bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incidence, Predictors and Outcome of Prosthesis-Patient Mismatch after Transcatheter Aortic Valve Replacement: a Systematic Review and Meta-analysis
Authors: Liao Yan-biao , Li Yi-jian , Jun-li Li , Zhao Zhen-gang , Wei Xin , Tsauo Jiay-yu , Xiong Tian-yuan , Xu Yuan-ning , Feng Yuan , Chen Mao 
Published: November 2017

AbstractThe aim of this study was to investigate the incidence, predictors and outcome of prosthesis-patient mismatch (PPM) following transcatheter aortic valve replacement (TAVR). A total of 30 articles incorporating 4,691 patients were identified. The pooled incidences of overall, moderate and severe PPM following TAVR were 33.0%, 25.0% and 11.0% respectively. Medtronic CoreValve (MCV) had lower incidence of overall (32% vs: 40%, P < 0.0001) and moderate (23% vs 32%, P < 0.0001) than Edwards Sapien (ESV). PPM was associated with a younger age, smaller annulus diameter and lower left ventricular ejection fraction in comparison with those patients without PPM. Post-dilation (OR, 0.51, 95% CI, 0.38 to 0.68, p < 0.001) during TAVR would decrease the incidence of PPM. Although PPM was common after TAVR, no significant differences were observed both in short- and mid-term all-cause mortality (30 day: OR: 1.1, 95% CI, 0.70 to 1.73 and 2 year: OR: 1.01, 95% CI, 0.74 to 1.38) between patients with PPM and those without PPM. In conclusion, despite being common after TAVR, the incidence of PPM was lower than that of surgical aortic valve replacement (SAVR) and decreased with the experience accumulating, and PPM was not seen to impact on short- and mid-term survival, regardless of its magnitude.
Magnesium homeostasis protects Salmonella against nitrooxidative stress
Authors: Bourret Travis J. , Liu Lin , Shaw Jeff A. , Husain Maroof , Vázquez-Torres Andrés 
Published: November 2017

AbstractThe PhoPQ two-component regulatory system coordinates the response of Salmonella enterica serovar Typhimurium to diverse environmental challenges encountered during infection of hosts, including changes in Mg2+ concentrations, pH, and antimicrobial peptides. Moreover, PhoPQ-dependent regulation of gene expression promotes intracellular survival of Salmonella in macrophages, and contributes to the resistance of this pathogen to reactive nitrogen species (RNS) generated from the nitric oxide produced by the inducible nitric oxide (NO) synthase of macrophages. We report here that Salmonella strains with mutations of phoPQ are hypersensitive to killing by RNS generated in vitro. The increased susceptibility of ∆phoQ Salmonella to RNS requires molecular O2 and coincides with the nitrotyrosine formation, the oxidation of [4Fe-4S] clusters of dehydratases, and DNA damage. Mutations of respiratory NADH dehydrogenases prevent nitrotyrosine formation and abrogate the cytotoxicity of RNS against ∆phoQ Salmonella, presumably by limiting the formation of peroxynitrite (ONOO−) arising from the diffusion-limited reaction of exogenous NO and endogenous superoxide (O2•−) produced in the electron transport chain. The mechanism underlying PhoPQ-mediated resistance to RNS is linked to the coordination of Mg2+ homeostasis through the PhoPQ-regulated MgtA transporter. Collectively, our investigations are consistent with a model in which PhoPQ-dependent Mg2+ homeostasis protects Salmonella against nitrooxidative stress.
Single-cell Co-expression Subnetwork Analysis
Authors: Bartlett Thomas E. , Müller Sören , Diaz Aaron 
Published: November 2017

AbstractSingle-cell transcriptomic data have rapidly become very popular in genomic science. Genomic science also has a long history of using network models to understand the way in which genes work together to carry out specific biological functions. However, working with single-cell data presents major challenges, such as zero inflation and technical noise. These challenges require methods to be specifically adapted to the context of single-cell data. Recently, much effort has been made to develop the theory behind statistical network models. This has lead to many new models being proposed, and has provided a thorough understanding of the properties of existing models. However, a large amount of this work assumes binary-valued relationships between network nodes, whereas genomic network analysis is traditionally based on continuous-valued correlations between genes. In this paper, we assess several established methods for genomic network analysis, we compare ways that these methods can be adapted to the single-cell context, and we use mixture-models to infer binary-valued relationships based on gene-gene correlations. Based on these binary relationships, we find that excellent results can be achieved by using subnetwork analysis methodology popular amongst network statisticians. This methodology thereby allows detection of functional subnetwork modules within these single-cell genomic networks.
A fast fabrication of copper nanowire transparent conductive electrodes by using pulsed laser irradiation
Authors: Tran Nguyen-Hung , Duong Thanh-Hung , Kim Hyun-Chul 
Published: November 2017

AbstractCopper nanowires have shown promise for use in next-generation conducting materials for transparent electrodes owing to their low sheet resistance, natural abundance, and high transmittance properties. Additionally, copper nanowires can be easily synthesized via low-cost solution-based processes. However, copper requires a uniform film to coat the nanowires on the substrate and removing film former residue in the post-treatment process remains a challenge. This lead to the high cost and complexity of fabricating transparent electrode. In this study, we demonstrate a simple, time-saving production method using a combination of laser irradiation and acid dipping to fabricate high-quality copper nanowire transparent electrodes. Preparation of electrodes was achieved by scanning pulsed laser on a copper nanowire film and then dipping in glacial acetic acid. The electrode exhibited excellent properties and the film former was totally erased from the electrode surface. Moreover, to demonstrate their capability, the as-fabricated electrodes were applied in touch-sensor fabrication.
Isoprenylated Phenolic Compounds from Morus macroura as Potent Tyrosinase Inhibitors
Authors: Wang Yifan , Xu Liangjin , Gao Wen , Niu Lixin , Huang Chunyue , Yang Peiming , Hu Xiao 
Published: November 2017

AbstractThree new Diels-Alder adducts, macrourins E – G (1–3), one new 2-arylbenzofuran, macrourin H (4), and eight known Diels-Alder adducts (5–12) were isolated from Morus macroura. Their structures were elucidated through extensive analysis of spectroscopic data. The 1H NMR and ECD trends in the determination of the configurations of these Diels-Alder adducts were summarized. The tyrosinase inhibitory activities of all compounds isolated were evaluated, and the new compounds (1–4) as well as the eight known compounds (5–12) were found to be potent with IC50 values ranging from 0.39 to 4.54 µM. Among them, 1 showed the best tyrosinase inhibitory activity with an IC50 value of 0.39 µM, approximately 50 times stronger than the positive control, kojic acid.
Numerical investigations of internal stresses on carbon steel based on ultrasonic LCR waves
Authors: Ramasamy R , Ibrahim Z , Chai H K 
Published: October 2017

Abstract
Internal stresses or residual stresses in the structural elements are very crucial in carrying out in-service evaluations and fitness-for-purpose assessments. The generation of these internal stresses can occur as result of the fabrication of the steel members, installation sequence or other ad-hoc events such as accidents or impact. The accurate prediction of the internal stresses will contribute towards estimating the integrity state of the structural elements, with respect to their material allowable stresses. This paper investigates the explicit FE based numerical modelling of the ultrasonic based non-destructive technique, utilising the measurable longitudinal critical refracted wave (LCR) and relating these to the internal stresses within the structural elements by the evaluation of the material dependent acoustoelastic factors. The subsurface travel path of the LCR wave inside the structural elements makes it a sub-surface stress measurement technique and the linearised relationship with corresponding internal stresses can be systematically applied repeatedly. The numerical results are compared against laboratory tests data to correlate the findings and to establish modelling feasibility for future proof-of-concepts. It can be concluded from this numerical investigation, that the subsurface ultrasonic LCR wave has great potential to be implemented for in-situ structural residual stress measurements, as compared to other available surface measurements such as strain gauges or x-ray diffraction.
CommWalker: correctly evaluating modules in molecular networks in light of annotation bias
Authors: Luecken M D , Page M J T , Crosby A J , Mason S , Reinert G , Deane C M 
Published: November 2017

Abstract

Motivation
Detecting novel functional modules in molecular networks is an important step in biological research. In the absence of gold standard functional modules, functional annotations are often used to verify whether detected modules/communities have biological meaning. However, as we show, the uneven distribution of functional annotations means that such evaluation methods favor communities of well-studied proteins.

Results
We propose a novel framework for the evaluation of communities as functional modules. Our proposed framework, CommWalker, takes communities as inputs and evaluates them in their local network environment by performing short random walks. We test CommWalker’s ability to overcome annotation bias using input communities from four community detection methods on two protein interaction networks. We find that modules accepted by CommWalker are similarly co-expressed as those accepted by current methods. Crucially, CommWalker performs well not only in well-annotated regions, but also in regions otherwise obscured by poor annotation. CommWalker community prioritization both faithfully captures well-validated communities and identifies functional modules that may correspond to more novel biology.

Availability and implementation
The CommWalker algorithm is freely available at opig.stats.ox.ac.uk/resources or as a docker image on the Docker Hub at hub.docker.com/r/lueckenmd/commwalker/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Short sea migration and precocious maturation in reared Atlantic salmon post-smolts in the northern Baltic Sea
Authors: Orell Panu , Erkinaro Jaakko , Kiljunen Mikko , Torniainen Jyrki , Sutela Tapio , Jaukkuri Mikko , Mäki-Petäys Aki 
Published: November 2017

Abstract
Atlantic salmon (Salmo salar L.) display significant variation in life history traits, including migration patterns and age at maturity. Hatchery rearing has been shown to affect the life history, and rearing-induced changes may include unfavourable consequences, e.g. shortened sea migration period and smaller size at maturity. We report on a new phenomenon of life history of reared Atlantic salmon in the Baltic Sea area: small-sized salmon returning to freshwater only a few months after release as smolts. These “one-sea-summer (1SS)” salmon were ca. 35 cm in length and weighed ca. 400 g, being clearly larger than smolts, but substantially smaller than one-sea-winter (1SW) salmon from the same cohorts. Almost all 1SS salmon were mature males and, at release, had been longer than the overall mean. Stable isotope analysis suggested that the 1SS salmon had been feeding in different sea areas than 1SW and multi-sea-winter salmon, likely in nearby Bothnian Bay, which is typically not a salmon feeding area. If an increasing proportion of the released salmon are not undertaking a normal marine migration (≥1SW) and are returning to estuaries and rivers as 1SS fish, the success and profitability of the reared salmon releases will decline even more than the reduced post-smolt survival is suggesting. We suggest that alternative rearing practices (e.g. enriched rearing environments and advanced diets) should be considered in hatchery production for shaping the reared smolts towards a closer resemblance to wild smolts.
Impact of donor and recipient human cytomegalovirus status on kidney transplantation
Authors: Zieliński Maciej , Tarasewicz Agnieszka , Zielińska Hanna , Jankowska Magdalena , Moszkowska Grażyna , Dębska-Ślizień Alicja , Rutkowski Bolesław , Trzonkowski Piotr 
Published: November 2017

Abstract
Human cytomegalovirus (HCMV) is considered to be a major pathogen that affects the outcome of solid organ transplantation (TX). Both recipient and donor may be HCMV positive, therefore HCMV re-infection is possible after TX. However, little is known how cytomegalovirus (CMV) transmitted from an infected donor to an infected recipient modulates the recipient’s already suppressed immunity, and what the clinical consequences are. To investigate these issues, 52 kidney recipients were followed up for 2 years after TX. T, B and natural killer (NK) lymphocytes, naive and memory T subsets, CD28 expression, relative telomere length, CMV-specific lymphocytes and serum cytokines were measured several times post-TX. Patients were monitored for signs of CMV viremia and other infections. The most important observation was that CMV-specific lymphocytes expand vastly in HCMV-infected recipients who received kidneys from infected donors, in comparison with uninfected donors. Despite this, a higher rate of HCMV viremia was found. Immune deterioration was confirmed by an increased number of CD28-negative T lymphocytes, inverted CD4/CD8 index and shortened telomeres. This was superior in HCMV-infected recipients transplanted from infected donors, when compared with uninfected. In conclusion, CMV alters the immune system in kidney transplant recipients and promotes immune exhaustion.
Applications of community detection techniques to brain graphs: Algorithmic considerations and implications for neural function
Authors: Garcia Javier O. , Ashourvan Arian , Muldoon Sarah F. , Vettel Jean M. , Bassett Danielle S. 
Published: October 2017

ABSTRACTThe human brain can be represented as a graph in which neural units such as cells or small volumes of tissue are heterogeneously connected to one another through structural or functional links. Brain graphs are parsimonious representations of neural systems that have begun to offer fundamental insights into healthy human cognition, as well as its alteration in disease. A critical open question in network neuroscience lies in how neural units cluster into densely interconnected groups that can provide the coordinated activity that is characteristic of perception, action, and adaptive behaviors. Tools that have proven particularly useful for addressing this question are community detection approaches, which can be used to identify communities or modules in brain graphs: groups of neural units that are densely interconnected with other units in their own group but sparsely interconnected with units in other groups. In this paper, we describe a common community detection algorithm known as modularity maximization, and we detail its applications to brain graphs constructed from neuroimaging data. We pay particular attention to important algorithmic considerations, especially in recent extensions of these techniques to graphs that evolve in time. After recounting a few fundamental insights that these techniques have provided into brain function, we highlight potential avenues of methodological advancements for future studies seeking to better characterize the patterns of coordinated activity in the brain that accompany human behavior. This tutorial provides a naive reader with an introduction to theoretical considerations pertinent to the generation of brain graphs, an understanding of modularity maximization for community detection, a resource of statistical measures that can be used to characterize community structure, and an appreciation of the utility of these approaches in uncovering behaviorally-relevant network dynamics in neuroimaging data.
Hydraulic constraints of reproduction do not explain sexual dimorphism in the genus Leucadendron (Proteaceae)
Authors: Roddy Adam B. , van Blerk Justin , Midgley Jeremy J. , West Adam G. 
Published: October 2017

AbstractBecause of the importance of reproduction in plant life history, the physiological costs of reproduction often influence vegetative structure and function. In dioecious species, these effects can be quite obvious, as different costs of male and female reproductive functions are entirely separated among different individuals in a population. In fire-prone ecosystems, in which recruitment is driven by fire frequency, many plants will maintain their seeds in the canopy, only to be released after a fire. The dioecious genus Leucadendron is a notable case of this, as females can maintain their seed cones for years, and, even more interestingly, species in the genus differ substantially in the degree to which males and females are sexually dimorphic. A recent study (Harris and Pannell 2010) argued that the hydraulic costs of maintaining seed cones for many years would effect the degree of sexual dimorphism among species. However, this assumed that shoot hydraulic architecture would be related to traits exhibiting sexual dimorphism. Here we explicitly test this hypothesis on two Leucadendron species. We found (1) that metrics of branch ramification used in the previous study to characterize dimorphism do not conform to known scaling relationships and (2) that sexual dimorphism in shoot architecture has no effect on hydraulic efficiency. Both of these results seriously question the pattern described by Harris and Pannell (2010) and suggest that the hydraulic costs of prolonged seed retention in Leucadendron do not significantly affect branch architecture.
Neurodevelopmental disease genes implicated byde novomutation and CNV morbidity
Authors: Coe Bradley P. , Stessman Holly A.F. , Sulovari Arvis , Geisheker Madeleine , Hormozdiari Fereydoun , Eichler Evan E. 
Published: October 2017

ABSTRACTWe combinedde novomutation (DNM) data from 10,927 cases of developmental delay and autism to identify 301 candidate neurodevelopmental disease genes showing an excess of missense and/or likely gene-disruptive (LGD) mutations. 164 genes were predicted by two different DNM models, including 116 genes with an excess of LGD mutations. Among the 301 genes, 76% show DNM in both autism and intellectual disability/developmental delay cohorts where they occur in 10.3% and 28.4% of the cases, respectively. Intersecting these results with copy number variation (CNV) morbidity data identifies a significant enrichment for the intersection of our gene set and genomic disorder regions (36/301, LR+ 2.53, p=0.0005). This analysis confirms many recurrent LGD genes and CNV deletion syndromes (e.g.,KANSL1, PAFAH1B1, RA1,etc.), consistent with a model of haploinsufficiency. We also identify genes with an excess of missense DNMs overlapping deletion syndromes (e.g.,KIF1Aand the 2q37 deletion) as well as duplication syndromes, such as recurrentMAPK3missense mutations within the chromosome 16p11.2 duplication, recurrentCHD4missense DNMs in the 12p13 duplication region, and recurrentWDFY4missense DNMs in the 10q11.23 duplication region. Finally, we also identify pathogenic CNVs overlapping more than one recurrently mutated gene (e.g., Sotos and Kleefstra syndromes) raising the possibility that multiple gene-dosage imbalances may contribute to phenotypic complexity of these disorders. Network analyses of genes showing an excess of DNMs confirm previous well-known enrichments but also highlight new functional networks, including cell-specific enrichments in the D1+ and D2+ spiny neurons of the striatum for both recurrently mutated genes and genes where missense mutations cluster.
Bursts of amino acid replacements in protein evolution
Authors: Stolyarova Anastasia V. , Bazykin Georgii A. , Neretina Tatyana V. , Kondrashov Alexey S. 
Published: October 2017

AbstractEvolution can occur both gradually and through alternating episodes of stasis and rapid changes. However, the prevalence and magnitude of fluctuations of the rate of evolution remains obscure. Detecting a rapid burst of changes requires a detailed record of past evolution, so that events that occurred within a short time interval can be identified. Here, we use the phylogenies of the Baikal Lake amphipods and of Catarrhini, which contain very short internal edges facilitating this task. We detect 6 radical bursts of evolution of individual proteins during such short time periods, each involving between 6 and 38 amino acid substitutions. These bursts were extremely unlikely to have occurred neutrally, and were apparently caused by positive selection. On average, in the course of a time interval required for one synonymous substitution per site, a protein undergoes a strong burst of rapid evolution with probability at least ~0.01.
Genomic characterisation and conservation genetics of the indigenous Irish Kerry cattle breed
Authors: Browett Sam , McHugo Gillian , Richardson Ian W. , Magee David A. , Park Stephen D. E. , Fahey Alan G. , Kearney John F. , Correia Carolina N. , Randhawa Imtiaz A. S. , MacHugh David E. 
Published: October 2017

AbstractKerry cattle are an endangered landrace heritage breed of cultural importance to Ireland. In the present study we have used genome-wide SNP data (Illumina®BovineSNP50 array) to evaluate genomic diversity within the Kerry cattle population and between Kerry cattle and other European cattle breeds. Visualisation of patterns of genetic differentiation and gene flow among cattle breeds using phylogenetic trees with ancestry graphs highlighted, in particular, historical gene flow from the British Shorthorn breed into the ancestral population of modern Kerry cattle. Principal component analysis (PCA) and genetic clustering emphasised the genetic distinctiveness of Kerry cattle relative to comparator British and European cattle breeds. Modelling of genetic effective population size (Ne) revealed a demographic trend of diminishingNeover time and that recent estimatedNevalues for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity (FROH) showed that genomic inbreeding has increased significantly during the 20 years between 1992 and 2012. Finally, signatures of selection revealed genomic regions subject to natural and artificial selection as Kerry cattle adapted to the climate, physical geography and agro-ecology of southwest Ireland.Note 1:This is an Associate Editor (D.E.M) Inaugural Article submission toFrontiers in Genetics: Livestock GenomicsNote 2:British English language style preferred for publication of this article.
Quantifying the effects of single mutations on viral escape from broad and narrow antibodies to an H1 influenza hemagglutinin
Authors: Doud Michael B. , Lee Juhye M. , Bloom Jesse D. 
Published: October 2017

ABSTRACTInfluenza virus can completely escape most antibodies with single mutations. However, rare antibodies broadly neutralize many viral strains. It is unclear how easily influenza virus might escape such antibodies if it was under strong pressure to do so. Here we map all single amino-acid mutations that increase resistance to broad antibodies targeting an H1 hemagglutinin. Crucially, our approach not only identifies antigenic mutations but also quantifies their effect sizes. All antibodies select mutations, but the effect sizes vary widely. The virus can escape a broad antibody that targets residues in hemagglutinin’s receptor-binding site the same way it escapes narrow strain-specific antibodies: via single mutations with huge effects. In contrast, broad antibodies targeting hemagglutinin’s stalk only select mutations with small effects. Therefore, among the antibodies we have examined, breadth is an imperfect indicator of the potential for viral escape via single mutations. Broadly neutralizing antibodies targeting the H1 hemagglutinin stalk are quantifiably harder to escape than the other antibodies tested here.