bluuebunny/crossref_metadata_2025_split huggingface dataset:
The genetic architecture of the network underlying flowering time variation inArabidopsis thaliana
Authors: Sasaki Eriko , Frommlet Florian , Nordborg Magnus 
Published: August 2017

ABSTRACTFlowering time is a key adaptive trait in plants and is tightly controlled by a complex regulatory network that responds to seasonal signals. In a rapidly changing climate, understanding the genetic basis of flowering time variation is important for both agriculture and ecology. Genetic mapping has revealed many genetic variants affecting flowering time, but the effects on the gene regulatory networks in population-scale are still largely unknown. We dissected flowering time networks using multi-layered Swedish population data fromArabidopsis thaliana, consisting of flowering time and transcriptome collected under constant 10°C growth temperature in addition to full genome sequence data. Our analysis identified multiple alleles of the key flowering time geneFLOWERING LOCUS C(FLC) as the primary determinant of the network underlying flowering time variation under our condition. Genetic variation ofFLCaffects multiple-pathways through known flowering-time genes includingFLOWERING LOCUS T(FT), andSUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1(SOC1). We demonstrated that an extremely simple single-locus model ofFLCinvolving allelic variation and expression explains almost a half of flowering time variation, with 60% of the effect being mediated throughFLCexpression. Furthermore, the accuracy of the model fitted at 10°C is almost unchanged at 16°C.
Pegivirus avoids immune recognition but does not attenuate acute-phase disease in a macaque model of HIV infection
Authors: Bailey Adam L. , Buechler Connor R. , Matson Daniel R. , Peterson Eric J. , Brunner Kevin G. , Mohns Mariel S. , Breitbach Meghan , Stewart Laurel M. , Ericsen Adam J. , Capuano Saverio , Simmons Heather A. , Yang David T. , O’Connor David H. 
Published: August 2017

AbstractHuman pegivirus (HPgV) protects HIV+ people from HIV-associated disease, but the mechanism of this protective effect remains poorly understood. We sequentially infected cynomolgus macaques with simian pegivirus (SPgV) and simian immunodeficiency virus (SIV) to model HIV+HPgV co-infection. SPgV had no effect on acute-phase SIV pathogenesis – as measured by SIV viral load, CD4+ T cell destruction, and immune activation – suggesting that HPgV’s protective effect is exerted primarily during the chronic phase of HIV infection. We also examined the immune response to SPgV in unprecedented detail, and found that this virus elicits virtually no activation of the immune system despite persistently high titers in the blood over long periods of time. Overall, this study expands our understanding of the pegiviruses – an understudied group of viruses with a high prevalence in the global human population – and suggests that the protective effect observed in HIV+HPgV co-infected people occurs primarily during the chronic phase of HIV infection.One Sentence SummaryPegivirus avoids immune recognition but does not attenuate acute-phase disease in a macaque model of HIV infection.Short TitlePegivirus and AIDS-virus co-infectionAccessible SummaryPeople infected with HIV live longer, healthier lives when they are co-infected with the human pegivirus (HPgV) – an understudied virus with a high prevalence in the global human population. To better understand how HPgV protects people with HIV from HIV-associated disease, we infected macaques with simian versions of these two viruses (SPgV and SIV). We found that SPgV had no impact on the incidence of SIV-associated disease early during the course of SIV infection – a time when SIV and HIV are known to cause irreversible damage to the immune system. Oddly, we found that the immune system did not recognize SPgV; a finding that warrants further investigation. Overall, this study greatly expands on our understanding of the pegiviruses and their interaction with the immune system.
Asymmetric cell volume changes regulate epithelial morphogenesis in zebrafish Kupffer’s vesicle
Authors: Dasgupta Agnik , Merkel Matthias , Jacob Andrew E. , Dawson Jonathan , Lisa Manning M. , Amack Jeffrey D. 
Published: August 2017

ABSTRACTHow epithelial cell behaviors are coordinately regulated to sculpt tissue architecture is a fundamental question in biology. Kupffer's vesicle (KV), a transient organ with a fluid - filled lumen, provides a simple system to investigate the interplay between intrinsic cellular mechanisms and external forces during epithelial morphogenesis. Using 3 - dimensional (3D) analyses of single cells we identify asymmetric cell volume changes along the anteroposterior axis of KV that coincide with asymmetric cell shape changes. Blocking ion flux prevents these cell volume changes and cell shape changes. Vertex simulations suggest cell shape changes do not depend on lumen expansion. Consistent with this prediction, asymmetric changes in KV cell volume and shape occur normally when KV lumen growth fails due to leaky cell adhesions. These results indicate ion flux mediates asymmetric cell volume changes that contribute to asymmetric cell shape changes in KV, and that these changes in epithelial morphology are separable from lumen - generated forces.
The evolution of tumour composition during fractionated radiotherapy: implications for outcome
Authors: Lewin Thomas D. , Maini Philip K , Moros Eduardo G , Enderling Heiko , Byrne Helen M 
Published: August 2017

AbstractCurrent protocols for delivering radiotherapy are based primarily on tumour stage and nodal and metastases status, even though it is well known that tumours and their microenvironments are highly heterogeneous. It is well established that the local oxygen tension plays an important role in radiation-induced cell death, with hypoxic tumour regions responding poorly to irradiation. Therefore, to improve radiation response, it is important to understand more fully the spatiotemporal distribution of oxygen within a growing tumour before and during fractionated radiation. To this end, we have extended a spatially-resolved mathematical model of tumour growth first proposed by Greenspan (Stud. Appl. Math., 1972) to investigate the effects of oxygen heterogeneity on radiation-induced cell death. In more detail, cell death due to radiation at each location in the tumour, as determined by the well-known linear-quadratic model, is assumed also to depend on the local oxygen concentration. The oxygen concentration is governed by a reaction-diffusion equation that is coupled to an integro-differential equation that determines the size of the assumed spherically-symmetric tumour. We combine numerical and analytical techniques to investigate radiation response of tumours with different intra-tumoral oxygen distribution profiles. Model simulations reveal a rapid transient increase in hypoxia upon re-growth of the tumour spheroid post-irradiation. We investigate the response to different radiation fractionation schedules and identify a tumour-specific relationship between inter-fraction time and dose per fraction to achieve cure. The rich dynamics exhibited by the model suggest that spatial heterogeneity may be important for predicting tumour response to radiotherapy for clinical applications.
Partisan effects in morality policy making
Authors: BUDDE EMMA , HEICHEL STEPHAN , HURKA STEFFEN , KNILL CHRISTOPH 
Published: August 2017

AbstractCurrent comparative policy research gives no clear answer to the question of whether partisan politics in general or the partisan composition of governments in particular matter for different morality policy outputs across countries and over time. This article addresses this desideratum by employing a new encompassing dataset that captures the regulatory permissiveness in six morality policies that are homosexuality, same‐sex partnership, prostitution, pornography, abortion and euthanasia in 16 European countries over five decades from 1960 to 2010. Given the prevalent scepticism about a role for political parties for morality policies in existing research, this is a ‘hard’ test case for the ‘parties do matter’ argument. Starting from the basic theoretical assumption that different party families, if represented in national governments to varying degrees, ought to leave differing imprints on morality policy making, this research demonstrates that parties matter when accounting for the variation in morality policy outputs. This general statement needs to be qualified in three important ways. First, the nature of morality policy implies that party positions or preferences cannot be fully understood by merely focusing on one single cleavage alone. Instead, morality policy is located at the interface of different cleavages, including not only left‐right and secular‐religious dimensions, but also the conflicts between materialism and postmaterialism, green‐alternative‐libertarian and traditional‐authoritarian‐nationalist (GAL‐TAN) parties, and integration and demarcation. Second, it is argued in this article that the relevance of different cleavages for morality issues varies over time. Third, partisan effects can be found only if individual cabinets, rather than country‐years, are used as the unit of analysis in the research design. In particular, party families that tend to prioritise individual freedom over collective interests (i.e., left and liberal parties) are associated with significantly more liberal morality policies than party families that stress societal values and order (i.e., conservative/right and religious parties). While the latter are unlikely to overturn previous moves towards permissiveness, these results suggest that they might preserve the status quo at least. Curiously, no systematic effects of green parties are found, which may be because they have been represented in European governments at later periods when morality policy outputs were already quite permissive.
Microbial ecology‐based engineering of Microbial Electrochemical Technologies
Authors: Koch Christin , Korth Benjamin , Harnisch Falk 
Published: August 2017

SummaryMicrobial ecology is devoted to the understanding of dynamics, activity and interaction of microorganisms in natural and technical ecosystems. Bioelectrochemical systems represent important technical ecosystems, where microbial ecology is of highest importance for their function. However, whereas aspects of, for example, materials and reactor engineering are commonly perceived as highly relevant, the study and engineering of microbial ecology are significantly underrepresented in bioelectrochemical systems. This shortfall may be assigned to a deficit on knowledge and power of these methods as well as the prerequisites for their thorough application. This article discusses not only the importance of microbial ecology for microbial electrochemical technologies but also shows which information can be derived for a knowledge‐driven engineering. Instead of providing a comprehensive list of techniques from which it is hard to judge the applicability and value of information for a respective one, this review illustrates the suitability of selected techniques on a case study. Thereby, best practice for different research questions is provided and a set of key questions for experimental design, data acquisition and analysis is suggested.
Increasing the accuracy and precision of relative telomere length estimates by RT qPCR
Authors: Eastwood Justin R. , Mulder Ellis , Verhulst Simon , Peters Anne 
Published: August 2017

AbstractAs attrition of telomeres, DNA caps that protect chromosome integrity, is accelerated by various forms of stress, telomere length (TL) has been proposed as an indicator of lifetime accumulated stress. In ecological studies, it has been used to provide insights into ageing, life history trade‐offs, the costs of reproduction and disease. qPCR is a high‐throughput and cost‐effective tool to measure relative TL (rTL) that can be applied to newly collected and archived ecological samples. However, qPCR is susceptible to error both from the method itself and pre‐analytical steps. Here, repeatability was assessed overall and separately across multiple levels (intra‐assay, inter‐assay and inter‐extraction) to elucidate the causes of measurement error, as a step towards improving precision. We also tested how accuracy, defined as the correlation between the “gold standard” for TL estimation (telomere restriction fragment length analysis with in‐gel hybridization), could be improved. We find qPCR repeatability (intra‐ and inter‐assay levels) to be at similar levels across three common storage media (ethanol, Longmire's and Queen's). However, inter‐extraction repeatability was 50% lower for samples stored in Queen's lysis buffer, indicating storage medium can influence precision. Precision as well as accuracy could be increased by estimating rTL from multiple qPCR reactions and from multiple extractions. Repetition increased statistical power equivalent to a 25% (single extraction analysed twice) and 17% (two extractions) increase in sample size. Overall, this study identifies novel sources of variability in high‐throughput telomere quantification and provides guidance on sampling strategy design and how to increase rTL precision and accuracy.
Do Mutual Fund Investors Care About Auditor Quality?
Authors: Goldie Bradley A. , Li Lei , Masli Adi 
Published: August 2017

AbstractWe study the influence of perceived auditor quality on investment decisions by bond mutual fund investors. Audits of bond mutual funds require significant auditor expertise. Fund managers estimate daily the fair market values of holdings that are often opaque and illiquid. Managers can use their discretion to manipulate their fund's performance results. While it is known that investment flows into funds that report good past performance, little evidence exists about whether investors' confidence in the reliability of fund financial reports is influenced by auditor quality. Using hand‐collected data from SEC filings, we find that the positive association between reported performance and investment flows is stronger for funds with auditors who are industry specialists and are longer‐tenured, as well as for funds that pay higher audit fees. We do not find that auditor office size strengthens the association. We also find that the presence of industry‐specialist auditors, long‐tenured auditors, and higher audit fees lead to additional disclosure in the form of emphasis‐of‐matter. This study contributes to the streams of research investigating perceived audit quality, fund investment decisions, and auditing for financial services.
Diet tracing in ecology: Method comparison and selection
Authors: Nielsen Jens M. , Clare Elizabeth L. , Hayden Brian , Brett Michael T. , Kratina Pavel 
Published: August 2017

Abstract

Determining diet is a key prerequisite for understanding species interactions, food web structure and ecological dynamics. In recent years, there has been considerable development in both the methodology and application of novel and more traditional dietary tracing methods, yet there is no comprehensive synthesis that systematically and quantitatively compares the different approaches.

Here we conceptualise diet tracing in ecology, provide recommendations for method selection, and illustrate the advantages of method integration. We summarise empirical evidence on how different methods quantify diet mixtures, by contrasting estimates of dietary proportions from multiple methods applied to the same consumer‐resource datasets, or from experimental studies with known diet compositions.

Our data synthesis revealed an urgent need for more experiential comparisons among the dietary methods. The comparison of diet quantifications from field observations showed that different techniques aligned well in cases with less than six diet items, but diverged considerably when applied to more complex diet mixtures.

Efforts are ongoing to further advance dietary estimation, including how reliably compound specific stable isotope analyses and fatty acid profiles can quantify more prey items than bulk stable isotope analyses. Similarly, DNA analyses, which can depict trophic interactions at a higher resolution than any other method, are generating new ways to better quantify diets and differentiate among life‐stages of prey. Such efforts, combined with more empirical testing of each dietary method and establishment of open data repositories for dietary data, promise to greatly advance community and ecosystem ecology.
Mendelian randomisation analysis provides no evidence for a relationship between adult height and testicular cancer risk
Authors: Levy M. , Hall D. , Sud A. , Law P. , Litchfield K. , Dudakia D. , Haugen T. B. , Karlsson R. , Reid A. , Huddart R. A. , Grotmol T. , Wiklund F. , Houlston R. S. , Turnbull C. 
Published: August 2017

SummaryObservational studies have suggested anthropometric traits, particularly increased height are associated with an elevated risk of testicular cancer (testicular germ cell tumour). However, there is an inconsistency between study findings, suggesting the possibility of the influence of confounding factors. To examine the association between anthropometric traits and testicular germ cell tumour using an unbiased approach, we performed a Mendelian randomisation study. We used genotype data from genome wide association studies of testicular germ cell tumour totalling 5518 cases and 19,055 controls. Externally weighted polygenic risk scores were created and used to evaluate associations with testicular germ cell tumour risk per one standard deviation (s.d) increase in genetically‐defined adult height, adult BMI, adult waist hip ratio adjusted for BMI (WHRadjBMI), adult hip circumference adjusted for BMI (HIPadjBMI), adult waist circumference adjusted for BMI (WCadjBMI), birth weight (BW) and childhood obesity. Mendelian randomisation analysis did not demonstrate an association between any anthropometric trait and testicular germ cell tumour risk. In particular, despite good power, there was no global evidence for association between height and testicular germ cell tumour. However, three SNPs for adult height individually showed association with testicular germ cell tumour (rs4624820: OR = 1.47, 95% CI: 1.41–1.55, p = 2.7 × 10−57; rs12228415: OR = 1.17, 95% CI: 1.11–1.22, p = 3.1 × 10−10; rs7568069: OR = 1.13, 95% CI: 1.07–1.18, p = 1.1 × 10−6). This Mendelian randomisation analysis, based on the largest testicular germ cell tumour genome wide association dataset to date, does not support a causal etiological association between anthropometric traits and testicular germ cell tumour aetiology. Our findings are more compatible with confounding by shared environmental factors, possibly related to prenatal growth with exposure to these risk factors occurring in utero.
Bonding, bridging and linking social networks: A qualitative study of the emergency management of Cyclone Pam, Vanuatu
Authors: Vachette Astrid , King David , Cottrell Alison 
Published: August 2017

AbstractCyclone Pam (March 2015) was an unprecedented event in Vanuatu forcing the simultaneous involvement of national and long‐term international actors, well integrated into the national disaster governance system, as well as numerous short‐term international actors, unfamiliar with the geopolitical and cultural disaster context of the country. Cooperation between these three groups of actors evolved through the three scales of bonding, bridging and linking social networking. This paper questions the different drivers and challenges within and across these scales of social networks affecting cooperation among the three different groups of actors during an emergency. Using a mixed methodology based on social network analysis, this paper utilises the case study of Cyclone Pam in Vanuatu to study the strengths and weaknesses of the disaster governance system in place based on bonding and bridging social capital to conduct disaster risk management and to prepare the integration of linking social capital when external support is needed. This paper contributes to the identification of key considerations in the development of resilience‐building strategies: the interactions of diverse actors to address disaster management needs and the reciprocal impacts of these interactions within and across the three different scales of social networks.
A Matrix-based Method of Moments for Fitting Multivariate Network Meta-analysis Models with Multiple Outcomes and Random Inconsistency Effects
Authors: Jackson Dan , Bujkiewicz Sylwia , Law Martin , Riley Richard D. , White Ian R. 
Published: August 2017

Summary
Random-effects meta-analyses are very commonly used in medical statistics. Recent methodological developments include multivariate (multiple outcomes) and network (multiple treatments) meta-analysis. Here, we provide a new model and corresponding estimation procedure for multivariate network meta-analysis, so that multiple outcomes and treatments can be included in a single analysis. Our new multivariate model is a direct extension of a univariate model for network meta-analysis that has recently been proposed. We allow two types of unknown variance parameters in our model, which represent between-study heterogeneity and inconsistency. Inconsistency arises when different forms of direct and indirect evidence are not in agreement, even having taken between-study heterogeneity into account. However, the consistency assumption is often assumed in practice and so we also explain how to fit a reduced model which makes this assumption. Our estimation method extends several other commonly used methods for meta-analysis, including the method proposed by DerSimonian and Laird (1986). We investigate the use of our proposed methods in the context of both a simulation study and a real example.
Associations between behaviours that challenge in adults with intellectual disability, parental perceptions and parental mental health
Authors: Waite Jane , Rose John , Wilde Lucy , Eden Kate , Stinton Chris , Moss Jo , Oliver Chris 
Published: August 2017

ObjectivesThis study examined parental perceptions of behaviours that challenge (CB) in their adult children with intellectual disability (ID), and explored whether perceptions mediated associations between CB and parental psychological distress.DesignA within‐group correlational design was employed.MethodsSixty‐five parents reported on individuals with genetic syndromes and ID who had chronic CB. Parents completed the Illness Perception Questionnaire‐Revised (IPQ‐R) adapted to measure perceptions of self‐injury, aggression or property destruction, alongside assessments of parental locus of control, attributions about behaviour, parental psychological distress, and CB.ResultsA high proportion of parents evidenced anxiety and depression at clinically significant levels (56.9% and 30.8%, respectively). Contrary to predictions, psychological distress was not significantly associated with CB. The perception that the adult with ID exerted control over the parent's life mediated the association between CB and parental psychological distress. Few parents endorsed operant reinforcement as a cause of CB (< 10%).ConclusionsThe high levels of psychological distress in parents is notable and of concern. Further research should consider the reasons why parents have causal attributions that might be inconsistent with contemporary interventions.Practitioner points

Parents experience high levels of psychological distress while supporting adults with ID who engage in chronic behaviours that challenge.

A stronger belief that the adult with ID exerts control over the parent's life may mediate an association between CB exhibited by the individual with ID and parental psychological distress.

Few parents endorsed operant reinforcement as a cause of behaviours that challenge.