bluuebunny/crossref_metadata_2025 huggingface dataset:
Score Establishment and Brazilian Portuguese version of the Pregnancy Sexual Response Inventory (PSRI)
Authors: Rudge Cibele Vieira Cunha , Calderon Iracema de Mattos Paranhos , Almeida Ana Paula Machado de , Piculo Fernanda , Rudge Marilza Vieira Cunha , Barbosa Angélica Mércia Pascon
Published: July 2018

Objective To establish the Pregnancy Sexual Response Inventory (PSRI) scores for each domain before and during pregnancy, and to publish the Brazilian Portuguese version of the PSRI.

Methods Pregnant women were recruited during antenatal care; the PSRI was administered to 244 women prenatally at Faculdade de Medicina de Botucatu, at Universidade do Estado de São Paulo (UNESP, in the Portuguese acronym). The PSRI scores were estimated based on the Kings Health Questionnaire (KHQ) and the Medical Outcomes Study 36-item short form survey (SF-36). The raw scale type was used to standardize the minimal value and amplitude of each domain. For each domain, the score varied from 0 to 100, and the composite score was obtained as the domain average. The composite score before and during pregnancy was determined by the sum of the scores of all specific domains for each divided by the full domain number. The categorization of the scale into quartiles was established when all PSRI-specific and composite scores were combined.

Results The composite and specific scores for each domain were categorized into quartiles: 0 < 25 as “very bad;” 25 < 50 as “bad;” 50 < 75 as “good” and 75 to 100 as “excellent.” The mean scores were lower during pregnancy than before pregnancy in 8 of the 10 domains. The Brazilian Portuguese PSRI version is presented.

Conclusion This study allowed the establishment of the PSRI composite and specific scores for each domain, and the categorization of scores into quartiles: very bad, bad, good and excellent. In addition, the Brazilian Portuguese version of the PSRI is presented in full for application in the Brazilian population.
Biofilm Biology and Vaccine Strategies for Otitis Media Due to Nontypeable Haemophilus influenzae
Authors: Novotny Laura , Brockman Kenneth , Mokrzan Elaine , Jurcisek Joseph , Bakaletz Lauren
Published: July 2018

Otitis media (OM) is one of the most common diseases of childhood, and nontypeable Haemophilus influenzae (NTHI) is the predominant causative agent of chronic and recurrent OM, as well as OM for which treatment has failed. Moreover, NTHI is now as important a causative agent of acute OM as the pneumococcus. NTHI colonizes the human nasopharynx asymptomatically. However, upon perturbation of the innate and physical defenses of the airway by upper respiratory tract viral infection, NTHI can replicate, ascend the Eustachian tube, gain access to the normally sterile middle ear space, and cause disease. Bacterial biofilms within the middle ear, including those formed by NTHI, contribute to the chronic and recurrent nature of this disease. These multicomponent structures are highly resistant to clearance by host defenses and elimination by traditional antimicrobial therapies. Herein, we review several strategies utilized by NTHI to persist within the human host and interventions currently under investigation to prevent and/or resolve NTHI-induced diseases of the middle ear and uppermost airway.
Pediatric Deep Neck Space Infections: A Medical and Surgical Perspective
Authors: Gregory Stacie , Chun Robert , Huppler Anna , Mohandas Sindhu
Published: July 2018

Pediatric deep neck space infections (DNSI) are common in children. If unrecognized, DNSIs can rapidly progress with the potential for developing serious complications. Children fair better than their adult counterparts in the face of complications such as mediastinitis, but early recognition and aggressive management is key to prevent mortality and limit morbidity. Knowledge of the anatomy related to the deep neck spaces helps in anticipating and managing the potential complications. In this article, we review the clinical presentation, complications, and management in pediatric DNSI from the point of view of the pediatric infectious disease physician and the otolaryngologist. We discuss the best management based on current available evidence and the experience of the authors.
Revascularization of AlloDerm Used during Endoscopic Skull Base Surgery
Authors: Taufique Zahrah , Bhatt Nupur , Zagzag David , Lebowitz Richard , Lieberman Seth
Published: July 2018

Objectives AlloDerm is an acellular dermal matrix often used for reconstruction throughout the body. AlloDerm has been shown to undergo revascularization when used to reconstruct soft tissue such as in abdominal wall reconstruction. In this study, the authors review the literature on revascularization of AlloDerm and demonstrate the histologic findings of AlloDerm after implantation during skull base reconstruction.

Study Design Literature review and case reports.

Setting Tertiary Care Institution

Participants Patients from a tertiary care institution

Main Outcome Measures Histologic slides are evaluated and compared with nonimplanted AlloDerm.

Methods The authors review a case of explanted AlloDerm that had been used for skull base reconstruction after endoscopic skull base surgery.

Results Upon reviewing the histologic slides of explanted AlloDerm to nonimplanted AlloDerm, we demonstrate revascularization of AlloDerm when used in skull base reconstruction. Representative slides will be included.

Conclusions AlloDerm undergoes revascularization when used for skull base reconstruction.
Electronic properties of GaSe/MoS2 and GaS/MoSe2 heterojunctions from first principles calculations
Authors: Pham Khang D. , Phuc Huynh V. , Hieu Nguyen N. , Hoi Bui D. , Nguyen Chuong V.
Published: July 2018

In this work, we theoretically investigate electronic properties of GaSeMoS2 and GaSMoSe2 heterojunctions using density functional theory based on first-principles calculations. The results show that both GaSeMoS2 and GaSMoSe2 heterojunctions are characterized by the weak vdW interactions with a corresponding interlayer distance of 3.45 Å and 3.54 Å, and the binding energy of −0.16 eV per GaSeGaS cell. Furthermore, one can observe that both the GaSeMoS2, and GaSMoSe2 heterojunctions are found to be indirect band gap semiconductors with a corresponding band gap of 1.91 eV and 1.23 eV, respectively. We also find that the band gaps of these semiconductors belong to type II band alignment. A type–II band alignment in both GaSeMoS2 and GaSMoSe2 heterojunctions open their potential applications as novel materials such as in designing and fabricating new generation of photovoltaic and optoelectronic devices.
Experimental study on friction coefficients between tire tread rubber and ice
Authors: Zhang Yuanchao , Gao Jingwei , Li Qiao
Published: July 2018

The tire tread pattern affects driving significantly on icy roads, and different kinds of rubber pattern mean different friction coefficients when moving on the ice surface. Based on the latest friction test rig, a simulation method of such tests was created. Therefore, the continuous sampling at low slip velocity was proposed. During the sampling, the typical pattern of the rubber specimen was employed. The friction test of the tire tread specimen on the ice surface was implemented with different slip velocities and pressure, and the results were fitted and analyzed. To research the effect of tire tread on the friction coefficient, the rubber ratio parameter (the ratio of the rubber contact area to the total contact area) was given for proper evaluation. It is found that rubber as the major component of the tire possesses a special friction property, which is against Coulomb’s law. In addition to that, the friction coefficient of rubber is influenced by the contact state to a great extent, especially in some extreme conditions. The experiment of rubber friction on ice can serve as an important reference for the study on tire mechanical properties.
Compact discrete breathers on flat-band networks
Authors: Danieli C. , Maluckov A. , Flach S.
Published: July 2018

Linear wave equations on flat-band networks host compact localized eigenstates (CLS). Nonlinear wave equations on translationally invariant flat-band networks can host compact discrete breathers-time-periodic and spatially compact localized solutions. Such solutions can appear as one-parameter families of continued linear compact eigenstates, or as discrete sets on families of non-compact discrete breathers, or even on purely dispersive networks with fine-tuned nonlinear dispersion. In all cases, their existence relies on destructive interference. We use CLS amplitude distribution properties and orthogonality conditions to derive existence criteria and stability properties for compact discrete breathers as continued CLS.
Identification of flood area in the coastal region using remote sensing in Karawang Regency, West Java
Authors: Riadi Bambang , Barus Baba , Widiatmaka  , Yanuar Moh , Pramudya Bambang
Published: July 2018

Flooding often occurs in the lowlands, while the area is usually a rice production centres which affects the rice crop. Rice fields is generally located on fluvial plains and usually located in coastal areas, with relatively lower altitudes than roads or settlements. Physically wetland is an area flooding hazard and wetlands tend to longer floods than surrounding areas. Flood-hazard areas are formed due to sedimentation and usually at the confluence of river. This area is a fertile area for agriculture, has shallow ground water which is well suited for residential and urban areas. Karawang regency is one of the largest producers of rice commodities in West Java, therefore the Karawang regency government faces a challenge in maintaining the level of rice production due to global climate change that worsen the threat of flood hazard, in addition to land use change and increasing population. Based on the results of the spatial analysis from period of 2000 to 2006 the wetland area have been converted up to 7,493 ha. For the period of 2006 to 2015 wetland area have been converted up to 14,416 ha. Utilization of Geographic Information System with a model of Cellular Automata - Marcov Chain is an appropriate method for studying the phenomenon of expansion of build ups land in coastal region. The primary data used in the research is a land cover map of 2000, 2006 and 2015, which were the results of the multispectral classification of Landsat. The prediction of land cover change for the next fifteen years shows a continuous increase in built up area. The expansion of built up area and the possibility of widespread flood hazard areas, have inverse relationship with the decreasing of agricultural land area.
Interpretation of differential gene expression results of RNA-seq data: review and integration
Authors: McDermaid Adam , Monier Brandon , Zhao Jing , Liu Bingqiang , Ma Qin
Published: July 2018

Differential gene expression (DGE) analysis is one of the most common applications of RNA-sequencing (RNA-seq) data. This process allows for the elucidation of differentially expressed genes across two or more conditions and is widely used in many applications of RNA-seq data analysis. Interpretation of the DGE results can be nonintuitive and time consuming due to the variety of formats based on the tool of choice and the numerous pieces of information provided in these results files. Here we reviewed DGE results analysis from a functional point of view for various visualizations. We also provide an R/Bioconductor package, Visualization of Differential Gene Expression Results using R, which generates information-rich visualizations for the interpretation of DGE results from three widely used tools, Cuffdiff, DESeq2 and edgeR. The implemented functions are also tested on five real-world data sets, consisting of one human, one Malus domestica and three Vitis riparia data sets.
FLYCOP: metabolic modeling-based analysis and engineering microbial communities
Authors: García-Jiménez Beatriz , García José Luis , Nogales Juan
Published: July 2018

Motivation

Synthetic microbial communities begin to be considered as promising multicellular biocatalysts having a large potential to replace engineered single strains in biotechnology applications, in pharmaceutical, chemical and living architecture sectors. In contrast to single strain engineering, the effective and high-throughput analysis and engineering of microbial consortia face the lack of knowledge, tools and well-defined workflows. This manuscript contributes to fill this important gap with a framework, called FLYCOP (FLexible sYnthetic Consortium OPtimization), which contributes to microbial consortia modeling and engineering, while improving the knowledge about how these communities work. FLYCOP selects the best consortium configuration to optimize a given goal, among multiple and diverse configurations, in a flexible way, taking temporal changes in metabolite concentrations into account.

Results

In contrast to previous systems optimizing microbial consortia, FLYCOP has novel characteristics to face up to new problems, to represent additional features and to analyze events influencing the consortia behavior. In this manuscript, FLYCOP optimizes a Synechococcus elongatus-Pseudomonas putida consortium to produce the maximum amount of bio-plastic (PHA, polyhydroxyalkanoate), and highlights the influence of metabolites exchange dynamics in a four auxotrophic Escherichia coli consortium with parallel growth. FLYCOP can also provide an explanation about biological evolution driving evolutionary engineering endeavors by describing why and how heterogeneous populations emerge from monoclonal ones.

Availability and implementation

Code reproducing the study cases described in this manuscript are available on-line: https://github.com/beatrizgj/FLYCOP

Supplementary information

Supplementary data are available at Bioinformatics online.
Bayesian inference on stochastic gene transcription from flow cytometry data
Authors: Tiberi Simone , Walsh Mark , Cavallaro Massimo , Hebenstreit Daniel , Finkenstädt Bärbel
Published: July 2018

Motivation

Transcription in single cells is an inherently stochastic process as mRNA levels vary greatly between cells, even for genetically identical cells under the same experimental and environmental conditions. We present a stochastic two-state switch model for the population of mRNA molecules in single cells where genes stochastically alternate between a more active ON state and a less active OFF state. We prove that the stationary solution of such a model can be written as a mixture of a Poisson and a Poisson-beta probability distribution. This finding facilitates inference for single cell expression data, observed at a single time point, from flow cytometry experiments such as FACS or fluorescence in situ hybridization (FISH) as it allows one to sample directly from the equilibrium distribution of the mRNA population. We hence propose a Bayesian inferential methodology using a pseudo-marginal approach and a recent approximation to integrate over unobserved states associated with measurement error.

Results

We provide a general inferential framework which can be widely used to study transcription in single cells from the kind of data arising in flow cytometry experiments. The approach allows us to separate between the intrinsic stochasticity of the molecular dynamics and the measurement noise. The methodology is tested in simulation studies and results are obtained for experimental multiple single cell expression data from FISH flow cytometry experiments.

Availability and implementation

All analyses were implemented in R. Source code and the experimental data are available at https://github.com/SimoneTiberi/Bayesian-inference-on-stochastic-gene-transcription-from-flow-cytometry-data.

Supplementary information

Supplementary data are available at Bioinformatics online.
A Boolean network inference from time-series gene expression data using a genetic algorithm
Authors: Barman Shohag , Kwon Yung-Keun
Published: July 2018

Motivation

Inferring a gene regulatory network from time-series gene expression data is a fundamental problem in systems biology, and many methods have been proposed. However, most of them were not efficient in inferring regulatory relations involved by a large number of genes because they limited the number of regulatory genes or computed an approximated reliability of multivariate relations. Therefore, an improved method is needed to efficiently search more generalized and scalable regulatory relations.

Results

In this study, we propose a genetic algorithm-based Boolean network inference (GABNI) method which can search an optimal Boolean regulatory function of a large number of regulatory genes. For an efficient search, it solves the problem in two stages. GABNI first exploits an existing method, a mutual information-based Boolean network inference (MIBNI), because it can quickly find an optimal solution in a small-scale inference problem. When MIBNI fails to find an optimal solution, a genetic algorithm (GA) is applied to search an optimal set of regulatory genes in a wider solution space. In particular, we modified a typical GA framework to efficiently reduce a search space. We compared GABNI with four well-known inference methods through extensive simulations on both the artificial and the real gene expression datasets. Our results demonstrated that GABNI significantly outperformed them in both structural and dynamics accuracies.

Conclusion

The proposed method is an efficient and scalable tool to infer a Boolean network from time-series gene expression data.

Supplementary information

Supplementary data are available at Bioinformatics online.
Large-Degree Asymptotics of Rational Painlevé-IV Functions Associated to Generalized Hermite Polynomials
Authors: Buckingham Robert
Published: July 2018

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

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

Let $\Lambda <SL(2,\mathbb{Z})$ 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 $\delta>0.999950$.
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

The 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

Correlations 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

We 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.
Inference, validation and predictions about statistics and propagation of cortical spiking in vivo
Authors: Wilting J. , Priesemann V.
Published: July 2018

Electrophysiological recordings of spiking activity can only access a small fraction of all neurons simultaneously. This spatial subsampling has hindered characterizing even most basic properties of collective spiking in cortex. In particular, two contradictory hypotheses prevailed for over a decade: the first proposed an asynchronous irregular, the second a critical state. While distinguishing them is straightforward in models, we show that in experiments classical approaches fail to infer them correctly, because subsampling can bias measures as basic as the correlation strength. Deploying a novel, subsampling-invariant estimator, we find evidence that in vivo cortical dynamics clearly differs from asynchronous or critical dynamics, and instead occupies a narrow “reverberating” regime, consistently across multiple mammalian species and cortical areas. These results enabled us to predict cortical properties that are difficult or impossible to obtain experimentally, including responses to minimal perturbations, intrinsic network timescales, and the strength of external input compared to recurrent activation.
Hydrophobic organic contaminants are not linked to microplastic uptake in Baltic Sea herring
Authors: Ogonowski Martin , Wenman Viktoria , Barth Andreas , Hamacher-Barth Evelyne , Danielsson Sara , Gorokhova Elena
Published: July 2018

It is commonly accepted that microplastic (MP) ingestion can lead to lower food intake and bioaccumulation of hydrophobic organic contaminants (HOCs) in aquatic organisms. However, causal links between MP and contaminant levels in biota are poorly understood and in situ data are very limited. Here, we investigated whether HOC concentrations in herring muscle tissue (Clupea harengus membras) are related to MP ingestion using fish caught along the West coast of the Baltic Sea. The MP occurrence exhibited a large geographic variability, with MP found in 22.3% of the fish examined. The population average was 1.0 MP ind-1; however, when only individuals containing MP were considered, the average MP burden was 4.4 MP ind-1. We also found that MP burden decreased with reproductive stage of the fish but increased with its body size. To predict MP abundance in fish guts, we constructed a mass-balance model using literature data on MP in the water column and physiological rates on ingestion and gut evacuation for clupeids of a similar size. The model output was in agreement with the observed values, thus supporting the validity of the results. Contaminant concentrations in the muscle tissue were unrelated to the MP levels in fish, suggesting a lack of direct links between the levels of HOCs and MP ingestion. Thus, despite their ubiquity, MP are unlikely to have a measurable impact on food intake or the total body burden of hydrophobic contaminants in Baltic herring.
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

Determining 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 contributions

JP 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 availability

Mitochondrial 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

Background

Transposable 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.

Results

TEs 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.

Conclusions

The 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

The 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

As 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

Very 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.

Importance

Primary 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.
The influence of task outcome on implicit motor learning
Authors: Kim Hyosub , Parvin Darius , Ivry Richard
Published: July 2018

Recent studies have demonstrated that task success signals can modulate learning during sensorimotor adaptation tasks, primarily through engaging explicit processes. Here we examine the influence of task outcome on implicit adaptation, using a reaching task in which adaptation is induced by feedback that is not contingent on actual performance. We imposed an invariant perturbation (rotation) on the feedback cursor while varying the target size. In this way, the cursor either hit or missed the target, with the former producing a marked attenuation of implicit motor learning. We explored different computational architectures that might account for how task outcome information interacts with implicit adaptation. The results fail to support an architecture in which adaptation operates in parallel with a model-free operant reinforcement process. Rather, task outcome may serve as a gain on implicit adaptation or provide a distinct error signal for a second model-based process, in addition to implicit adaptation.
Collective decision making by rational individuals
Authors: Mann Richard P.
Published: July 2018

The patterns and mechanisms of collective decision making in humans and animals have attracted both empirical and theoretical attention. Of particular interest has been the variety of social feedback rules, and the extent to which these behavioural rules can be explained and predicted from theories of rational estimation and decision making. However, models that aim to model the full range of social information use have incorporated ad hoc departures from rational decision-making theory to explain the apparent stochasticity and variability of behaviour. In this paper I develop a model of social information use and collective decision making by fully rational agents that reveals how a wide range of apparently stochastic social decision rules emerge from fundamental information asymmetries both between individuals, and between the decision-makers and the observer of those decisions. As well as showing that rational decision making is consistent with empirical observations of collective behaviour, this model makes several testable predictions about how individuals make decisions in groups, and offers a valuable perspective on how we view sources of variability in animal, and human, behaviour.
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

Roots 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

Listening 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.
Two N,N′-bis(pyridin-4-yl)pyridine-2,6-dicarboxamide coordination compounds
Authors: Guo Yue-Xin , Ma Hong-Cui , Bo Ren , Zhao Ning , Zhao Li-Gang , Li Jin-Peng , Hou Hong-Wei
Published: July 2018

The molecular structures of tetraaqua[N,N′-bis(pyridin-4-yl)pyridine-2,6-dicarboxamide]sulfatomanganese(II) dihydrate, [Mn(SO4)(C17H13N5O2)(H2O)4]·2H2O or [Mn(H2
L
1)(SO4)(H2O)4]·2H2O, (I), and tetraaquabis[N,N′-bis(pyridin-4-yl)pyridine-2,6-dicarboxamide]cadmium(II) sulfate tetrahydrate, [Cd(C17H13N5O2)2(H2O)4]SO4·4H2O or [Cd(H2O)4(H2
L
1)2]·SO4·4H2O, (II), both contain a central metal atom in a distorted octahedral geometry coordinated equatorially by four oxygen atoms from water molecules. In (I), the axial positions are occupied by a nitrogen atom from H2
L
1 and an oxygen atom from the sulfate anion, whereas in (II), the axial positions contain two nitrogen atoms from two different H2
L
1 ligands and the sulfate anion acts as the charge-balancing ion. π–π stacking between pyridine rings and a network of hydrogen bonds involving the water molecules and the sulfate anions play a crucial role in the molecular self-assembly of the two structures.
Crystal structure and Hirshfeld surface analysis of (2E)-3-(3-bromo-4-fluorophenyl)-1-(3,4-dimethoxyphenyl)prop-2-en-1-one
Authors: Sheshadri S. N. , Atioğlu Zeliha , Akkurt Mehmet , Veeraiah M. K. , Quah Ching Kheng , Chidan Kumar C. S. , Siddaraju B. P.
Published: July 2018

In the molecule of the title compound, C17H14BrFO3, the aromatic rings are tilted with respect to the enone bridge by 13.63 (14) and 4.27 (15)°, and form a dihedral angle 17.91 (17)°. In the crystal, centrosymmetrically related molecules are linked by pairs of C—H...O hydrogen bonds into dimeric units, forming rings of R
2
2(14) graph-set motif. The dimers are further connected by weak C—H...O hydrogen interactions, forming layers parallel to (10\overline{1}). Hirshfeld surface analysis shows that van der Waals interactions constitute the major contribution to the intermolecular interactions, with H...H contacts accounting for 29.7% of the surface.
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.