bluuebunny/crossref_metadata_2025_split huggingface dataset:
“Theory, practice, and conservation in the age of genomics: the Galápagos giant tortoise as a case study”
Authors: Gaughran Stephen J , Quinzin Maud C , Miller Joshua M , Garrick Ryan C , Edwards Danielle L , Russello Michael A , Poulakakis Nikos , Ciofi Claudio , Beheregaray Luciano B , Caccone Adalgisa 
Published: September 2017

AbstractHigh-throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms (SNPs) in non-model species. Population genetic theory predicts that this large number of independent markers should provide detailed insights into population structure, even when only a few individuals are sampled. Still, sampling design can have a strong impact on such inferences. Here, we use simulations and empirical SNP data to investigate the impacts of sampling design on estimating genetic differentiation among populations that represent three species of Galápagos giant tortoises (Chelonoidisspp.). Though microsatellite and mitochondrial DNA analyses have supported the distinctiveness of these species, a recent study called into question how well these markers matched with data from genomic SNPs, thereby questioning decades of studies in non-model organisms. Using >20,000 genome-wide SNPs from 30 individuals from three Galápagos giant tortoise species, we find distinct structure that matches the relationships described by the traditional genetic markers. Furthermore, we confirm that accurate estimates of genetic differentiation in highly structured natural populations can be obtained using thousands of SNPs and 2-5 individuals, or hundreds of SNPs and 10 individuals, but only if the units of analysis are delineated in a way that is consistent with evolutionary history. We show that the lack of structure in the recent SNP-based study was likely due to unnatural grouping of individuals and erroneous genotype filtering. Our study demonstrates that genomic data enable patterns of genetic differentiation among populations to be elucidated even with few samples per population, and underscores the importance of sampling design. These results have specific implications for studies of population structure in endangered species and subsequent management decisions.“Modern molecular techniques provide unprecedented power to understand genetic variation in natural populations. Nevertheless, application of this information requires sound understanding of population genetics theory.”- Fred Allendorf (2017, p. 420)
Statistical machine learning of sleep and physical activity phenotypes from sensor data in 96,220 UK Biobank participants
Authors: Willetts Matthew , Hollowell Sven , Aslett Louis , Holmes Chris , Doherty Aiden 
Published: September 2017

ABSTRACTCurrent public health guidelines on physical activity and sleep duration are limited by a reliance on subjective self-reported evidence. Using data from simple wrist-worn activity monitors, we developed a tailored machine learning model, using balanced random forests with Hidden Markov Models, to reliably detect a number of activity modes. We show that physical activity and sleep behaviours can be classified with 87% accuracy in 159,504 minutes of recorded free-living behaviours from 132 adults. These trained models can be used to infer fine resolution activity patterns at the population scale in 96,220 participants. For example, we find that men spend more time in both low- and high-intensity behaviours, while women spend more time in mixed behaviours. Walking time is highest in spring and sleep time lowest during the summer. This work opens the possibility of future public health guidelines informed by the health consequences associated with specific, objectively measured, physical activity and sleep behaviours.
Exome chip meta-analysis elucidates the genetic architecture of rare coding variants in smoking and drinking behavior
Authors: Liu Dajiang J. , Brazel David M. , Turcot Valérie , Zhan Xiaowei , Gong Jian , Barnes Daniel R. , Bertelsen Sarah , Chou Yi-Ling , Erzurumluoglu A. Mesut , Faul Jessica D. , Haessler Jeff , Hammerschlag Anke R. , Hsu Chris , Kapoor Manav , Lai Dongbing , Le Nhung , de Leeuw Christiaan A , Loukola Ana , Mangino Massimo , Melbourne Carl A. , Pistis Giorgio , Qaiser Beenish , Rohde Rebecca , Shao Yaming , Stringham Heather , Wetherill Leah , Zhao Wei , Agrawal Arpana , Beirut Laura , Chen Chu , Eaton Charles B. , Goate Alison , Haiman Christopher , Heath Andrew , Iacono William G. , Martin Nicholas G. , Polderman Tinca J. ,   CHD Exome+ Consortium,   Consortium for Genetics of Smoking Behavior, Reiner Alex , Rice John , Schlessinger David , Scholte H. Steven , Smith Jennifer A. , Tardif Jean-Claude , Tindle Hilary A. , van der Leij Andreis R , Boehnke Michael , Chang-Claude Jenny , Cucca Francesco , David Sean P. , Foroud Tatiana , Kardia Sharon L.R. , Kooperberg Charles , Laakso Markku , Lettre Guillaume , Madden Pamela , McGue Matt , North Kari , Posthuma Danielle , Spector Timothy , Stram Daniel , Weir David R. , Kaprio Jaakko , Abecasis Gonçalo R. , Vrieze Scott 
Published: September 2017

AbstractBackgroundSmoking and alcohol use behaviors in humans have been associated with common genetic variants within multiple genomic loci. Investigation of rare variation within these loci holds promise for identifying causal variants impacting biological mechanisms in the etiology of disordered behavior. Microarrays have been designed to genotype rare nonsynonymous and putative loss of function variants. Such variants are expected to have greater deleterious consequences on gene function than other variants, and significantly contribute to disease risk.MethodsIn the present study, we analyzed ∼250,000 rare variants from 17 independent studies. Each variant was tested for association with five addiction-related phenotypes: cigarettes per day, pack years, smoking initiation, age of smoking initiation, and alcoholic drinks per week. We conducted single variant tests of all variants, and gene-based burden tests of nonsynonymous or putative loss of function variants with minor allele frequency less than 1%.ResultsMeta-analytic sample sizes ranged from 70,847 to 164,142 individuals, depending on the phenotype. Known loci tagged by common variants replicated, but there was no robust evidence for individually associated rare variants, either in gene based or single variant tests. Using a modified method-of-moment approach, we found that all low frequency coding variants, in aggregate, contributed 1.7% to 3.6% of the phenotypic variation for the five traits (p<.05).ConclusionsThe findings indicate that rare coding variants contribute to phenotypic variation, but that much larger samples and/or denser genotyping of rare variants will be required to successfully identify associations with these phenotypes, whether individual variants or gene‐ based associations.
The FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis
Authors: Frost Jennifer M. , Kim M. Yvonne , Park Guen-Tae , Hsieh Ping-Hung , Nakamura Miyuki , Lin Samuel , Yoo Hyunjin , Choi Jaemyung , Ikeda Yoko , Kinoshita Tetsu , Choi Yeonhee , Zilberman Daniel , Fischer Robert L. 
Published: September 2017

AbstractThe DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1), subunit of the chromatin remodeler FAcilitates Chromatin Transactions (FACT), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We find that FACT co-localizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin.
Mitochondrial Dual-coding Genes inTrypanosomabrucei
Authors: Kirby Laura E. , Koslowsky Donna 
Published: September 2017

AbstractTrypanosoma bruceiis transmitted between mammalian hosts by the tsetse fly. In the mammal, they are exclusively extracellular, continuously replicating within the bloodstream. During this stage, the mitochondrion lacks a functional electron transport chain (ETC). Successful transition to the fly, requires activation of the ETC and ATP synthesis via oxidative phosphorylation. This life cycle leads to a major problem: in the bloodstream, the mitochondrial genes are not under selection and are subject to genetic drift that endangers their integrity. Exacerbating this,T. bruceiundergoes repeated population bottlenecks as they evade the host immune system that would create additional forces of genetic drift. These parasites possess several unique genetic features, including RNA editing of mitochondrial transcripts. RNA editing creates open reading frames by the guided insertion and deletion of U-residues within the mRNA. A major question in the field has been why this metabolically expensive system of RNA editing would evolve and persist. Here, we show that many of the edited mRNAs can alter the choice of start codon and the open reading frame by alternative editing of the 5’ end. Analyses of mutational bias indicate that six of the mitochondrial genes may be dual-coding and that RNA editing allows access to both reading frames. We hypothesize that dual-coding genes can protect genetic information by essentially hiding a non-selected gene within one that remains under selection. Thus, the complex RNA editing system found in the mitochondria of trypanosomes provides a unique molecular strategy to combat genetic drift in non-selective conditions.Author SummaryIn African trypanosomes, many of the mitochondrial mRNAs require extensive RNA editing before they can be translated. During this process, each edited transcript can undergo hundreds of cleavage/ligation events as U-residues are inserted or deleted to generate a translatable open reading frame. A major paradox has been why this incredibly metabolically expensive process would evolve and persist. In this work, we show that many of the mitochondrial genes in trypanosomes are dual-coding, utilizing different reading frames to potentially produce two very different proteins. Access to both reading frames is made possible by alternative editing of the 5’ end of the transcript. We hypothesize that dual-coding genes may work to protect the mitochondrial genes from mutations during growth in the mammalian host, when many of the mitochondrial genes are not being used. Thus, the complex RNA editing system may be maintained because it provides a unique molecular strategy to combat genetic drift.
Data-driven Modeling of Thrombus Size and Shape in Aortic Dissections: Role of Hemodynamics
Authors: Yazdani Alireza , Li He , Bersi Matthew R. , Di Achille Paolo , Insley Joseph , Humphrey Jay D. , Karniadakis George Em 
Published: September 2017

AbstractAortic dissection is a pathology that manifests due to micro-structural defects in the aortic wall. Blood enters the damaged wall through an intimal tear, thereby creating a so-calledfalse lumenand exposing the blood to thrombogenic intramural constituents such as collagen. The natural history of this acute vascular injury thus depends, in part, on thrombus formation, maturation, and possible healing within the false lumen. A key question is: Why do some false lumens thrombose completely while other thrombose partially or little at all? An ability to predict the location and extent of thrombus in subjects with dissection could contribute significantly to clinical decision-making, including interventional design. We develop, for the first time, a data-drivenparticle-continuummodel for thrombus formation in a murine model of aortic dissection. In the proposed model, we simulate a final-value problem in lieu of the original initial-value problem with significantly fewer particles that may grow in size upon activation, representing the local concentration of blood-borne species. Numerical results confirm that geometry and local hemodynamics play significant roles in the acute progression of thrombus. Despite geometrical differences between murine and human dissections, mouse models can provide considerable insight and have gained in popularity owing to their reproducibility. Our results for three classes of geometrically different false lumens show that thrombus forms and extends to a greater extent in regions with lower bulk shear rates. Dense thrombi are less likely to form in high-shear zones and in the presence of strong vortices. The present data-driven study suggests that the proposed model is robust and can be employed to assess thrombus formation in human aortic dissections.
A zombieLIFgene in elephants is up-regulated by TP53 to induce apoptosis in response to DNA damage
Authors: Vazquez Juan Manuel , Sulak Michael , Chigurupati Sravanthi , Lynch Vincent J. 
Published: September 2017

AbstractLarge bodied organisms have more cells that can potentially turn cancerous than smallbodied organisms with fewer cells, imposing an increased risk of developing cancer. This expectation predicts a positive correlation between body size and cancer risk, however, there is no correlation between body size and cancer risk across species (‘Peto’s Paradox’). Here we show that elephants and their extinct relatives (Proboscideans) may have resolved Peto’s Paradox in part through re-functionalizing aleukemia inhibitory factorpseudogene (LIF6) with pro-apoptotic functions. TheLIF6gene is transcriptionally up-regulated by TP53 in response to DNA damage, and translocates to the mitochondria where it induces apoptosis. Phylogenetic analyses of living and extinct ProboscideanLIF6genes indicates its TP53 response element evolved coincident with the evolution of large body sizes in the Proboscidean stem-lineage. These results suggest that re-functionalizing of a pro-apoptotic LIF pseudogene may have been permissive (though not sufficient) for the evolution of large body sizes in Proboscideans.
Towards a neuro-computational account of prism adaptation
Authors: Petitet Pierre , O’Reilly Jill X. , O’Shea Jacinta 
Published: September 2017

AbstractPrism adaptation has a long history as an experimental paradigm used to investigate the functional and neural processes that underlie sensorimotor control. In the neuropsychology literature, functional explanations of prism adaptation are typically framed within a traditional cognitive psychology ‘box-and-arrow’ framework that distinguishes putative component functions thought to give rise to behaviour (i.e. ‘strategic control’ versus ‘spatial realignment’). However, this kind of theoretical framework lacks precision and explanatory power. Here, we advocate for a computational framework that offers several advantages: 1) analgorithmicexplanatory account of the computations and operations that drive behaviour; 2) expressed in quantitative mathematical terms; 3) embedded within a principled theoretical framework (Bayesian decision theory, state-space modelling); 4) that offers a means to generate and test quantitative behavioural predictions. This computational framework offers a route toward mechanistic explanations of prism adaptation behaviour. Thus it constitutes a conceptual advance compared to the traditional theoretical framework. In this paper, we illustrate how Bayesian decision theory and state-space models offer principled explanations for a range of behavioural phenomena in the field of prism adaptation (e.g. visual capture, magnitude of visual versus proprioceptive realignment, spontaneous recovery and dynamics of adaptation memory). We argue that this explanatory framework offers to advance understanding of the functional and neural mechanisms that implement prism adaptation behaviour, by enabling quantitative tests of hypotheses that go beyond mere descriptive mapping claims that ‘brain area X is (somehow)involvedin psychological process Y’.
Incentive value and spatial certainty combine additively to determine visual priorities
Authors: Garner K.G. , Bowman H. , Raymond J.E. 
Published: September 2017

AbstractHow does the brain combine information predictive of the value of a visually guided task (incentive value) with information predictive of where task relevant stimuli may occur (spatial certainty)? Human behavioural evidence indicates that these two predictions may be combined additively to bias visual selection (additive hypothesis), whereas neuroeconomic studies posit that they may be multiplicatively combined (expected value hypothesis). We sought to adjudicate between these two alternatives. Participants viewed two coloured placeholders that specified the potential value of correctly identifying an imminent letter target if it appeared in that placeholder. Then, prior to the target’s presentation, an endogenous spatial cue was presented indicating the target’s more likely location. Spatial cues were parametrically manipulated with regards to the information gained (in bits). Across two experiments, performance was better for targets appearing in high versus low value placeholders and better when targets appeared in validly cued locations. Interestingly, as shown with a Bayesian model selection approach, these effects did not interact, clearly supporting the additive hypothesis. Even when conditions were adjusted to increase the optimality of a multiplicative operation, support for it remained. These findings refute recent theories that expected value computations are the singular mechanism driving the deployment of endogenous spatial attention. Instead, incentive value and spatial certainty seem to act independently to influence visual selection.
Obtaining 3D Super-resolution Information from 2D Super-resolution Images through a 2D-to-3D Transformation Algorithm
Authors: Ruba Andrew , Luo Wangxi , Kelich Joseph , Yang Weidong 
Published: September 2017

AbstractCurrently, it is highly desirable but still challenging to obtain three-dimensional (3D) superresolution information of structures in fixed specimens as well as dynamic processes in live cells with a high spatiotemporal resolution. Here we introduce an approach, without using 3D superresolution microscopy or real-time 3D particle tracking, to achieve 3D sub-diffraction-limited information with a spatial resolution of ≤ 1 nm. This is a post-localization analysis that transforms 2D super-resolution images or 2D single-molecule localization distributions into their corresponding 3D spatial probability information. The method has been successfully applied to obtain structural and functional information for 25-300 nm sub-cellular organelles that have rotational symmetry. In this article, we will provide a comprehensive analysis of this method by using experimental data and computational simulations.
News media coverage and initial public offerings in Germany: explaining flotation performance
Authors: Strauß Nadine , van der Meer Toni G.L.A. 
Published: September 2017

PurposeThe purpose of this paper is to investigate the relationships of news media coverage and the performance of initial public offerings (IPOs) in Germany. The aim is to find out how media attention, media sentiment, corporate information, and recency of news are related to the flotation performance of firms that go public.Design/methodology/approach50 IPOs that went public in Germany between January 2011 and December 2015 were investigated. In total, 3,644 German speaking articles dealing with the IPOs were manually analyzed. Hierarchical OLS regressions were performed to find out how news media variables relate with the flotation performance of German IPOs (cf. underpricing, share price percentage gain after second day of trading). It was furthermore distinguished between news media coverage six days prior to the IPO and coverage on the day of the IPO itself.FindingsWhile more media attention devoted to the IPOs on the day of their flotation might lead to a share price percentage gain after the second day of trading, negativity in the news media and information about new products and products of the IPO firm might be negatively related with their flotation performance. However, information about the strategy change of the IPO firms seems to be positively related with the underpricing of IPOs. Furthermore, news media coverage on the day of the IPO itself seems to be more influential for the flotation performance with regard to negative sentiment and information about new products.Practical implicationsFinancial communication professionals should manage media representations of IPO firms before and on the day of the IPO itself. In this vein, negative media coverage should be prevented and information about new products and products of the IPO firm should be considered with caution. Instead, talking about the strategy of the IPO firm might be advantageous for the flotation performance.Originality/valueThis study evolved from a lack of empirical research on the interrelationships between news media and stock market prices in communication science, particularly with regard to IPOs. The study contributes to previous research in paying attention to corporate information and the recency of news when trying to explain IPO performances. The findings of this study provide implications for strategic financial communication and the role of managing news media of firms that go public.
Quality reporting of corporate philanthropy
Authors: Valor Carmen , Zasuwa Grzegorz 
Published: September 2017

PurposeThe purpose of this paper is twofold: first, to outline a framework for corporate philanthropy (CP) reporting that could help differentiate between symbolic and substantive reporting; and second, to test whether the reporting practices of large corporate donors are symbolic or substantive.Design/methodology/approachFirst, to construct a framework for CP reporting, the authors draw from research on corporate social responsibility communication, CP and reputational capital-building. Second, the philanthropy disclosures found in non-financial reports of the largest donors from the list of Fortune 100 corporations were examined using content analysis.FindingsThe theoretical framework identifies key ingredients of disclosure quality such as goals, causes, support, partners and impacts. The empirical findings show that disclosures regarding CP are more symbolic than meaningful. The largest donors provide descriptive information regarding the CP plan that primarily focuses on projects and causes. However, they fail to provide an explicit account of their decisions and the results of their philanthropic activities.Research limitations/implicationsThe framework could also be applied with small changes to other communication outlets including social media and corporate websites.Originality/valueThis paper addresses an important gap in non-financial reporting research: the lack of a CP accounting model. To the authors’ knowledge, the framework developed in this paper represents the first conceptualization of the quality of CP disclosure that may enable scholars to differentiate symbolic from substantive CP and in this way advances the debate on CP communication. This framework can also help companies sincerely engaged in philanthropy to benefit from these activities.