bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large-Degree Asymptotics of Rational Painlevé-IV Functions Associated to Generalized Hermite Polynomials
Authors: Buckingham Robert 
Published: July 2018

Abstract
The Painlevé-IV equation has three families of rational solutions generated by the generalized Hermite polynomials. Each family is indexed by two positive integers $m$ and $n$. These functions have applications to nonlinear wave equations, random matrices, fluid dynamics, and quantum mechanics. Numerical studies suggest the zeros and poles form a deformed $n\times m$ rectangular grid. Properly scaled, the zeros and poles appear to densely fill certain curvilinear rectangles as $m,n\to \infty $ with $r:=m/n$ a fixed positive real number. Generalizing a method of Bertola and Bothner [2] used to study rational Painlevé-II functions, we express the generalized Hermite rational Painlevé-IV functions in terms of certain non-Hermitian orthogonal polynomials. Using the Deift–Zhou nonlinear steepest-descent method, we asymptotically analyze the associated Riemann–Hilbert problem in the limit $n\to \infty $ with $m=r\cdot n$ for $r$ fixed. We obtain an explicit characterization of the boundary curve and determine the leading-order asymptotic expansion of the rational Painlevé-IV functions associated to generalized Hermite polynomials in the pole-free region.
Applications of Mutations in the Derived Categories of Weighted Projective Lines to Lie and Quantum Algebras
Authors: Deng Bangming , Ruan Shiquan , Xiao Jie 
Published: July 2018

Abstract
Let $\textrm{coh}\ \mathbb{X}$ be the category of coherent sheaves over a weighted projective line $\mathbb{X}$ and let $D^b(\textrm{coh}\ \mathbb{X})$ be its bounded derived category. The present paper focuses on the study of the right and left mutation functors arising in $D^b(\textrm{coh}\ \mathbb{X})$ attached to certain line bundles. As applications, we first show that these mutation functors give rise to simple reflections for the Weyl group of the star-shaped quiver ${Q}$ associated with $\mathbb{X}$. By further dealing with the Ringel–Hall algebra of $\mathbb{X}$, we show that these functors provide a realization for Tits’ automorphisms of the Kac–Moody algebra ${\mathfrak g}_{Q}$ associated with ${Q}$, as well as for Lusztig’s symmetries of the quantum enveloping algebra of ${\mathfrak g}_{Q}$.
On Representation of Integers from Thin Subgroups of SL(2, ℤ) with Parabolics
Authors: Zhang Xin 
Published: July 2018

Abstract
Let $\Lambda &lt;SL(2,\mathbb{Z})$ be a finitely generated, nonelementary Fuchsian group of the 2nd kind, and $\mathbf{v},\mathbf{w}$ be two primitive vectors in $\mathbb{Z}^2\!-\!\mathbf{0}$. We consider the set $\mathcal{S}\!=\!\{\left \langle \mathbf{v}\gamma ,\mathbf{w}\right \rangle _{\mathbb{R}^2}\!:\!\gamma\! \in\! \Lambda \}$, where $\left \langle \cdot ,\cdot \right \rangle _{\mathbb{R}^2}$ is the standard inner product in $\mathbb{R}^2$. Using Hardy–Littlewood circle method and some infinite co-volume lattice point counting techniques developed by Bourgain, Kontorovich, and Sarnak, together with Gamburd’s 5/6 spectral gap, we show that if $\Lambda $ has parabolic elements, and the critical exponent $\delta $ of $\Lambda $ exceeds 0.998317, then a density-one subset of all admissible integers (i.e., integers passing all local obstructions) are actually in $\mathcal{S}$, with a power savings on the size of the exceptional set (i.e., the set of admissible integers failing to appear in $\mathcal{S}$). This supplements a result of Bourgain–Kontorovich, which proves a density-one statement for the case when $\Lambda $ is free, finitely generated, has no parabolics, and has critical exponent $\delta&gt;0.999950$.
Fast and flexible bacterial genomic epidemiology with PopPUNK
Authors: Lees John A. , Harris Simon R. , Tonkin-Hill Gerry , Gladstone Rebecca A. , Lo Stephanie W. , Weiser Jeffrey N. , Corander Jukka , Bentley Stephen D. , Croucher Nicholas J. 
Published: July 2018

AbstractThe routine use of genomics for disease surveillance provides the opportunity for high-resolution bacterial epidemiology.However, current whole-genome clustering and multi-locus typing approaches do not fully exploit core and accessory genomic variation, and cannot both automatically identify, and subsequently expand, clusters of significantly-similar isolates in large datasets and across species.Here we describe PopPUNK (Population Partitioning Using Nucleotide K-mers; https://poppunk.readthedocs.io/en/latest/). software implementing scalable and expandable annotation- and alignment-free methods for population analysis and clustering.Variable-length k-mer comparisons are used to distinguish isolates’ divergence in shared sequence and gene content, which we demonstrate to be accurate over multiple orders of magnitude using both simulated data and real datasets from ten taxonomically-widespread species. Connections between closely-related isolates of the same strain are robustly identified, despite variation in the discontinuous pairwise distance distributions that reflects species’ diverse evolutionary patterns. PopPUNK can process 103-104 genomes as single batch, with minimal memory use and runtimes up to 200-fold faster than existing methods. Clusters of strains remain consistent as new batches of genomes are added, which is achieved without needing to re-analyse all genomes de novo.This facilitates real-time surveillance with stable cluster naming and allows for outbreak detection using hundreds of genomes in minutes. Interactive visualisation and online publication is streamlined through automatic output of results to multiple platforms.PopPUNK has been designed as a flexible platform that addresses important issues with currently used whole-genome clustering and typing methods, and has potential uses across bacterial genetics and public health research.
Genetic correlations between pain phenotypes and depression and neuroticism
Authors: Meng Weihua , Adams Mark J , Deary Ian J , Palmer Colin NA , McIntosh Andrew M , Smith Blair H 
Published: July 2018

AbstractCorrelations between pain phenotypes and psychiatric traits such as depression and the personality trait of neuroticism are not fully understood. The purpose of this study was to identify whether eight pain phenotypes, depressive symptoms, major depressive disorders, and neuroticism are correlated for genetic reasons. Eight pain phenotypes were defined by a specific pain-related question in the UK Biobank questionnaire. First we generated genome-wide association summary statistics on each pain phenotype, and estimated the common SNP-based heritability of each trait using GCTA. We then estimated the genetic correlation of each pain phenotype with depressive symptoms, major depressive disorders and neuroticism using the the cross-trait linkage disequilibrium score regression (LDSC) method integrated in the LD Hub. Third, we used the LDSC software to calculate genetic correlations among pain phenotypes. All pain phenotypes were heritable, with pain all over the body showing the highest heritability (h2=0.31, standard error=0.072). All pain phenotypes, except hip pain and knee pain, had significant and positive genetic correlations with depressive symptoms, major depressive disorders and neuroticism. The largest genetic correlations occurred between neuroticism and stomach or abdominal pain (rg=0.70, P=2.4 x 10−9). In contrast, hip pain and knee pain showed weaker evidence of shared genetic architecture with these negative emotional traits. In addition, many pain phenotypes had positive and significant genetic correlations with each other indicating shared genetic mechanisms. Pain at a variety of body sites is heritable and genetically correlated with depression and neuroticism. This suggests that pain, neuroticism and depression share partially overlapping genetic risk factors.
Genomic underpinnings of lifespan allow prediction and reveal basis in modern risks
Authors: Timmers Paul RHJ , Mounier Ninon , Läll Kristi , Fischer Krista , Ning Zheng , Feng Xiao , Bretherick Andrew , Clark David W , Consortium eQTLGen , Shen Xia , Esko Tōnu , Kutalik Zoltán , Wilson James F , Joshi Peter K 
Published: July 2018

AbstractWe use a multi-stage genome-wide association of 1 million parental lifespans of genotyped subjects and data on mortality risk factors to validate previously unreplicated findings near CDKN2B-AS1, ATXN2/BRAP, FURIN/FES, ZW10, PSORS1C3, and 13q21.31, and identify and replicate novel findings near GADD45G, KCNK3, LDLR, POM121C, ZC3HC1, and ABO. We also validate previous findings near 5q33.3/EBF1 and FOXO3, whilst finding contradictory evidence at other loci. Gene set and tissue-specific analyses show that expression in foetal brain cells and adult dorsolateral prefrontal cortex is enriched for lifespan variation, as are gene pathways involving lipid proteins and homeostasis, vesicle-mediated transport, and synaptic function. Individual genetic variants that increase dementia, cardiovascular disease, and lung cancer –but not other cancers-explain the most variance, possibly reflecting modern susceptibilities, whilst cancer may act through many rare variants, or the environment. Resultant polygenic scores predict a mean lifespan difference of around five years of life across the deciles.
A framework for estimating the effects of sequential reproductive barriers: implementation using Bayesian models with field data from cryptic species
Authors: Peccoud Jean , Pleydell David R. J. , Sauvion Nicolas 
Published: July 2018

AbstractDetermining how reproductive barriers modulate gene flow between populations represents a major step towards understanding the factors shaping the course of speciation. Although many indices quantifying reproductive isolation (RI) have been proposed, they do not permit the quantification of cross direction-specific RI under varying species frequencies and over arbitrary sequences of barriers. Furthermore, techniques quantifying associated uncertainties are lacking, and statistical methods unrelated to biological process are still preferred for obtaining confidence intervals and p-values. To address these shortcomings, we provide new RI indices that model changes in gene flow for both directions of hybridization, and we implement them in a Bayesian model. We use this model to quantify RI between two species of the psyllid Cacopsylla pruni based on field genotypic data for mating individuals, inseminated spermatophores and progeny. The results showed that pre-insemination isolation was strong, mildly asymmetric and undistinguishably different between study sites despite large differences in species frequencies; that post-insemination isolation strongly affected the more common hybrid type; and that cumulative isolation was close to complete. In the light of these results, we discuss how these developments can strengthen comparative RI studies.Author contributionsJP and NS initiated the study and obtained biological data. JP and DRJP developed the porosity-based approach. DRJP conceived the Bayesian implementation and code. JP, DRJP and NS wrote the manuscript.Data availabilityMitochondrial sequence data will be available at Genbank, source code is available at xxx.
Impact of transposable elements on genome structure and evolution in bread wheat
Authors: Wicker Thomas , Gundlach Heidrun , Spannagl Manuel , Uauy Cristobal , Borrill Philippa , Ramírez-González Ricardo H. , De Oliveira Romain ,   International Wheat Genome Sequencing Consortium, Mayer Klaus F. X. , Paux Etienne , Choulet Frédéric 
Published: July 2018

AbstractBackgroundTransposable elements (TEs) are ubiquitous components of genomes and they are the main contributors to genome evolution. The reference sequence of the hexaploid bread wheat (Triticum aestivum L.) genome enabled for the first time a comprehensive genome-wide view of the dynamics of TEs that have massively proliferated in the A, B, and D subgenomes.ResultsTEs represent 85% of the genome. We traced back TE amplification dynamics in the evolutionary history of wheat and did not find large bursts in the wake of either the tetra- or the hexaploidization. Despite the massive turnover of TEs since A, B, and D diverged, 76% of TE families are present in similar proportions in the three subgenomes. Moreover, spacing between homeologous genes was also conserved. TE content around genes is very different from the TE space comprising large intergenic regions and families that are enriched or depleted from gene promoters are the same in the three subgenomes.ConclusionsThe chromosome-scale assembly of the wheat genome provided an unprecedented genome-wide view of the organization and impact of TEs in such a complex genome. Our results suggest that TEs play a role at the structural level and that the overall chromatin structure is likely under selection pressure.
Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data
Authors: Alaux Michael , Rogers Jane , Letellier Thomas , Flores Raphaël , Alfama Françoise , Pommier Cyril , Mohellibi Nacer , Durand Sophie , Kimmel Erik , Michotey Célia , Guerche Claire , Loaec Mikaél , Lainé Mathilde , Steinbach Delphine , Choulet Frédéric , Rimbert Hélène , Leroy Philippe , Guilhot Nicolas , Salse Jérôme , Feuillet Catherine ,   International Wheat Genome Sequencing Consortium, Paux Etienne , Eversole Kellye , Adam-Blondon Anne-Françoise , Quesneville Hadi 
Published: July 2018

AbstractThe Wheat@URGI portal (https://wheat-urgi.versailles.inra.fr) has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.
A hybrid approach for automated mutation annotation of the extended human mutation landscape in scientific literature
Authors: Yepes Antonio Jimeno , MacKinlay Andrew , Gunn Natalie , Schieber Christine , Faux Noel , Downton Matthew , Goudey Benjamin , Martin Richard L. 
Published: July 2018

AbstractAs the cost of DNA sequencing continues to fall, an increasing amount of information on human genetic variation is being produced that could help progress precision medicine. However, information about such mutations is typically first made available in the scientific literature, and is then later manually curated into more standardized genomic databases. This curation process is expensive, time-consuming and many variants do not end up being fully curated, if at all. Detecting mutations in the literature is the first key step towards automating this process. However, most of the current methods have focused on identifying mutations that follow existing nomenclatures. In this work, we show that there is a large number of mutations that are missed by using this standard approach. Furthermore, we implement the first mutation annotator to cover an extended mutation landscape, and we show that its F1 performance is the same performance as human annotation (F1 78.29 for manual annotation vs F1 79.56 for automatic annotation).
Genetic evidence for two carbon fixation pathways in symbiotic and free-living bacteria: The Calvin-Benson-Bassham cycle and the reverse tricarboxylic acid cycle
Authors: Rubin-Blum Maxim , Dubilier Nicole , Kleiner Manuel 
Published: July 2018

AbstractVery few bacteria are able to fix carbon via both the reverse tricarboxylic acid (rTCA) and the Calvin-Benson-Bassham (CBB) cycles, such as symbiotic, sulfur-oxidizing bacteria that are the sole carbon source for the marine tubeworm Riftia pachyptila, the fastest growing invertebrate. To date, this co-existence of two carbon fixation pathways had not been found in a cultured bacterium and could thus not be studied in detail. Moreover, it was not clear if these two pathways were encoded in the same symbiont individual, or if two symbiont populations, each with one of the pathways, co-existed within tubeworms. With comparative genomics, we show that Thioflavicoccus mobilis, a cultured, free-living gammaproteobacterial sulfur oxidizer, possesses the genes for both carbon fixation pathways. Here, we also show that both the CBB and rTCA pathways are likely encoded in the genome of the sulfur-oxidizing symbiont of the tubeworm Escarpia laminata from deep-sea asphalt volcanoes in the Gulf of Mexico. Finally, we provide genomic and transcriptomic data suggesting a potential electron flow towards the rTCA cycle carboxylase 2-oxoglutarate:ferredoxin oxidoreductase, via a rare variant of NADH dehydrogenase/heterodisulfide reductase. This electron bifurcating complex, together with NAD(P)+ transhydrogenase and Na+ translocating Rnf membrane complexes may improve the efficiency of the rTCA cycle in both the symbiotic and the free-living sulfur oxidizer.ImportancePrimary production on Earth is dependent on autotrophic carbon fixation, which leads to the incorporation of carbon dioxide into biomass. Multiple metabolic pathways have been described for autotrophic carbon fixation, but most autotrophic organisms were assumed to have the genes for only one of these pathways. Our finding of a cultivable bacterium with two carbon fixation pathways in its genome opens the possibility to study the potential benefits of having two pathways and the interplay between these pathways. Additionally, this will allow the investigation of the unusual, and potentially very efficient mechanism of electron flow that could drive the rTCA cycle in these autotrophs. Such studies will deepen our understanding of carbon fixation pathways and could provide new avenues for optimizing carbon fixation in biotechnological applications.
Genetic screening for mutants with altered seminal root numbers in hexaploid wheat using a high-throughput root phenotyping platform
Authors: Shorinola Oluwaseyi , Kaye Ryan , Golan Guy , Peleg Zvi , Kepinski Stefan , Uauy Cristobal 
Published: July 2018

ABSTRACTRoots are the main channel for water and nutrient uptake in plants. Optimisation of root architecture provides a viable strategy to improve nutrient and water uptake efficiency and maintain crop productivity under water-limiting and nutrient-poor conditions. We know little, however, about the genetic control of root development in wheat, a crop supplying 20% of global calorie and protein intake. To improve our understanding of the genetic control of seminal root development in wheat, we conducted a high-throughput screen for variation in seminal root number using an exome-sequenced mutant population derived from the hexaploid wheat cultivar Cadenza. The screen identified seven independent mutants with homozygous and stably altered seminal root number phenotypes. One mutant, Cadenza0900, displays a recessive extra seminal root number phenotype, while six mutants (Cadenza0062, Cadenza0369, Cadenza0393, Cadenza0465, Cadenza0818 and Cadenza1273) show lower seminal root number phenotypes most likely originating from defects in the formation and activation of seminal root primordia. Segregation analysis in F2 populations suggest that the phenotype of Cadenza0900 is controlled by multiple loci whereas the Cadenza0062 phenotype fits a 3:1 mutant:wild-type segregation ratio characteristic of dominant single gene action. This work highlights the potential to use the sequenced wheat mutant population as a forward genetic resource to uncover novel variation in agronomic traits, such as seminal root architecture.
Distracting Linguistic Information Impairs Neural Tracking of Attended Speech
Authors: Dai Bohan , McQueen James M. , Terporten René , Hagoort Peter , Kösem Anne 
Published: July 2018

AbstractListening to speech is difficult in noisy environments, and is even harder when the interfering noise consists of intelligible speech as compared to unintelligible sounds. This suggests that the competing linguistic information interferes with the neural processing of target speech. Interference could either arise from a degradation of the neural representation of the target speech, or from increased representation of distracting speech that enters in competition with the target speech. We tested these alternative hypotheses using magnetoencephalography (MEG) while participants listened to a target clear speech in the presence of distracting noise-vocoded speech. Crucially, the distractors were initially unintelligible but became more intelligible after a short training session. Results showed that the comprehension of the target speech was poorer after training than before training. The neural tracking of target speech in the delta range (1–4 Hz) reduced in strength in the presence of a more intelligible distractor. In contrast, the neural tracking of distracting signals was not significantly modulated by intelligibility. These results suggest that the presence of distracting speech signals degrades the linguistic representation of target speech carried by delta oscillations.
Self-adaptive migration NSGA and optimal design of inductors for magneto-fluid hyperthermia
Authors: Sieni Elisabetta , Di Barba Paolo , Dughiero Fabrizio , Forzan Michele 
Published: July 2018

Purpose
The purpose of this paper is to present a modified version of the non-dominated sorted genetic algorithm with an application in the design optimization of a power inductor for magneto-fluid hyperthermia (MFH).

Design/methodology/approach
The proposed evolutionary algorithm is a modified version of migration-non-dominated sorting genetic algorithms (M-NSGA) that now includes the self-adaption of migration events- non-dominated sorting genetic algorithms (SA-M-NSGA). Moreover, a criterion based on the evolution of the approximated Pareto front has been activated for the automatic stop of the computation. Numerical experiments have been based on both an analytical benchmark and a real-life case study; the latter, which deals with the design of a class of power inductors for tests of MFH, is characterized by finite element analysis of the magnetic field.

Findings
The SA-M-NSGA substantially varies the genetic heritage of the population during the optimization process and allows for a faster convergence.

Originality/value
The proposed SA-M-NSGA is able to find a wider Pareto front with a computational effort comparable to a standard NSGA-II implementation.