bluuebunny/crossref_metadata_2025_split huggingface dataset:
Taxonomies of psychological individual differences: biological perspectives on millennia-long challenges
Authors: Trofimova I. , Robbins T. W. , Sulis W. H. , Uher J. 
Published: February 2018

This Editorial highlights a unique focus of this theme issue on the biological perspectives in deriving psychological taxonomies coming from neurochemistry, neuroanatomy, neurophysiology, genetics, psychiatry, developmental and comparative psychology—as contrasted to more common discussions of socio-cultural concepts (personality) and methods (lexical approach). It points out the importance of the distinction between temperament and personality for studies in human and animal differential psychophysiology, psychiatry and psycho-pharmacology, sport and animal practices during the past century. It also highlights the inability of common statistical methods to handle nonlinear, feedback, contingent, dynamical and multi-level relationships between psychophysiological systems of consistent psychological traits discussed in this theme issue.This article is part of the theme issue ‘Diverse perspectives on diversity: multi-disciplinary approaches to taxonomies of individual differences'.
Inter-individual differences in the impulsive/compulsive dimension: deciphering related dopaminergic and serotonergic metabolisms at rest
Authors: Dellu-Hagedorn Françoise , Rivalan Marion , Fitoussi Aurélie , De Deurwaerdère Philippe 
Published: February 2018

Several impulse control disorders such as ADHD, mania, personality disorders or substance abuse share common behavioural traits, like impulsiveness, risk-taking or inflexible behaviour. These disorders are treated with drugs targeting dopamine (DA) and/or serotonin (5-HT). However, the patient's monoamine imbalance that these neurotransmitters compensate is unclear. This study aims to investigate the patterns of DA and 5-HT metabolisms at rest within selected brain regions related to inter-individual variability in six main components of impulsivity/compulsivity (anticipatory hyperactivity, premature responses, delay discounting, risk-taking, perseveration, flexibility). Rats with adaptive and highly inadaptive behaviours were identified in each task and a sensitive biochemical approach allowed mapping of post-mortem endogenous monoamine tissue content in 20 brain areas. Distinct patterns of 5-HT and DA metabolisms were revealed according to the behavioural traits. Except for hyperactive responses, lower control of actions was mainly associated with a lower DA or 5-HT metabolism in prefrontal and/or subcortical areas (i.e. in orbitofrontal cortex (DA), amygdala and anterior cingulate cortex (5-HT) for inflexible and risk-prone rats). Our results reveal the complex nature of behavioural traits related to impulse control disorders through their associated monoaminergic networks at rest, paving the way for understanding the link between mental disorders and drug therapeutic actions.
This article is part of the theme issue ‘Diverse perspectives on diversity: multi-disciplinary approaches to taxonomies of individual differences'.
Genetics of biologically based psychological differences
Authors: Sallis Hannah , Davey Smith George , Munafò Marcus R. 
Published: February 2018

In recent years, substantial effort has gone into disentangling the genetic contribution to individual differences in behaviour (such as personality and temperament traits). Heritability estimates from twin and family studies, and more recently using whole genome approaches, suggest a substantial genetic component to these traits. However, efforts to identify the genes that influence these traits have had relatively little success. Here, we review current work investigating the heritability of individual differences in behavioural traits and provide an overview of the results from genome-wide association analyses of these traits to date. In addition, we discuss the implications of these findings for the potential applications of Mendelian randomization.
This article is part of the theme issue ‘Diverse perspectives on diversity: multi-disciplinary approaches to taxonomies of individual differences'.
Phospho-regulation of Atoh1 is required for plasticity of secretory progenitors and tissue regeneration
Authors: Tomic Goran , Morrissey Edward , Kozar Sarah , Ben-Moshe Shani , Hoyle Alice , Azzarelli Roberta , Kemp Richard , Chilamakuri Chandra Sekhar Reddy , Itzkovitz Shalev , Philpott Anna , Winton Douglas J. 
Published: February 2018

SUMMARYThe intestinal epithelium is maintained by a small number of self-renewing stem cells in homeostasis. In addition committed progenitors can contribute to the functional stem cell compartment at a low level during homeostasis and substantially during regeneration following tissue damage. However the mechanism of, and requirement for, progenitor plasticity in mediating pathological response has not been demonstrated. Here we show that multisite phosphorylation of the transcription factor Atoh1 is required both for the contribution of secretory progenitors to the intestinal stem cell pool and for a robust regenerative response following damage. In lineage tracing experiments Atoh1+ cells (Atoh1(WT)CreERT2 mice) show stem cell activity by giving rise to multilineage intestinal clones both in the steady state and after tissue damage. Notably in the colonic epithelium a single generation of Atoh1+ progenitors sustains 1 in 15 stem cells. In an activating Atoh1(9S/T-A)CreERT2 line, the loss of phosphorylation sites on the Atoh1 protein promotes secretory differentiation and inhibits the contribution of these cells to self-renewal. Finally, in a chemical colitis model the Atoh1+ cells of Atoh1(9S/T-A)CreERT2 mice have reduced clonogenic capacity that impacts overall regenerative response of the epithelium. Thus progenitor plasticity plays an integral part in maintaining robust self-renewal in the intestinal epithelium and the balance between stem and progenitor fate behaviour is directly co-ordinated by Atoh1 multi-site phosphorylation.
SELF-PRUNINGaffects auxin responses synergistically with the cyclophilin A DIAGEOTROPICA in tomato
Authors: Silva Willian B. , Vicente Mateus H. , Robledo Jessenia M. , Reartes Diego S. , Ferrari Renata C. , Bianchetti Ricardo , Araújo Wagner L. , Freschi Luciano , Peres Lázaro E. P. , Zsögön Agustin 
Published: February 2018

SummaryThe antiflorigenic signal SELF-PRUNING, which controls growth habit, exerts its effects through auxin transport, signaling and metabolism in tomato.AbstractTheSELF PRUNING(SP) gene is a key regulator of growth habit in tomato (Solanum lycopersicum). It is an ortholog ofTERMINAL FLOWER 1, a phosphatidyl-ethanolamine binding protein with anti-florigenic activity inArabidopsis thaliana. A spontaneous loss-of-functionspmutation has been bred into a large number of industrial tomato cultivars, as it produces a suite of pleiotropic effects that are favorable for mechanical harvesting, including determinate growth habit, short plant stature and simultaneous fruit ripening. However, the physiological basis for these phenotypic differences has not been thoroughly explained. Here, we show that thespmutation alters polar auxin transport as well as auxin responses such gravitropic curvature and elongation of excised hypocotyl segments. We further demonstrate that free auxin levels and auxin-regulated gene expression patterns are altered insp, with epistatic effects ofdiageotropica, a mutation in a cyclophilin A protein-encoding gene. Our results indicate that SP impacts growth habit in tomato, at least in part, via changes in auxin transport and responsiveness. These findings hint at novel targets that could be manipulated in the control of growth habit and productivity.
Complete assembly of parental haplotypes with trio binning
Authors: Koren Sergey , Rhie Arang , Walenz Brian P. , Dilthey Alexander T. , Bickhart Derek M. , Kingan Sarah B. , Hiendleder Stefan , Williams John L. , Smith Timothy P. L. , Phillippy Adam M. 
Published: February 2018

AbstractReference genome projects have historically selected inbred individuals to minimize heterozygosity and simplify assembly. We challenge this dogma and present a new approach designed specifically for heterozygous genomes. “Trio binning” uses short reads from two parental genomes to partition long reads from an offspring into haplotype-specific sets prior to assembly. Each haplotype is then assembled independently, resulting in a complete diploid reconstruction. On a benchmark human trio, this method achieved high accuracy and recovered complex structural variants missed by alternative approaches. To demonstrate its effectiveness on a heterozygous genome, we sequenced an F1 cross between cattle subspeciesBos taurus taurusandBos taurus indicus, and completely assembled both parental haplotypes with NG50 haplotig sizes >20 Mbp and 99.998% accuracy, surpassing the quality of current cattle reference genomes. We propose trio binning as a new best practice for diploid genome assembly that will enable new studies of haplotype variation and inheritance.
Pathogen susceptibility and fitness costs explain variation in immune priming across natural populations of flour beetles
Authors: Khan Imroze , Prakash Arun , Agashe Deepa 
Published: February 2018

AbstractIn many insects, individuals primed with low doses of pathogens live longer after being exposed to the same pathogen later in life. Yet, our understanding of the evolutionary and ecological history of priming of immune response in natural insect populations is limited. Previous work demonstrated population-, sex- and- stage specific variation in the survival benefit of priming response in flour beetles (Tribolium castaneum) infected with their natural pathogenBacillus thuringiensis. However, the evolutionary forces responsible for this natural variation remained unclear. Here, we tested whether the strength of the priming response (measured as the survival benefit after priming and subsequent infection relative to unprimed controls) was associated with multiple fitness parameters across 10 flour beetle populations. Our results suggest two major selective pressures that may explain the observed inter-population variation in priming: (A) Basal pathogen susceptibility – populations that were more susceptible to infection produced a stronger priming response, and (B) Reproductive success – populations where primed females produced more offspring had lower survival benefit, suggesting a trade-off between priming response and reproduction. Our work is the first empirical demonstration of multiple selective pressures that may govern the adaptive evolution of immune priming in the wild. We hope that this motivates further experiments to establish the role of pathogen-imposed selection and fitness costs in the evolution of priming in natural insect populations.
Association of Arg389Gly β1-adrenergic receptor polymorphism with effective dose of β blocker in congestive heart failure among Chinese Han population
Authors: Gu Rong , Shen Yu , Liu Jianhua , Qiao Shuaihua , Wang Lian , Xu Biao 
Published: February 2018

AbstractBackgroundTo investigate the relationship between β1-adrenergic receptor (ADRB1) gene polymorphisms and the response to medication in patients with congestive heart failure (CHF).Methods and ResultsTwo hundred and sixty patients with CHF were enrolled. Ser49Gly and Arg389Gly polymorphisms were identified. During one-year follow-up, differences of echocardiographic parameters and major adverse cardiac events (MACE) were analyzed. For Ser49Gly polymorphisms, there were no differences between AA genotype and AG/GG genotype of baseline clinical features and echocardiographic parameters as well as one-year incidence of MACE. For Arg389Gly polymorphisms, there were no significant differences in baseline clinical characteristics, LVDd and LVEF among the three genotypes. However, the increase amplitude of LVEF after one year among patients carrying GG genotype was significantly higher than those carrying CC genotype (11.7% vs 1.3%, P<0.05). The incidence of MACE among different genotypes of CC, CG and GG were 22.2%, 10.0% and 8.3%,with statistical difference (P=0.021).ConclusionsThe study suggested there was no relationship between Ser49Gly polymorphisms of the ADRB1 gene and the therapeutic effect and prognosis in CHF patients under the same dosage of drugs. However, the improvement of cardiac function and prognosis in patients carrying the Gly389 allele were significantly better than those of Arg389Arg homozygous.
RiboTag translatomic profiling ofDrosophilaoenocytes under aging and oxidative stress
Authors: Huang Kerui , Chen Wenhao , Zhu Fang , Bai Hua 
Published: February 2018

AbstractBackgroundAging is accompanied with loss of tissue homeostasis and accumulation of cellular damages. As one of the important metabolic centers, aged liver shows altered lipid metabolism, impaired detoxification pathway, increased inflammation and oxidative stress response. However, the mechanisms for these age-related changes still remain unclear. In fruit flies,Drosophila melanogaster, liver-like functions are controlled by two distinct tissues, fat body and oenocytes. Although the role of fat body in aging regulation has been well studied, little is known about how oenocytes age and what are their roles in aging regulation. To address these questions, we used cell-type-specific ribosome profiling (RiboTag) to study the impacts of aging and oxidative stress on oenocyte translatome inDrosophila.ResultsWe show that aging and oxidant paraquat significantly increased the levels of reactive oxygen species (ROS) in adult oenocytes ofDrosophila, and aged oenocytes exhibited reduced sensitivity to paraquat treatment. Through RiboTag sequencing, we identified 3324 and 949 differentially expressed genes in oenocytes under aging and paraquat treatment, respectively. Aging and paraquat exhibit both shared and distinct regulations on oenocyte translatome. Among all age-regulated genes, mitochondrial, proteasome, peroxisome, fatty acid metabolism, and cytochrome P450 pathways were down-regulated, whereas DNA replication and glutathione metabolic pathways were up-regulated. Interestingly, most of the peroxisomal genes were down-regulated in aged oenocytes, including peroxisomal biogenesis factors and beta-oxidation genes. Further analysis of the oenocyte translatome showed that oenocytes highly expressed genes involving in liver-like processes (e.g., ketogenesis). Many age-related transcriptional changes in oenocytes are similar to aging liver, including up-regulation of Ras/MAPK signaling pathway and down-regulation of peroxisome and fatty acid metabolism.ConclusionsOur oenocyte-specific translatome analysis identified many genes and pathways that are shared betweenDrosophilaoenocytes and mammalian liver, highlighting the molecular and functional similarities between the two tissues. Many of these genes are altered in both aged oenocytes and aged liver, suggesting a conserved molecular mechanism underlying oenocyte and liver aging. Thus, our translatome analysis will contribute significantly to the understanding of oenocyte biology, and its role in lipid metabolism, stress response and aging regulation.
ProtaBank: A repository for protein design and engineering data
Authors: Wang Connie Y. , Chang Paul M. , Ary Marie L. , Allen Benjamin D. , Chica Roberto A. , Mayo Stephen L. , Olafson Barry D. 
Published: February 2018

AbstractWe present ProtaBank, a repository for storing, querying, analyzing, and sharing protein design and engineering data in an actively maintained and updated database. ProtaBank provides a format to describe and compare all types of protein mutational data, spanning a wide range of properties and techniques. It features a user-friendly web interface and programming layer that streamlines data deposition and allows for batch input and queries. The database schema design incorporates a standard format for reporting protein sequences and experimental data that facilitates comparison of results across different data sets. A suite of analysis and visualization tools are provided to facilitate discovery, to guide future designs, and to benchmark and train new predictive tools and algorithms. ProtaBank will provide a valuable resource to the protein engineering community by storing and safeguarding newly generated data, allowing for fast searching and identification of relevant data from the existing literature, and exploring correlations between disparate data sets. ProtaBank invites researchers to contribute data to the database to make it accessible for search and analysis. ProtaBank is available athttps://protabank.org.ImpactThe ProtaBank database provides a central repository for researchers to store, query, analyze, and share all types of protein engineering data. This modern database will serve a pivotal role in organizing protein engineering data and leveraging the increasingly large amounts of mutational data being generated. Together with the analysis tools, it will help scientists gain insights into sequence-function relationships, support the development of new predictive tools and algorithms, and facilitate future protein engineering efforts.Abbreviations3Dthree-dimensionalAPIapplication programming interfaceAWSAmazon Web ServicesBLASTBasic Local Alignment Search ToolCmconcentration of denaturant at midpoint of unfolding transitionCSVcomma-separated valuesΔGGibbs free energy of folding/unfoldingGβ1β1 domain of Streptococcal protein GGdmClguanidinium chloridekcatcatalytic rate constantKddissociation constantMICminimum inhibitory concentrationPDBProtein Data BankPEprotein engineeringRDSRelational Database ServicesRESTRepresentation State TransferTmmelting temperature
VirTect: a computational method for detecting virus species from RNA-Seq and its application in head and neck squamous cell carcinoma
Authors: Khan Atlas , Liu Qian , Chen Xuelian , Zeng Yunjing , Stucky Andres , Sedghizadeh Parish P. , Adelpour Daniel , Zhang Xi , Wang Kai , Zhong Jiang F. 
Published: February 2018

AbstractNext generation sequencing (NGS) provides an opportunity to detect viral species from RNA-seq data on human tissues, but existing computational approaches do not perform optimally on clinical samples. We developed a bioinformatics method called VirTect for detecting viruses in neoplastic human tissues using RNA-seq data. Here, we used VirTect to analyze RNA-seq data from 363 HNSCC (head and neck squamous cell carcinoma) patients and identified 22 HPV-induced HNSCCs. These predictions were validated by manual review of pathology reports on histopathologic specimens. Compared to two existing prediction methods, VirusFinder and VirusSeq, VirTect demonstrated superior performance with many fewer false positives and false negatives. The majority of HPV carcinogenesis studies thus far have been performed on cervical cancer and generalized to HNSCC. Our results suggest that HPV-induced HNSCC involves unique mechanisms of carcinogenesis, so understanding these molecular mechanisms will have a significant impact on therapeutic approaches and outcomes. In summary, VirTect can be an effective solution for the detection of viruses with NGS data, and can facilitate the clinicopathologic characterization of various types of cancers with broad applications for oncology.Significance StatementWe developed a new bioinformatics tool, and reported the new inside of HPV carcinogenesis mechanism in HPV-induced head and neck squamous cell carcinoma (HNSCC). This novel bioin-formatics tool and the new knowledge of HPV-induced HNSCC will facilitate the development of target therapies for treating HNSCC.
Numerical simulation of flow field in the Invar alloy laser–MIG hybrid welding pool based on different heat source models
Authors: Zhan Xiaohong , Zhang Qi , Wang Qibing , Chen Jie , Liu Hongbing , Wei Yanhong 
Published: February 2018

Purpose
The purpose of this paper is to establish a three-dimensional flow field model of the Invar alloy laser–metal inert gas (laser–MIG) hybrid welding process to investigate the influence of different heat sources between different layers and to analyze the flow field based on the two different heat source models for the multilayer welding.

Design/methodology/approach
The Invar steel plates with 19.5 mm thickness are welded into three layers’ seam using the hybrid laser–MIG welding technology. The flow field based on different heat source models is studied and then used to investigate the influence of different heat sources in different layers during the laser–MIG hybrid welding process. The simulation results of flow field using two different heat source models are compared with experiments.

Findings
The flow field simulations results show that using the Gaussian rotating body heat source model to simulate the temperature field is more consistent with the experiment of the hybrid laser–MIG welding where its flow field between different layers better reflects the characteristics of the hybrid laser–MIG welding.

Originality/value
The findings will be useful in the study of a variety of thick-plate laser–MIG hybrid welding process fluid flows.
Effect of work of adhesion on deep bed filtration process
Authors: Przekop Rafał , Jackiewicz-Zagórska Anna , Woźniak Michał , Gradoń Leon 
Published: February 2018

Purpose
The purpose of this work was to study the influence of particles and fiber material properties on the deposition efficiency. Collection of aerosol particles in the particular steps of their production, and purification of the air at the workplace and the atmospheric environment requires the efficient method of separation of particulate matter from the carrier gas. There are many papers published in the past years in which the deposition of particles on fibrous collectors is considered. Most of them assume that collisions between particles and collector surfaces are 100% effective.

Design/methodology/approach
For the purpose of this work, the lattice Boltzmann model was used to describe fluid dynamics, whereas the solid particles motion was modeled by the Brownian dynamics. The interactions between particles and surfaces were modeled using an energy-balanced oscillatory model.

Findings
The results show significant impact of material properties on filter performance.

Practical implications
Obtained results may provide useful information for the proper design of a filtration process and the production of filters with long service life.

Originality/value
In addition, the results presented in this work show that some assumptions of the classical filtration theory lead to an overestimation of deposition efficiency.