bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defense Style of Children and Adolescents
Authors: Wolmer Leo , Erez Chen , Toren Paz 
Published: March 2020

Abstract
This study assessed the defense style of children referred to an outpatient clinic and examined what this style contributes to discriminating among various disorder categories, beyond internalizing and externalizing symptoms. A sample of 433 children and adolescents were grouped into four disorder categories: disruptive, depressive, anxiety, and attention deficit hyperactivity disorder. Their parents completed the Comprehensive Assessment of Defense Style (CADS: mature, self-oriented, and other-oriented) and the Child Behavior Checklist (CBCL: internalizing and externalizing symptoms). The disorder categories differed in the use of other-oriented defenses (e.g., acting-out, projection), whereas the CADS helped in properly discriminating most diagnostic categories beyond the CBCL. Information provided by the children themselves was missing, as was a subsample of nonclinical participants; these sources could strengthen the conclusions of the study. Assessing children's defense style together with their symptoms may result in better statistical discrimination among diagnostic categories.
A transcription-centric model of SNP-Age interaction
Authors: Wang Kun , Basu Mahashweta , Malin Justin , Hannenhalli Sridhar 
Published: March 2020

AbstractComplex age-associated phenotypes are caused, in part, by an interaction between an individual’s genotype and age. The mechanisms governing such interactions are however not entirely understood. Here, we provide a novel transcriptional mechanism-based framework – SNiPage, to investigate such interactions, whereby a transcription factor (TF) whose expression changes with age (age-associated TF), binds to a polymorphic regulatory element in an allele-dependent fashion, rendering the target gene’s expression dependent on both, the age and the genotype. Applying SNiPage to GTEx, we detected ~637 interacting TF-SNP-Gene triplets on average across 25 tissues, where the TF binds to a regulatory SNP in the gene’s promoter or putative enhancer and potentially regulates its expression in an age- and allele-dependent fashion. The detected SNPs are enriched for epigenomic marks indicative of regulatory activity, exhibit allele-specific chromatin accessibility, and spatial proximity to their putative gene targets. Furthermore, the TF-SNP interaction-dependent target genes have established links to aging and to age-associated diseases. In six hypertension-implicated tissues, detected interactions significantly inform hypertension state of an individual. Lastly, the age-interacting SNPs exhibit a greater proximity to the reported phenotype/diseases-associated SNPs than eSNPs identified in an interaction-independent fashion. Overall, we present a novel mechanism-based model, and a novel framework SNiPage, to identify functionally relevant SNP-age interactions in transcriptional control and illustrate their potential utility in understanding complex age-associated phenotypes.
Establishing Preclinical Withdrawal Syndrome Symptomatology Following Heroin Self-Administration in Male and Female Rats
Authors: Gipson Cassandra D. , Dunn Kelly E. , Bull Amanda , Ulangkaya Hanaa , Hossain Aronee 
Published: March 2020

AbstractOpioid use disorder (OUD) is a significant health problem, and understanding mechanisms of various aspects of OUD including drug use and withdrawal is important. Preclinical models provide an ideal opportunity to evaluate mechanisms underlying opioid withdrawal. Current models are limited by their reliance upon forced opioid administration, focus on the acute (and not protracted) syndrome, and exclusion of females. In this study, male and female rats self-administered heroin (maintenance dose of 12.5 μg/kg/infusion) opioid withdrawal following abrupt discontinuation was measured. In Phase 1, acute withdrawal symptoms were rated in male and female rats at 0, 16, 48, and 72 hrs following the last self-administration session. Total somatic signs increased until 48 hrs (predominantly in females), and heroin intake positively correlated with total somatic signs at the 48 and 72 hr timepoints. Measures of hyperactivity and anxiety-like behavior increased by 16 and 48 hrs, respectively. In Phase 2, symptoms were assessed at baseline, acute, and protracted (168 and 312 hrs after self-administration) timepoints in a subset of male and female rats from Phase 1. The total number of somatic signs did not differ across timepoints, though females displayed significantly higher body temperature at all timepoints compared to males, indicating sex-specific protracted withdrawal symptomatology. These data provide a thorough characterization of rodent opioid withdrawal symptomatology following self-administration and abrupt discontinuation that serve as a foundation for future studies designed to mimic the human experience, and demonstrate the importance of characterizing acute and protracted withdrawal with sex-specificity in preclinical models of opioid self-administration.
A draft genome assembly of the eastern banjo frog Limnodynastes dumerilii dumerilii (Anura: Limnodynastidae)
Authors: Li Qiye , Guo Qunfei , Zhou Yang , Tan Huishuang , Bertozzi Terry , Zhu Yuanzhen , Li Ji , Donnellan Stephen , Zhang Guojie 
Published: March 2020

AbstractAmphibian genomes are usually challenging to assemble due to large genome size and high repeat content. The Limnodynastidae is a family of frogs native to Australia, Tasmania and New Guinea. As an anuran lineage that successfully diversified on the Australian continent, it represents an important lineage in the amphibian tree of life but lacks reference genomes. Here we sequenced and annotated the genome of the eastern banjo frog Limnodynastes dumerilii dumerilii to fill this gap. The total length of the genome assembly is 2.38 Gb with a scaffold N50 of 285.9 kb. We identified 1.21 Gb of non-redundant sequences as repetitive elements and annotated 24,548 protein-coding genes in the assembly. BUSCO assessment indicated that more than 94% of the expected vertebrate genes were present in the genome assembly and the gene set. We anticipate that this annotated genome assembly will advance the future study of anuran phylogeny and amphibian genome evolution.
Force-Field Benchmarking by Alternatives: A Systematic Study of Ten Small α- and β-Proteins
Authors: Jana Kalyanashis , Kepp Kasper P. 
Published: March 2020

AbstractPredicting protein structure from sequence is a central challenge of biochemistry, yet different force fields feature distinct structural biases that are hard to quantify, preventing clear assessment of results. Since structural transitions occur on milliseconds to seconds, sampling is out of reach in almost all routine studies, we inherently rely on local sampled structures, and benchmarks have emphasized the ability to reproduce these local structures. Here we approach the force field bias problem in a different way, viaalternatives, by revisiting the old question: How unique is the sequence-structure relationship when studied computationally? To circumvent the sampling problem, the system-bias (specific structure choices affect apparent force field structural preference) and the complexity of tertiary structure, we studied ten small α- and β-proteins (20-35 amino acids) with one helix or sheet. For each of the ten sequences, we then designed alternative β- or α-structures and subjected all 20 proteins to molecular dynamics simulations. We apply this “alternative structure” benchmark to five of the best modern force fields: Amber ff99SB-ILDN, Amber ff99SB*-ILDN, CHARMM22*, CHARMM36, and GROMOS54A8. Surprisingly, we find thatallsequences with reported β-structures also feature stable native-like α-structures with all five force fields. In contrast, only the alternative β-1T5Q and to some extent β-1CQ0 and β-1V1D resembled native β-proteins. With full phase space sampling being impossible in almost all cases, our benchmark by alternatives, which samples another local part of phase space in direct comparison, is a useful complement to millisecond benchmarks when these become more common.
Hsp27 reduces glycation-induced toxicity and aggregation of α-synuclein
Authors: Miranda Hugo Vicente , Chegão Ana , Oliveira Márcia , Gomes Bárbara Fernandes , Enguita Francisco J. , Outeiro Tiago Fleming 
Published: March 2020

Abstractα-synuclein (aSyn) is a major player in Parkinson’s disease (PD) and a group of other disorders collectively known as synucleinopathies, but the precise molecular mechanisms involved are still unclear. aSyn, as virtually all proteins, undergoes a series of posttranslational modifications (PTMs) during its lifetime which can affect its biology and pathobiology. We recently showed that glycation of aSyn by methylglyoxal (MGO) potentiates its oligomerization and toxicity, induces dopaminergic neuronal cell loss in mice, and affects motor performance in flies. Small heat-shock proteins (sHsps) are molecular chaperones that facilitate the folding of proteins or target misfolded proteins for clearance. Importantly, sHsps were shown to prevent aSyn aggregation and cytotoxicity. Upon treating cells with increasing amounts of methylglyoxal, we found that the levels of Hsp27 decreased in a dose-dependent manner. Therefore, we hypothesized that restoring the levels of Hsp27 in glycating environments could alleviate the pathogenicity of aSyn. Consistently, we found that Hsp27 reduced MGO-induced aSyn aggregation in cells, leading to the formation of non-toxic aSyn species. Remarkably, increasing the levels of Hsp27 suppressed the deleterious effects induced by MGO. Our findings suggest that in glycating environments, the levels of Hsp27 are important for modulating the glycation-associated cellular pathologies in synucleinopathies.
Reducing reference bias using multiple population reference genomes
Authors: Chen Nae-Chyun , Solomon Brad , Mun Taher , Iyer Sheila , Langmead Ben 
Published: March 2020

AbstractMost sequencing data analyses start by aligning sequencing reads to a linear reference genome. But failure to account for genetic variation causes reference bias and confounding of results downstream. Other approaches replace the linear reference with structures like graphs that can include genetic variation, incurring major computational overhead. We propose the “reference flow” alignment method that uses multiple population reference genomes to improve alignment accuracy and reduce reference bias. Compared to the graph aligner vg, reference flow achieves a similar level of accuracy and bias avoidance, but with 14% of the memory footprint and 5.5 times the speed.
Development of Wheat-Aegilops caudataIntrogression Lines and Their Characterisation Using Genome-Specific KASP Markers
Authors: Grewal Surbhi , Othmeni Manel , Walker Jack , Edwards Stella Hubbart , Yang Cai-yun , Scholefield Duncan , Ashling Stephen , Isaac Peter , King Ian P. , King Julie 
Published: March 2020

ABSTRACTAegilops caudataL. [syn.Ae. markgrafii(Greuter) Hammer], a diploid wild relative of wheat (2n = 2x = 14, CC), is an important source for new genetic variation for wheat improvement due to a variety of disease resistance factors along with tolerance for various abiotic stresses. Its practical utilisation in wheat improvement can be facilitated through the generation of genome-wide introgressions leading to a variety of different wheat–Ae. caudatarecombinant lines. In this study, we report the generation of nine such wheat–Ae. caudatarecombinant lines which were characterized using wheat genome-specific KASP (Kompetitive Allele Specific PCR) markers and multi-colour genomicin situhybridization (mcGISH). Of these, six lines have stable homozygous introgressions fromAe. caudataand will be used for future trait analysis. Through a combination of molecular and cytological analysis of all the recombinant lines, we were able to physically map 182 KASP markers onto the sevenAe. caudatachromosomes, of which 155 were polymorphic specifically with only one wheat subgenome. Comparative analysis of the physical positions of these markers in theAe. caudataand wheat genomes confirmed that the former had chromosomal rearrangements with respect to wheat, as previously reported. These wheat–Ae. caudatarecombinant lines and KASP markers provide a useful genetic resource for wheat improvement with the latter having a wider impact as a tool for detection of introgressions from other Aegilops species into wheat.
Reprogramming progressive cells display low CAG promoter activity
Authors: Hu Xiao , Wu Qiao , Zhang Jian , Chen Xinyue , Hartman Amaleah , Eastman Anna , Guo Shangqin 
Published: March 2020

AbstractThere is wide variability in the propensity of somatic cells to reprogram into pluripotency in response to the Yamanaka factors. How to segregate these variability to enrich for cells of specific traits that reprogram efficiently remains challenging. Here we report that the variability in reprogramming propensity is associated with the activity of the MKL1/SRF transcription factor and concurs with small cell size as well as rapid cell cycle. Reprogramming progressive cells can be prospectively identified by their low activity of a widely used synthetic promoter, CAG. CAGlowcells arise and expand during cell cycle acceleration in the early reprogramming culture of both mouse and human fibroblasts. Our work illustrate a molecular scenario underlying the distinct reprogramming propensities and demonstrate a convenient practical approach for their enrichment.
CryoEM structure of the Vibrio cholerae Type IV competence pilus secretin PilQ
Authors: Weaver Sara J. , Sazinsky Matthew H. , Dalia Triana N. , Dalia Ankur B. , Jensen Grant J. 
Published: March 2020

AbstractNatural transformation is the process by which bacteria take up genetic material from their environment and integrate it into their genome by homologous recombination. It represents one mode of horizontal gene transfer and contributes to the spread of traits like antibiotic resistance. InVibrio cholerae, the Type IV competence pilus is thought to facilitate natural transformation by extending from the cell surface, binding to exogenous DNA, and retracting to thread this DNA through the outer membrane secretin, PilQ. A lack of structural information has hindered our understanding of this process, however. Here, we solved the first ever high-resolution structure of a Type IV competence pilus secretin. A functional tagged allele of VcPilQ purified from nativeV. choleraecells was used to determine the cryoEM structure of the PilQ secretin in amphipol to ∼2.7 Å. This structure highlights for the first time key differences in the architecture of the Type IV competence pilus secretin from the Type II and Type III Secretin System secretins. Based on our cryoEM structure, we designed a series of mutants to interrogate the mechanism of PilQ. These experiments provide insight into the channel that DNA likely traverses to promote the spread of antibiotic resistance via horizontal gene transfer by natural transformation. We prove that it is possible to reduce pilus biogenesis and natural transformation by sealing the gate, suggesting VcPilQ as a new drug target.
Structure and mechanism of a primate ferroportin
Authors: Ren Zhenning , Gao Shuai , Shen Jiemin , Wang Lie , Xu Zhichun , Yu Ye , Bachina Preetham , Zhang Hanzhi , Laganowsky Arthur , Yan Nieng , Zhou Ming , Pan Yaping 
Published: March 2020

AbstractFerroportin is the only cellular iron exporter in human and essential for iron homoeostasis. Mutations in ferroportin are associated with hemochromatosis or ferroportin diseases characterized by a paradoxical combination of anemia and abnormal accumulation of iron in cells. Ferroportin is also the target of hepcidin, which is a hormone that downregulates ferroportin activity. However, due to a lack of three-dimensional structures, the mechanism of iron transport by ferroportin and its regulation by hepcidin remains unclear. Here we present the structure of a ferroportin from the primate Philippine tarsier (TsFpn) at 3.0 Å resolution determined by cryo-electron microscopy. TsFpn has a structural fold common to major facilitator superfamily of transporters and the current structure is in an outward-open conformation. The structure identifies two potential ion binding sites with each site coordinated by two residues. Functional studies demonstrate that TsFpn is a H+/Fe2+antiporter and that transport of one Fe2+is coupled to the transport of two H+in the opposite direction such that the transport cycle is electroneutral. Further studies show that the two ion binding sites affect transport of H+and Fe2+differently. The structure also provides mechanistic interpretation for mutations that cause ferroportin diseases.
Influence of the area of a thermal pad on optical and thermal parameters of LED modules
Authors: Górecki Krzysztof , Ptak Przemysław Piotr 
Published: March 2020

Purpose
The purpose of this paper is to present and discuss the results of measurements illustrating influence of the area of a thermal pad and the kind of the used base on thermal and optical parameters of LED modules.

Design/methodology/approach
LED modules including six power LEDs are designed. In the layout of these modules, different areas of a thermal pad of each LED are used. These modules are made using the classical FR-4 base and metal core printed circuit board (MCPCB). Thermal and optical parameters of all the tested modules are measured using the method elaborated by the authors.

Findings
The obtained results of measurements prove that increasing the area of a thermal pad causes a decrease in thermal resistance of the tested LED modules and an increase in power density of the emitted light. The role of the area of a thermal pad is more important for the classical FR-4 base than for MCPCB.

Research limitations/implications
Investigations were performed for only two values of the area of thermal pads and selected values of LEDs forward current.

Originality/value
The presented results of investigations show how the used layout and type of the used base of these modules influence optical and thermal parameters of LED modules. Changing the base of a module can cause even a double decrease in thermal resistance and a double increase in power density of the emitted light.
Gender, technology and decision-making: insights from an experimental conjoint analysis
Authors: Bendell Bari L. , Sullivan Diane M. , Hanek Kathrin J. 
Published: March 2020

PurposeThe purpose of this paper is to investigate differences in how men and women small- and medium-sized enterprise (SME) entrepreneurs make decisions regarding whether to invest in technologies for their firms. Answering recent calls for a gendered perspective in entrepreneurial decision-making, this study integrates premises from social identity theory and role congruity theory to help explain innovation investment decisions among male and female SME entrepreneurs.Design/methodology/approachUsing data from 121 SME entrepreneurs in the dry cleaning industry, the authors employ a conjoint experimental methodology to capture decisions SME entrepreneurs make to adopt or reject an environment-friendly dry cleaning technology. The authors examine the role gender, firm revenue, technology price, and technology complexity play in entrepreneur investment decisions.FindingsThe authors find that gender indirectly impacts innovation purchase decisions through interactions with firm revenue and key innovation characteristics. Women SME entrepreneurs were less likely to purchase the technology than their male counterparts at low (and high) firm revenue, high innovation price, and high innovation complexity—all highly risky, masculine, choice contexts.Research limitations/implicationsThese findings suggest that men and women's entrepreneurial investment decisions might be shaped by gender stereotypes. Future research should sample additional industries and determine the norms guiding gendered decision-making.Originality/valueBeyond the decision to launch a new venture, this multi-level analysis, using the lens of social identity and role congruity theories, helps illuminate how men and women SME entrepreneurs approach innovation investment decision-making in significantly different—and gender role consistent—ways.
NIMBYs for the rich and YIMBYs for the poor: analyzing the property price effects of infill development
Authors: Brunes Fredrik , Hermansson Cecilia , Song Han-Suck , Wilhelmsson Mats 
Published: March 2020

PurposeThis paper aims to analyze how nearby property prices are affected by new construction projects in Stockholm. If there is an impact on property prices, the authors endeavor to investigate whether the effects vary among different areas within the municipality, for different groups of inhabitants and for different types of housing (i.e. public versus private housing).Design/methodology/approachThe authors use a difference-in-difference specification in a hedonic model, and the sample consists of more than 90,000 observations over the period 2005-2013.FindingsThe results are robust and indicate that house prices in nearby areas increase following the completion of infill development. The results also indicate that infill development has a positive spillover effect on nearby dwelling prices only in areas with lower incomes, more public housing units and more inhabitants born abroad.Originality/valueIt provides an analysis on how nearby property prices are affected by new construction projects by creating a restricted control area, so as to make the treatment group and the control group more homogeneous. Thus, it mitigates any potential problems with spatial dependency, which can cause biased standard errors.
Mandatory adoption of IFRS and its effect on international stock listings in Canada
Authors: Khan Shahid , Abdou Khaled , Ghosh Sudip 
Published: March 2020

PurposeThe purpose of this study is to investigate if non-US/non-Canada (international) equity listings in the Canadian stock exchanges increased with the adoption of International Financial Reporting Standards (IFRS) in Canada. A question of interest is whether the adoption of common global accounting standards (IFRS) was beneficial in attracting international firms to the Canadian exchanges.Design/methodology/approachThe authors use difference-in-difference ordinary least square methodology to conduct inter-country (between Canada and the USA) and intra-country (between the Toronto Stock Exchange [TSX] and the TSX Venture Exchange [TSXV]) tests to investigate whether there is increased listings of international firms on Canada’s exchanges associated with mandatory adoption of IFRS in Canada compared to such listings in the American exchanges.FindingsThe authors did not find evidence of a relative increase in listings by international firms on the TSX and the TSXV after Canadian adoption of IFRS, but they did find that listings by international firms on the TSX, Canada’s primary exchange, increased when the authors include the year before mandatory Canadian adoption as part of the IFRS adoption period. The authors also find that international listings from outside the North American, European and Australasian regions increased on the TSXV, consistent with IFRS adoption making the smaller Canadian exchange more attractive to listers from these regions.Originality/valueWith the increasing use of IFRS throughout the world, US regulators, the US Congress and other capital market participants seek to understand the costs and benefits of potential IFRS adoption in the USA. The authors contribute to this debate by examining the effect of Canada’s adoption of IFRS on growth in international stock listings in the Canadian stock exchanges.