bluuebunny/crossref_metadata_2025_split huggingface dataset:
The aryl hydrocarbon receptor and interferon gamma generate antiviral states via transcriptional repression
Authors: Kueck Tonya , Cassella Elena , Holler Jessica , Kim Baek , Bieniasz Paul D. 
Published: June 2018

SummaryThe aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor whose activation induces the expression of numerous genes, with many effects on cells. However, AhR activation is not known to affect the replication of viruses. We show that AhR activation in macrophages causes a block to HIV-1 and HSV-1 replication. We find that AhR activation transcriptionally represses cyclin-dependent kinase (CDK)1/2 and their associated cyclins, thereby reducing SAMHD1 phosphorylation, cellular dNTP levels and both HIV-1 and HSV-1 replication. Remarkably, a different antiviral stimulus, interferon gamma (IFN-γ), that induces a largely non-overlapping set of genes, also transcriptionally represses CDK1, CDK2 and their associated cyclins, resulting in similar dNTP depletion and antiviral effects. Concordantly, the SIV Vpx protein provides complete and partial resistance to the antiviral effects of AhR and IFN-γ, respectively. Thus, distinct antiviral signaling pathways converge on CDK/cyclin repression, causing inhibition of viral DNA synthesis and replication.
Optimal growth conditions and nutrient degradation characteristics of an aerobic denitrifying bacterium
Authors: Ling Sun , Juanjuan Shi 
Published: June 2018

AbstractAn efficient aerobic denitrifying bacterium, QX1, identified as Arthrobacter sp. by morphological observations, physiological-biochemical tests, and 16s rDNA sequence analysis, was isolated from burdock fields. A phylogenetic tree for this strain was built based on the 16s rDNA sequence, and the effects of nitrogen source, carbon source, pH value, and temperature on the growth of the strain, in addition to its denitrification characteristics, were evaluated. The results showed that under conditions of a gas bath with shaking at 160 rpm, suitable growth conditions for this strain were LB medium plus 1% acetic acid sodium, 30°C, and pH 8. With these conditions, the strain grew to the logarithmic phase after about 4 h, the logarithmic phase was maintained for 16 h, steady growth was observed for 24 h, and growth began to decline thereafter. QX1 exhibited alkali resistance and could tolerate low (15°C) and high temperatures (40°C). At 30°C, pH 8, and shaking at 160 rpm, strains could degrade nitrate, with a removal rate of 89.92% within 48 h in synthetic sewage. Thus, strain QX1 could have applications as an alkaline-tolerant, broad-spectrum temperature-tolerant, efficient denitrifying bacterium in the field of denitrification repair.
Innovative method for reducing uninformative calls in non-invasive prenatal testing
Authors: Budis Jaroslav , Gazdarica Juraj , Radvanszky Jan , Szucs Gabor , Kucharik Marcel , Strieskova Lucia , Gazdaricova Iveta , Harsanyova Maria , Duris Frantisek , Minarik Gabriel , Sekelska Martina , Nagy Balint , Turna Jan , Szemes Tomas 
Published: June 2018

AbstractMotivationNon-invasive prenatal testing or NIPT is currently among the top researched topic in obstetric care. While the performance of the current state-of-the-art NIPT solutions achieve high sensitivity and specificity, they still struggle with a considerable number of samples that cannot be concluded with certainty. Such uninformative results are often subject to repeated blood sampling and re-analysis, usually after two weeks, and this period may cause a stress to the future mothers as well as increase the overall cost of the test.ResultsWe propose a supplementary method to traditional z-scores to reduce the number of such uninformative calls. The method is based on a novel analysis of the length profile of circulating cell free DNA which compares the change in such profiles when random-based and length-based elimination of some fragments is performed. The proposed method is not as accurate as the standard z-score; however, our results suggest that combination of these two independent methods correctly resolves a substantial portion of healthy samples with an uninformative result. Additionally, we discuss how the proposed method can be used to identify maternal aberrations, thus reducing the risk of false positive and false negative calls.Availability and ImplementationA particular implementation of the proposed methods is not provided with the manuscript.ContactCorrespondence regarding the manuscript should be directed at Frantisek Duris (fduris@dcs.fmph.uniba.sk).Supplementary InformationNo additional supplementary information is available.
Food web networks shift across a precipitation gradient due to changes in community composition and species interactions
Authors: Guzman Laura Melissa , Vanschoenwinkel Bram , Farjalla Vinicius F. , Poon Anita , Srivastava Diane 
Published: June 2018

AbstractEcological networks change across spatial and environmental gradients due to (i) changes in species composition or (ii) changes in the frequency or strength of interactions. Here we use the communities of aquatic invertebrates inhabiting clusters of bromeliad phytotelms along the Brazilian coast as a model system for examining turnover in the properties of ecological networks. We first document the variation in the species pools of sites across a geographical climate gradient. Using the same sites, we also explored the geographic variation in species interaction strength using a newly developed Markov network approach. We found that community composition differed along a gradient of water volume within bromeliads due to the turnover of some species. From the Markov network analysis, we found that the top-down effects of certain predators differed geographically, which could also be explained by geographic differences in bromeliad water volumes. Overall, this study illustrates how a network can change across an environmental gradient through both changes in both species and their interactions.
Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR
Authors: Danks Gemma , Galbiati Heloisa , Raasholm Martina , Torres Cleuren Yamila N. , Valen Eivind , Navratilova Pavla , Thompson Eric M. 
Published: June 2018

AbstractIn phylogenetically diverse organisms, the 5’ ends of a subset of mRNAs are trans-spliced with a spliced leader (SL) RNA. The functions of SL trans-splicing, however, remain largely enigmatic. Here, we quantified translation genome-wide in the marine chordate, Oikopleura dioica, under inhibition of mTOR, a central growth regulator. Translation of trans-spliced TOP mRNAs was suppressed, showing that the SL sequence permits nutrient-dependent translational control of growth-related mRNAs. Under crowded, nutrient-limiting conditions, O. dioica continues to filter-feed, but arrests growth until favorable conditions return. Upon release from such conditions, initial recovery was independent of nutrient-responsive, trans-spliced genes, suggesting animal density sensing as a first trigger for resumption of development. Our results demonstrate a role for trans-splicing in the coordinated translational down-regulation of nutrient-responsive genes under limiting conditions.
Mammalian CST averts replication failure by preventing G-quadruplex accumulation
Authors: Liu Yang , Zhang Miaomiao , Wang Bing , Xiao Yingnan , Li Tingfang , Geng X , Li Guang , Liu Qiang , Price Carolyn M. , Wang Feng 
Published: June 2018

AbstractHuman CST (CTC1-STN1-TEN1) is an RPA-like complex that associates with G-rich single-strand DNA and helps resolve replication problems both at telomeres and genome-wide. We previously showed that CST binds and disrupts G-quadruplex (G4) DNAin vitro, suggesting that CST may preventin vivoblocks to replication by resolving G4 structures. Here, we demonstrate that CST binds and unfolds G4 with similar efficiency to RPA. In cells, CST is recruited to telomeric and non-telomeric chromatin upon G4 stabilization. STN1 depletion increases G4 accumulation and slows bulk genomic DNA replication. At telomeres, combined STN1 depletion and G4 stabilization causes multi-telomere FISH signals and telomere loss, hallmarks of deficient telomere duplex replication. Strand-specific telomere FISH indicates preferential loss of C-strand DNA while analysis of BrdU uptake during leading and lagging-strand telomere replication shows preferential under-replication of lagging telomeres. Together these results indicate a block to Okazaki fragment synthesis. Overall, our findings indicate a novel role for CST in maintaining genome integrity through resolution of G4 structures both ahead of the replication fork and on the lagging strand template.
A novel co-segregatingDCTN1splice site variant in a family with Bipolar Disorder may hold the key to understanding the etiology
Authors: Hallen André , Cooper Arthur J.L. 
Published: June 2018

AbstractA novel co-segregating splice site variant in theDynactin-1(DCTN1) gene was discovered by Next Generation Sequencing (NGS) in a family with a history of bipolar disorder (BD) and major depressive diagnosis (MDD). Psychiatric illness in this family follows an autosomal dominant pattern.DCTN1codes for the largest dynactin subunit, namely p150Glued, which plays an essential role in retrograde axonal transport and in neuronal autophagy. A GT→TT transversion in theDCTN1gene, uncovered in the present work, is predicted to disrupt the invariant canonical splice donor site IVS22+1G>T and result in intron retention and a premature termination codon (PTC). Thus, this splice site variant is predicted to trigger RNA nonsense-mediated decay (NMD) and/or result in a C-terminal truncated p150Gluedprotein (ct-p150Glued), thereby negatively impacting retrograde axonal transport and neuronal autophagy. BD prophylactic medications, and most antipsychotics and antidepressants, are known to enhance neuronal autophagy. This variant is analogous to the dominant-negativeGLUED Gl1mutation inDrosophilawhich is responsible for a neurodegenerative phenotype. The newly identified variant may reflect an autosomal dominant cause of psychiatric pathology in this affected family. Factors that affect alternative splicing of theDCTN1gene, leading to NMD and/or ct-p150Glued, may be of fundamental importance in contributing to our understanding of the etiology of BD as well as MDD.
A rapid visuomotor response on the human upper limb is selectively influenced by implicit, but not explicit, motor learning
Authors: Gu(顾超) Chao , Pruszynski J. Andrew , Gribble Paul L. , Corneil Brian D. 
Published: June 2018

SUMMARYHow do humans learn to adapt their motor actions to achieve task success? Recent behavioral and patient studies have challenged the classic notion that motor learning arises solely from the errors produced during a task, suggesting instead that explicit cognitive strategies can act in concert with the implicit, error“based, motor learning component. Here, we show that the earliest wave of directionally-tuned neuromuscular activity that occurs within ~100 ms of peripheral visual stimulus onset is selectively influenced by the implicit component of motor learning. In contrast, the voluntary neuromuscular activity associated with reach initiation, which evolves ~100 to 200 ms later is influenced by both the implicit and explicit components of motor learning. The selective influence of the implicit, but not explicit, component of motor learning on the earliest cascade of neuromuscular activity supports the notion that these components of motor learning can differentially influence descending motor pathways.
An essential mycolate remodeling program for mycobacterial adaptation in host cells
Authors: Peterson Eliza J.R. , Bailo Rebeca , Rothchild Alissa C. , Arrieta-Ortiz Mario , Kaur Amardeep , Pan Min , Mai Dat , Cooper Charlotte , Aderem Alan , Bhatt Apoorva , Baliga Nitin S. 
Published: June 2018

AbstractThe success ofMycobacterium tuberculosis(MTB) stems from its ability to remain hidden from the immune system within macrophages. Here, we report a new technology (Path-seq) to sequence miniscule amounts of MTB transcripts within up to million-fold excess host RNA. Using Path-seq we have discovered a novel transcriptional program forin vivomycobacterial cell wall remodeling when the pathogen infects alveolar macrophages in mice. We have discovered that MadR transcriptionally modulates two mycolic acid desaturasesdesA1/A2to initially promote cell wall remodeling uponin vitromacrophage infection and, subsequently, reduces mycolate biosynthesis upon entering dormancy. We demonstrate that disrupting MadR program is lethal to diverse mycobacteria making this evolutionarily conserved regulator a prime antitubercular target for both early and late stages of infection.One Sentence SummaryNovel technology (Path-seq) discovers cell wall remodeling program duringMycobacterium tuberculosisinfection of macrophages
An open trial of psychodynamic psychotherapy for people with mild-moderate intellectual disabilities with waiting list and follow up control
Authors: Skelly Allan , McGeehan Caoimhe , Usher Robert 
Published: June 2018

PurposeThe purpose of this paper is to examine the outcome of psychodynamic psychotherapy for people with intellectual disabilities (ID), which has a limited but supportive evidence base.Design/methodology/approachThe study is a systematic open trial of flexible-length psychodynamic therapy offered in an urban community to 30 people with mild and moderate ID, presenting with significant emotional distress on the Psychological Therapies Outcome Scale for people with intellectual disabilities (PTOS-ID). Allocation to therapy was made according to an established stepped care approach according to need, and the mean number of sessions was 22.03 (range 7–47). Treatment fidelity was checked via notes review and cases excluded from analysis where there were other significant psychological interventions.FindingsOn both self-report (PTOS-ID) and independent ratings (Health of the Nation Outcome Scales-Learning Disability (HoNOS-LD)) recipients of therapy: did not improve while waiting for therapy; improved significantly during therapy, with large pre–post effect sizes; and retained improvements at six-month follow-up.Research limitations/implicationsWhile it is important to conduct further controlled trials, the findings provide support for previous studies. High rates of abuse and neglect were found in the sample, suggesting that more trauma-informed and relational approaches should be explored for this client group.Originality/valueNo other study of this size has been completed which used dedicated standardised outcome measures, with this therapy type, with both waiting list and follow-up control and with account of model fidelity.
Gender mainstreaming as a strategy to achieve sustainable post-disaster reconstruction
Authors: Yumarni Tri , Amaratunga Dilanthi 
Published: June 2018

Purpose
The purpose of this paper is to discuss policy-relevant findings regarding strategies for mainstreaming gender in achieving sustainable post-disaster reconstruction (PDR).

Design/methodology/approach
An exploratory case study was used to explore the implementation of gender mainstreaming strategies and the link to sustainable PDR. The Bantul and Sleman regencies of Yogyakarta province provide a unique site for researching PDR as they are located in a region that is more strongly affected by earthquakes than nearly any other in Indonesia. Data were collected through interviews with 17 key stakeholders and 26 beneficiaries who were involved during and after the earthquake. To support the interview findings, surveys involving 50 policy makers and 150 beneficiaries were conducted. Content analysis and t-statistics were used in analyzing the data.

Findings
Gender mainstreaming strategies within sustainable reconstruction should incorporate strategies for protecting against gender vulnerabilities and for promoting gender capacities. Both are fundamental to the achievement of sustainable PDR.

Originality/value
The paper establishes comprehensive strategies for mainstreaming gender under three pillars (i.e. economic, social and environmental) of sustainable development. The findings benefit relevant policy makers by improving the policy performance of gender mainstreaming in the affected communities in enhancing sustainable PDR.
Reactions to men’s and women’s counterproductive work behavior
Authors: Botsford Morgan Whitney , Nelson Johnathan , King Eden B. , Mancini Victor S. 
Published: June 2018

PurposeThe purpose of this paper is to clarify the nature of counterproductive work behavior (CWB) gender stereotypicality, and to consider whether despite efforts to systematically evaluate employees through formalized performance appraisal processes, gender-stereotypic bias is likely to enter into performance management systems.Design/methodology/approachStudy 1 used archival data from 197 federal employees to explore actual punishment recommendations allocated to men and women who engaged in a variety of CWBs. Study 2 tested the causal effect of gender stereotypicality on punishment recommendations with 47 EMBA students who participated in a laboratory study.FindingsStudy 1 revealed an interaction between appellant gender and CWB stereotypicality with regard to termination decisions suggesting that women who engage in stereotypical (i.e. feminine) CWBs and men who engage in stereotypical (i.e. masculine) CWBs are more likely to be terminated than women and men who engage in gender counter-stereotypic CWB. Study 2 revealed that women (not men) tended to receive harsher punishment recommendations for stereotypical (i.e. feminine) CWB than for counter-stereotypical (i.e. masculine) CWB.Practical implicationsFindings illustrate that punishments are not universally extreme, as men and women are denigrated differentially depending on the stereotypicality of their behavior. The current research affirms that there are social constructions for evaluating performance that may continue to confound evaluations of performance.Originality/valueThis is one of the first studies to explore the gendered nature of CWB and supports the argument that prescriptive gender stereotypes shape reactions to CWBs.
Institutional regimes and profitability transitions: the case of Indian manufacturing firms
Authors: Majumdar Sumit K. , Bhattacharjee Arnab 
Published: June 2018

PurposeLiterature, spanning industrial organization and strategic management disciplines, uses variance decomposition to understand the relative importance of firm, industry and business group effects in shaping profitability variations. Some literature analyzes firm profitability under transition to liberalization. Previous research has taken a static before-and-after view on institutional change. This paper aims to focus on the dynamic process of liberalization in India, analyzing how different institutional regime changes alter firm behavior leading to changes in profitability patterns.Design/methodology/approachBased on a panel data set of several thousand Indian firms, spanning the 26-year period between 1980-1981 and 2005-2006, the authors determine the relative importance of firm, industry and business group effects in explaining manufacturing firms’ profitability variances across different institutional phases. The authors evaluate three propositions that help assess transition dynamics between phases. They determine the quantum of catch-up or falling behind by firms.FindingsDifferent industries emerge as profitability leaders, as the economy progresses through different liberalization phases. Business groups that have been more effective in resource appropriation, rent-seeking, politician management and non-market activities in a controlled regime are replaced as profit leaders by those that, in a free-market economy, can be capable of intra-business resource allocation tasks and leveraging corporate capabilities.Originality/valueThe approach demonstrates how to analyze the underlying detailed structure of firm-level data, and performance outcomes, to derive nuanced interpretation of factors giving rise to the effects that explain profitability variances, and how to assess the way these effects behave over time. The dynamic evidence-based approach highlights what factors matter, where, when and why, in influencing profitability variances, which are a key dimension of industrial and economic performance.
Accounting quality and media attention around seasoned equity offerings
Authors: Comiran Fernando , Fedyk Tatiana , Ha Joohyung 
Published: June 2018

Purpose
This paper aims to investigate how media coverage affects the quality of accounting information for seasoned equity offering (SEO) firms.

Design/methodology/approach
The sample includes SEOs completed between January 1993 and December 2014 in the USA that are available from Thomson Financial’s Securities Data Company. The FactSet database was used to measure the amount of media coverage. The paper considers two types of earnings management: accrual-based earnings management and real earnings management.

Findings
This study finds that the media serves as a watchdog for real earnings management but does not affect accrual manipulations. These findings hold when endogenous factors affecting firms’ earnings management choices are controlled for and also when alternative time windows for media coverage are examined.

Originality/value
This paper is the first to demonstrate that media attention affects the quality of accounting information during equity offerings, as it successfully reduces real earnings management.
A model of mobile payment usage among Arab consumers
Authors: Ramadan Reem , Aita Jawdat 
Published: June 2018

Purpose
The purpose of this paper is to investigate the impact of perceived satisfaction with mobile payment applications based on use experience, and subsequent stated expectations on brand loyalty and future use behavior using a theory-based research integrative model of factors that influence Arabs’ intentions to use mobile payment application(s).

Design/methodology/approach
A conceptual model was developed using the mixed research method approach. The focus group approach was used for the qualitative study and structural equation modeling for the quantitative study. Primary data were collected online. Participants were 305 Arab consumers from nine countries in the Middle East.

Findings
Satisfaction with the quality of mobile payment application(s) increased use experience and enhanced consumers’ expectations, which in turn positively affected loyalty and purchase intentions.

Research limitations/implications
The study encompassed mobile payment application(s) in nine countries rather than focusing on one market, or on one product type and business. The paper did not perform a comparative study between sampled Arab countries, but rather it sees all countries and respondents just as Arabs.

Practical implications
Service providers should build mobile application(s) based on the features of usability, availability, reliability, adaptability, accessibility, responsiveness and security.

Originality/value
This study is one of the first studies that empirically examines mobile payment consumer’s usage behavior from nine countries of the Arab world where there is scarce research on the topic in the region.