bluuebunny/crossref_metadata_2025_split huggingface dataset:
Habitat Associations of Juvenile Burbot in a Tributary of the Kootenai River
Authors: Beard Zachary S. , Quist Michael C. , Hardy Ryan S. , Ross Tyler J. 
Published: July 2017

AbstractBurbot Lota lota in the lower Kootenai River, Idaho, have been the focus of extensive conservation efforts, particularly conservation aquaculture. One of the primary management strategies has been the release of Burbot into small tributaries in the Kootenai River basin, such as Deep Creek. Since 2012, approximately 12,000 juvenile Burbot have been stocked into Deep Creek; however, little is known about the habitat use of stocked Burbot. The objective of this study was to evaluate habitat associations of juvenile Burbot in Deep Creek. Fish and habitat were sampled from 58 reaches of the creek. Regression models suggested that Burbot moved little after stocking and were associated with areas of high mean depth and coarse substrate. This study provides additional knowledge on habitat associations of juvenile Burbot and suggests that managers should consider selecting deep habitats with coarse substrate for stocking locations.Received December 15, 2016; accepted May 22, 2017 Published online July 31, 2017
Spawning Habitat of Hatchery Spring Chinook Salmon and Possible Mechanisms Contributing to Lower Reproductive Success
Authors: Hughes Michael S. , Murdoch Andrew R. 
Published: July 2017

AbstractSpawning is a critical stage in the life history of salmonids. Spawning location has been reported to be a significant factor in the fitness differences between natural‐ and hatchery‐origin (natural and hatchery, respectively) female spring Chinook Salmon Oncorhynchus tshawytscha, although the mechanisms responsible remain uncertain. The objectives of this study were to compare the spawning distributions of hatchery and natural female spring Chinook salmon within the Chiwawa River, Washington, and determine whether spawning characteristics differ between hatchery and natural female Chinook Salmon or between channel types within the Chiwawa River. Over a 10‐year period, locations of female carcasses were examined to assess differences in the spawning distribution of hatchery and natural females. Additionally, a suite of metrics was measured from redds of known origin females to characterize the spawning location and redd characteristics. A greater proportion of hatchery females spawned in the lower watershed within plane‐bed channels than spawned upstream. Conversely, the majority of natural females spawned farther upstream in pool‐riffle channels. The distribution of hatchery fish was presumably strongly influenced by the hatchery acclimation–release location in the lower river. Given the geomorphic characteristics of plane‐bed channels, salmon were unable to build redds there similar to those in more typical pool‐riffle channels. Redds constructed in plane‐bed channels were smaller, shallower, and closer to stream banks than redds in pool‐riffle channels. Limited differences were detected in redd characteristics between natural and hatchery females in pool‐riffle channels. Smaller hatchery females constructed smaller redds with lower tailspill relief than did larger natural fish. As the results of differences in spawning distribution and fish size, redds constructed by hatchery females were more susceptible to environmental sources of mortality than were redds constructed by natural females. This study provides insight into the possible mechanisms responsible for the reported lower reproductive success among hatchery females spawning in the natural environment.Received December 14, 2016; accepted May 24, 2017 Published online July 31, 2017
Connections between the human gut microbiome and gestational diabetes mellitus
Authors: Kuang Ya-Shu , Lu Jin-Hua , Li Sheng-Hui , Li Jun-Hua , Yuan Ming-Yang , He Jian-Rong , Chen Nian-Nian , Xiao Wan-Qing , Shen Song-Ying , Qiu Lan , Wu Ying-Fang , Hu Cui-Yue , Wu Yan-Yan , Li Wei-Dong , Chen Qiao-Zhu , Deng Hong-Wen , Papasian Christopher J. , Xia Hui-Min , Qiu Xiu 
Published: July 2017

Abstract
The human gut microbiome can modulate metabolic health and affect insulin resistance, and it may play an important role in the etiology of gestational diabetes mellitus (GDM). Here, we compared the gut microbial composition of 43 GDM patients and 81 healthy pregnant women via whole-metagenome shotgun sequencing of their fecal samples, collected at 21–29 weeks, to explore associations between GDM and the composition of microbial taxonomic units and functional genes. A metagenome-wide association study identified 154 837 genes, which clustered into 129 metagenome linkage groups (MLGs) for species description, with significant relative abundance differences between the 2 cohorts. Parabacteroides distasonis, Klebsiella variicola, etc., were enriched in GDM patients, whereas Methanobrevibacter smithii, Alistipes spp., Bifidobacterium spp., and Eubacterium spp. were enriched in controls. The ratios of the gross abundances of GDM-enriched MLGs to control-enriched MLGs were positively correlated with blood glucose levels. A random forest model shows that fecal MLGs have excellent discriminatory power to predict GDM status. Our study discovered novel relationships between the gut microbiome and GDM status and suggests that changes in microbial composition may potentially be used to identify individuals at risk for GDM.
Population-wide sampling of retrotransposon insertion polymorphisms using deep sequencing and efficient detection
Authors: Yu Qichao , Zhang Wei , Zhang Xiaolong , Zeng Yongli , Wang Yeming , Wang Yanhui , Xu Liqin , Huang Xiaoyun , Li Nannan , Zhou Xinlan , Lu Jie , Guo Xiaosen , Li Guibo , Hou Yong , Liu Shiping , Li Bo 
Published: July 2017

Abstract
Active retrotransposons play important roles during evolution and continue to shape our genomes today, especially in genetic polymorphisms underlying a diverse set of diseases. However, studies of human retrotransposon insertion polymorphisms (RIPs) based on whole-genome deep sequencing at the population level have not been sufficiently undertaken, despite the obvious need for a thorough characterization of RIPs in the general population. Herein, we present a novel and efficient computational tool called Specific Insertions Detector (SID) for the detection of non-reference RIPs. We demonstrate that SID is suitable for high-depth whole-genome sequencing data using paired-end reads obtained from simulated and real datasets. We construct a comprehensive RIP database using a large population of 90 Han Chinese individuals with a mean ×68 depth per individual. In total, we identify 9342 recent RIPs, and 8433 of these RIPs are novel compared with dbRIP, including 5826 Alu, 2169 long interspersed nuclear element 1 (L1), 383 SVA, and 55 long terminal repeats. Among the 9342 RIPs, 4828 were located in gene regions and 5 were located in protein-coding regions. We demonstrate that RIPs can, in principle, be an informative resource to perform population evolution and phylogenetic analyses. Taking the demographic effects into account, we identify a weak negative selection on SVA and L1 but an approximately neutral selection for Alu elements based on the frequency spectrum of RIPs. SID is a powerful open-source program for the detection of non-reference RIPs. We built a non-reference RIP dataset that greatly enhanced the diversity of RIPs detected in the general population, and it should be invaluable to researchers interested in many aspects of human evolution, genetics, and disease. As a proof of concept, we demonstrate that the RIPs can be used as biomarkers in a similar way as single nucleotide polymorphisms.
Drosophila embryonic type II neuroblasts: origin, temporal patterning, and contribution to the adult central complex
Authors: Walsh Kathleen T. , Doe Chris Q. 
Published: July 2017

ABSTRACTDrosophila neuroblasts are an excellent model for investigating how neuronal diversity is generated. Most brain neuroblasts generate a series of ganglion mother cells (GMCs) that each make two neurons (type I lineage), but sixteen brain neuroblasts generate a series of intermediate neural progenitors (INPs) that each produce 4-6 GMCs and 8-12 neurons (type II lineage). Thus, type II lineages are similar to primate cortical lineages, and may serve as models for understanding cortical expansion. Yet the origin of type II neuroblasts remains mysterious: do they form in the embryo or larva? If they form in the embryo, do their progeny populate the adult central complex, as do the larval type II neuroblast progeny? Here we present molecular and clonal data showing that all type II neuroblasts form in the embryo, produce INPs, and express known temporal transcription factors. Embryonic type II neuroblasts and INPs undergo quiescence, and produce embryonic-born progeny that contribute to the adult central complex. Our results provide a foundation for investigating the development of the central complex, and tools for characterizing early-born neurons in central complex function.
The ANTs Longitudinal Cortical Thickness Pipeline
Authors: Tustison Nicholas J. , Holbrook Andrew J. , Avants Brian B. , Roberts Jared M. , Cook Philip A. , Reagh Zachariah M. , Duda Jeffrey T. , Stone James R. , Gillen Daniel L. , Yassa Michael A. ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: July 2017

AbstractLongitudinal studies of development and disease in the human brain have motivated the acquisition of large neuroimaging data sets and the concomitant development of robust methodological and statistical tools for quantifying neurostructural changes. Longitudinal-specific strategies for acquisition and processing have potentially significant benefits including more consistent estimates of intra-subject measurements while retaining predictive power. In this work, we introduce the open-source Advanced Normalization Tools (ANTs) registration-based cortical thickness longitudinal processing pipeline and its application to the first phase of the Alzheimer’s Disease Neuroimaging Initiative (ADNI-1) comprising over 600 subjects with multiple time points from baseline to 36 months. We demonstrate in these data that the single-subject template construction and same orientation processing results in a simultaneous minimization of residual variability and maximization of between-subject variability immediately estimable from a longitudinal mixed-effects modeling strategy. It is known from the statistical literature that optimizing these dual criteria leads to greater scientific interpretability in terms of tighter confidence intervals in calculated mean trends, smaller prediction intervals, and narrower confidence intervals for determining cross-sectional effects. This strategy is evaluated over the entire cortex, as defined by the Desikan-Killiany-Tourville labeling protocol, where comparisons are made with the cross-sectional and longitudinal FreeSurfer processing streams. Subsequent linear mixed effects modeling for identifying diagnostic groupings within the ADNI cohort is provided as supporting evidence for the utility of the proposed ANTs longitudinal framework which provides unbiased structural neuroimage processing and competitive to superior power for longitudinal structural change detection.
Exploring repositioning opportunities and side-effects of statins: a Mendelian randomization study of HMG-CoA reductase inhibition with 55 complex traits
Authors: Hon-Cheong SO , Chau Carlos Kwan-long , Zhao Kai 
Published: July 2017

AbstractStatin is one of the most commonly prescribed medications worldwide. Besides reduction of cardiovascular risks, statins have been proposed for the prevention or treatment of other disorders, but results from clinical studies are mixed. There are also controversies concerning the adverse effects caused by statins.In this study we employed a Mendelian randomization (MR) approach across a wide range of complex traits to explore repositioning opportunities and side-effects of statins. MR is analogous to a “naturalistic” randomized controlled trial (RCT), which is much less susceptible to confounding and reverse causation as compared to observational studies.We employed two genetic instruments (rs12916 and rs17238484) in theHMGCRgene which have been shown to provide reliable estimates of the risk of statins on type 2 diabetes and weight gain. We observed in the single- and joint-SNP analysis that low density lipoprotein cholesterol (LDL-C) reduction from HMG-CoA reductase inhibition results in increased depressive symptoms. This finding appeared to be supported by nominally significant results of raised major depression risk in single-SNP MR analysis of rs17238484, and analyses using LDL-C as the exposure. Several other outcomes also reached nominal significance (p< 0.05) in single- or joint-SNP analyses; for example, we observed causal associations of LDL-C lowering from HMG-CoA reductase inhibition withreducedrisks of schizophrenia, anorexia nervosa, Alzheimer disease, Parkinson disease, as well as increased forearm bone mineral density, sleep duration and extreme longevity (highestq-value= 0.289). We also found evidence of casual relationships of LDL-C levels with schizophrenia, anorexia, sleep duration and longevity, following the same association directions as in analyses ofHMGCRvariants. These findings were at least partially supported by previous clinical studies. We did not observe associations with cognitive test profiles, renal outcomes, autoimmune diseases or cancers. While MR has its limitations and our findings remain to be confirmed in further studies, this work demonstrates the potential of a phenome-wide approach to reveal novel therapeutic indications and unknown drug side-effects.
Consequence of induced magnetic field on peristaltic motion of a Carreau nanofluid in a tapered asymmetric channel
Authors: Kothandapani M. , Pushparaj V. 
Published: July 2017

Purpose
This paper aims to investigate the consequence of the combined impacts of an induced magnetic field and thermal radiation on peristaltic transport of a Carreau nanofluid in a vertical tapered asymmetric channel. The model applied for the nanofluid comprises the effects of Brownian motion and thermophoresis.

Design/methodology/approach
The governing equations have been simplified under the widespread assumption of long-wavelength and low-Reynolds number approximations. The reduced coupled nonlinear equations of momentum and magnetic force function have also been solved analytically using the regular perturbation method.

Findings
The physical features of emerging parameters have been discussed by drawing the graphs of velocity, temperature, nanoparticle concentration profile, magnetic force function, current density, heat transfer coefficient and stream function. It has been realized that the magnetic force function is increased with the increase of Hartmann number, magnetic Reynolds number and mean flow rate.

Originality/value
It may be first paper in which the effect of induced magnetic field on peristaltic flow of non-Newtonian nanofluid in a tapered asymmetric channel has been studied.
Impact of Cattaneo-Christov heat flux on flow of two-types viscoelastic fluid in Darcy-Forchheimer porous medium
Authors: Abbasi Fahad Munir , Hayat Tasawar , Shehzad Sabir Ali , Alsaedi Ahmed 
Published: July 2017

Purpose
The aim of this works is to characterize the role of Cattaneo?Christov heat flux in two-dimensional flows of second-grade and Walter’s liquid B fluid models.

Design/methodology/approach
In this study similarity transformations have been used to transform the system into ordinary ones. Numerical and analytical solutions are computed through homotopic algorithm and shooting technique.

Findings
The numerical values of temperature gradient are tabulated, and the temperature gradient reduces rapidly with enhancing values of the Darcy parameter, but this reduction is very slow for Forchheimer parameter.

Originality/value
No such analyses have been reported in the literature.
The furthest left behind: the urgent need to scale up harm reduction in prisons
Authors: Sander Gen , Murphy Fionnuala 
Published: July 2017

Purpose
Raise awareness about the disproportionate impact of HIV and hepatitis C (HCV) on prisoners worldwide and the need for key harm reduction services such as needle and syringe programmes and opioid substitution therapy in prisons offer practical recommendations to assist policy makers in implementing or scaling up these services. The paper aims to discuss these issues.

Design/methodology/approach
This study is a desk review of existing data and evidence on HIV, HCV and harm reduction in prisons, analysis of political barriers and formulation of key policy recommendations.

Findings
Harm reduction works, yet service provision in prisons remains extremely limited. There is an urgent need for governments to enhance political leadership and funding for harm reduction in prisons. Authorities must also work to remove obstacles to the implementation of harm reduction services in prisons, enhance the monitoring and evaluation of laws, policies and programmes relating to HIV, HCV and drugs in prison settings, and recognise access to harm reduction in prisons as a fundamental human right. Until these obstacles are addressed, the world will not meet the Sustainable Development Goal of eradicating HIV and HCV by 2030.

Originality/value
More than just a desk review, this policy brief provides a political analysis of the harm reduction crisis in prisons and offers clear-cut recommendations for policy makers.
Relations between usage patterns of performance indicators and the role of individual firms in fresh fruit agri-food supply chains
Authors: Cunha Callado Antônio André , Jack Lisa 
Published: July 2017

PurposeThe purpose of this paper is to report the use of performance metrics among 121 Brazilian agribusiness companies, with the aim of helping accountants and academics to understand the actual use of performance metrics in non-integrated supply chains (SCs).Design/methodology/approachTo identify which performance metrics are used among SC partners, four independent clusters representing specific SC roles (input suppliers, farmers, distributors, and retailers) were formed. Data relating to 49 performance metrics were collected by questionnaire and analyzed statistically to isolate common measures.FindingsIt was found among suppliers, farmers, distributors, and retailers that the performance metrics for return on investment, responsiveness, and response time to clients are not being used whereas customer satisfaction obtained a usage pattern in all roles in the four groups. Hence, it appears that customer satisfaction rather than financial sustainability is the driver for discussion between SC partners.Research limitations/implicationsAlthough limited to a sample of firms within Brazil, the findings confirm evidence from similar SCs worldwide.Practical implicationsThese findings suggest that the common metrics approach to measure SC performance may be very difficult to achieve in practice and other alternatives should be investigated by management accountants.Social implicationsA predominance of customer satisfaction metrics to the exclusion of discussions on financial performance between partners in agri-food SC has implications for the sustainability of the industry and the ability of accountants and managers to negotiate when faced with increasing input costs.Originality/valueThis study contributes to the accountants’ understanding of how performance measurement works in fragmented SCs, whereas the majority of the literature is concerned with the integrated SCs.
Tax-induced fiscal year extension and earnings management
Authors: Sundvik Dennis 
Published: July 2017

Purpose
The purpose of this paper is to examine three different responses to the Finnish 2005 tax reform that, among other things, reduced the corporate tax rate and hiked dividend taxation. Focus lies on the factors influencing the decision to change the fiscal year-end and whether earnings management is more prevalent when the decision is not taken.

Design/methodology/approach
This study uses the financial statement data of Finnish private firms and studies 350 fiscal year-end changing firms and 700 non-changing firms with logistic and linear regression analysis. Discretionary accruals are the proxy for earnings management.

Findings
The results suggest that firms seize the window of opportunity and extend fiscal years depending on the magnitude of the expected tax savings. Firms that do not change their fiscal year-end engage in more tax-induced earnings management. In terms of economic consequences, the earnings management approach is less economically significant.

Research limitations/implications
This study only examines a limited number of firms that change their fiscal year-end, hence, care has been exercised in generalising the findings.

Practical implications
The findings may be considered when structuring future tax reforms, particularly when considering transition rules relating to changes in fiscal year-ends. The study may also have implications beyond tax reforms since the evidence of opportunistic changes in the fiscal year-end can be informative for tax authorities, independent auditors and creditors.

Originality/value
This study contributes to the relatively scarce literature on private firm responses to tax policy changes by analysing both upward and downward earnings management, as well as changes in the fiscal year-end. This is in contrast to previous research that mainly focusses on listed firms and absolute earnings management or earnings management in one direction.
Altruism born of suffering among emerging adults in Northern Ireland
Authors: Taylor Laura K. , Hanna Jeffrey R. 
Published: July 2017

PurposeThe purpose of this paper is to explore altruism born of suffering (ABS), a theory that explains how the experience of suffering within one’s own life may result in the motivation to help others, even outgroup members.Design/methodology/approachParticipants were 186 emerging adults (63 per cent female, 37 per cent male; 69 per cent Protestant, 41 per cent Catholic; average age =21.3, SD=2.57 years old) in Northern Ireland, a setting of protracted intergroup conflict. Participants were randomly assigned to an in/outgroup condition, read four types of adversity that occurred to same-sex victim(s), and indicated their empathetic response and how much they would like to help the victims.FindingsModerated mediation analyses revealed that empathy for the victim partially mediated the impact of perceived harm on desire to help; moreover, recent negative life events strengthened the link between harm and empathy. The path between empathy and helping was stronger in the outgroup compared to the ingroup condition.Practical implicationsThese findings support ABS, highlighting empathy as a key factor underlying more constructive intergroup relations in a divided society.Originality/valueThis paper extends previous research on ABS by focusing on a post-accord context. The value of the current analyses demonstrate the important role of fostering empathy to promote outgroup helping in settings of divisive group identities.