , Cabral Vitor , Maufrais Corinne , Nesseir Audrey , Maslanka Irena , Permal Emmanuelle , Rossignol Tristan , Walker Louise A. , Zeidler Ute , Znaidi Sadri , Schoeters Floris , Majgier Charlotte , Julien Renaud A. , Ma Laurence , Tichit Magali , Bouchier Christiane , Dijck Patrick Van , Munro Carol A. , d’Enfert Christophe 
Published: February 2018

ABSTRACTThe advent of the genomic era has made elucidating gene function at large scale a pressing challenge. ORFeome collections, whereby almost all ORFs of a given species are cloned and can be subsequently leveraged in multiple functional genomic approaches, represent valuable resources towards this endeavor. Here we provide novel, genome-scale tools for the study ofCandida albicans, a commensal yeast that is also responsible for frequent superficial and disseminated infections in humans. We have generated an ORFeome collection composed of 5,102 ORFs cloned in a Gateway™donor vector, representing 83% of the currently annotated coding sequences ofC. albicans. Sequencing data of the cloned ORFs are available in the CandidaOrfDB database athttp://candidaorfeome.eu. We also engineered 49 expression vectors with a choice of promoters, tags, and selection markers and demonstrated their applicability to the study of target ORFs transferred from theC. albicansORFeome. In addition, the use of the ORFeome in the detection of protein-protein interaction was demonstrated. Mating-compatible strains as well as Gateway™-compatible two-hybrid vectors were engineered, validated and used in a proof of concept experiment. These unique and valuable resources should greatly facilitate future functional studies inC. albicansand the elucidation of mechanisms that underlie its pathogenicity.
Regulation of Decellularized Tissue Remodeling via Scaffold-Mediated Lentiviral Delivery in Anatomically-Shaped Osteochondral Constructs
Authors: Rowland Christopher R. , Glass Katherine A. , Ettyreddy Adarsh R. , Gloss Catherine C. , Matthews Jared , Huynh Nguyen P.T. , Guilak Farshid 
Published: February 2018

AbstractCartilage-derived matrix (CDM) has emerged as a promising scaffold material for tissue engineering of cartilage and bone due to its native chondroinductive capacity and its ability to support endochondral ossification. Because it consists of native tissue, CDM can undergo cellular remodeling, which can promote integration with host tissue and enables it to be degraded and replaced by neotissue over time. However, enzymatic degradation of decellularized tissues can occur unpredictably and may not allow sufficient time for mechanically competent tissue to form, especially in the harsh inflammatory environment of a diseased joint. The goal of the current study was to engineer cartilage and bone constructs with the ability to inhibit aberrant inflammatory processes caused by the cytokine interleukin-1 (IL-1), through scaffold-mediated delivery of lentiviral particles containing a doxycycline-inducible IL-1 receptor antagonist (IL-1Ra) transgene on anatomically-shaped CDM constructs. Additionally, scaffold-mediated lentiviral gene delivery was used to facilitate spatial organization of simultaneous chondrogenic and osteogenic differentiation via site-specific transduction of a single mesenchymal stem cell (MSC) population to overexpress either chondrogenic, transforming growth factor-beta 3 (TGF-β3), or osteogenic, bone morphogenetic protein-2 (BMP-2), transgenes. Controlled induction of IL-1Ra expression protected CDM hemispheres from inflammation-mediated degradation, and supported robust bone and cartilage tissue formation even in the presence of IL-1. In the absence of inflammatory stimuli, controlled cellular remodeling was exploited as a mechanism for fusing concentric CDM hemispheres overexpressing BMP-2 and TGF-β3 into a single bi-layered osteochondral construct. Our findings demonstrate that site-specific delivery of inducible and tunable transgenes confers spatial and temporal control over both CDM scaffold remodeling and neotissue composition. Furthermore, these constructs provide a microphysiological, in vitro, joint, organoid model with site-specific, tunable, and inducible protein delivery systems for examining the spatiotemporal response to pro-anabolic and/or inflammatory signaling across the osteochondral interface.
Mapping diversification metrics in macroecological studies: Prospects and challenges
Authors: Velasco Julián A. , Pinto-Ledezma Jesús N. 
Published: February 2018

AbstractThe intersection of macroecology and macroevolution is one of the most active research areas today. Macroecological studies are increasingly using phylogenetic diversification metrics to explore the role of evolutionary processes in shaping present-day patterns of biodiversity. Evolutionary explanations of species richness gradients are key for our understanding of how diversity accumulated in a region. For instance, the present-day diversity in a region can be a result ofin situdiversification, extinction, or colonization from other regions, or a combination of all of these processes. However, it is unknown whether these metrics capture well these diversification and dispersal processes across geography. Some metrics (e.g., mean root distance -MRD-; lineage diversification-rate -DR-; evolutionary distinctiveness -ED-) seem to provide very similar geographical patterns regardless of how they were calculated (e.g., using branch lengths or not). The lack of appropriate estimates of extinction and dispersal rates in phylogenetic trees can limit our conclusions about how species richness gradients emerged. With a review of the literature and complemented by an empirical comparison, we show that phylogenetic metrics by itself are not capturing well the speciation, extinction and dispersal processes across the geographical gradients. Furthermore, we show how new biogeographic methods can improve our inference of past events and therefore our conclusions about the evolutionary mechanisms driving regional species richness. Finally, we recommend that future studies include several approaches (e.g., spatial diversification modelling, parametric biogeographic methods) to disentangle the relative the role of speciation, extinction and dispersal in the generation and maintenance of species richness gradients.