bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bootstrat: Population Informed Bootstrapping for Rare Variant Tests
Authors: Huang Hailiang , Peloso Gina M. , Howrigan Daniel , Rakitsch Barbara , Simon-Gabriel Carl Johann , Goldstein Jacqueline I. , Daly Mark J. , Borgwardt Karsten , Neale Benjamin M. 
Published: August 2016

AbstractRecent advances in genotyping and sequencing technologies have made detecting rare variants in large cohorts possible. Various analytic methods for associating disease to rare variants have been proposed, including burden tests, C-alpha and SKAT. Most of these methods, however, assume that samples come from a homogeneous population, which is not realistic for analyses of large samples. Not correcting for population stratification causes inflated p-values and false-positive associations. Here we propose a population-informed bootstrap resampling method that controls for population stratification (Bootstrat) in rare variant tests. In essence, the Bootstrat procedure uses genetic distance to create a phenotype probability for each sample. We show that this empirical approach can effectively correct for population stratification while maintaining statistical power comparable to established methods of controlling for population stratification. The Bootstrat scheme can be easily applied to existing rare variant testing methods with reasonable computational complexity.Author SummaryRecent technology advances have enabled large-scale analysis of rare variants, but properly testing rare variants remains a significant challenge as most rare variant testing methods assume a sample of homogenous ethnicity, an assumption often not true for large cohorts. Failure to account for this heterogeneity increases the type I error rate. Here we propose a bootstrap scheme applicable to most existing rare variant testing methods to control for population heterogeneity. This scheme uses a randomization layer to establish a null distribution of the test statistics while preserving the sample genetic relationships. The null distribution is then used to calculate an empirical p-value that accounts for population heterogeneity. We demonstrate how this scheme successfully controls the type I error rate without loss of statistical power.
ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions
Authors: Latif Haythem , Federowicz Stephen , Ebrahim Ali , Tarasova Janna , Szubin Richard , Utrilla Jose , Zengler Karsten , Palsson Bernhard O. 
Published: August 2016

ABSTRACTNumerousin vitrostudies have yielded a refined picture of the structural and molecular associations between Cyclic-AMP receptor protein (Crp), the DNA motif, and RNA polymerase (RNAP) holoenzyme. In this study, high-resolution ChIP-exonuclease (ChIP-exo) was applied to study Crp bindingin vivoand at genome-scale. Surprisingly, Crp was found to provide little to no protection of the DNA motif under activating conditions. Instead, Crp demonstrated binding patterns that closely resembled those generated by σ70. The binding patterns of both Crp and σ70are indicative of RNAP holoenzyme DNA footprinting profiles associated with stages during transcription initiation that occur post-recruitment. This is marked by a pronounced advancement of the template strand footprint profile to the +20 position relative to the transcription start site and a multimodal distribution on the nontemplate strand. This trend was also observed in the familial transcription factor, Fnr, but full protection of the motif was seen in the repressor ArcA. Given the time-scale of ChIP studies and that the rate-limiting step in transcription initiation is typically post recruitment, we propose a hypothesis where Crp is absent from the DNA motif but remains associated with RNAP holoenzyme post-recruitment during transcription initiation. The release of Crp from the DNA motif may be a result of energetic changes that occur as RNAP holoenzyme traverses the various stable intermediates towards elongation complex formation.
Rapid evolution of distinctHelicobacter pylorisubpopulations in the Americas
Authors: Thorell Kaisa , Yahara Koji , Berthenet Elvire , Lawson Daniel J. , Kato Ikuko , Mendez Alfonso , Canzian Federico , Bravo María Mercedes , Suzuki Rumiko , Yamaoka Yoshio , Torres Javier , Sheppard Samuel K , Falush Daniel 
Published: August 2016

AbstractFor the last 500 years, the Americas have been a melting pot both for genetically diverse humans and for the pathogenic and commensal organisms associated with them. One such organism is the stomach dwelling bacteriumHelicobacter pylori, which is highly prevalent in Latin America where it is a major current public health challenge because of its strong association with gastric cancer. By analyzing the genome sequence ofH. pyloriisolated in North, Central and South America, we found evidence for admixture betweenH. pyloriof European and African origin throughout the Americas, without substantial input from pre-Columbian (hspAmerind) bacteria. In the US, strains of African and European origin have remained genetically distinct, while in Colombia and Nicaragua, bottlenecks and rampant genetic exchange amongst isolates have led to the formation of national gene pools. We found four outer membrane proteins with atypical levels of Asian ancestry in American strains, including the adhesion factor AlpB, suggesting a role for the ethnic makeup of hosts in the colonization of incoming strains. Our results show that newH. pylorisubpopulations can rapidly arise, spread and adapt during times of demographic flux, and suggest that differences in transmission ecology between high and low prevalence areas may substantially affect the composition of bacterial populations.Author SummaryHelicobacter pyloriis one of the best studied examples of an intimate association between bacteria and humans, due to its ability to colonize the stomach for decades and to transmit from generation to generation. A number of studies have sought to link diversity inH. pylorito human migrations but there are some discordant signals such as an “out of Africa” dispersal within the last few thousand years that has left a much stronger signal in bacterial genomes than in human ones. In order to understand how such discrepancies arise, we have investigated the evolution ofH. pyloriduring the recent colonization of the Americas. We find that bacterial populations evolve quickly and can spread rapidly to people of different ethnicities. Distinct new bacterial subpopulations have formed in Colombia from a European source and in Nicaragua and the US from African sources. Genetic exchange between bacterial populations is rampant within Central and South America but is uncommon within North America, which may reflect differences in prevalence. Our results also suggest that adaptation of bacteria to particular human ethnic groups may be confined to a handful of genes involved in interaction with the immune system.
IMMAN: an R/Bioconductor package for Interolog protein network reconstruction, Mapping and Mining ANalysis
Authors: Ashtinai Minoo , Nickchi Payman , Jahangiri-Tazehkand Soheil , Safari Abdollah , Mirzaie Mehdi , Jafari Mohieddin 
Published: August 2016

SummaryIMMAN is a software for reconstructing Interolog Protein Network (IPN) by integrating several Protein-protein Interaction Networks (PPIN). Users can unify different PPINs to mine conserved common network among species. IMMAN helps to retrieve IPNs with different degrees of conservation to engage for protein function prediction analysis based on protein networks.AvailabilityIMMAN is freely available athttps://bioconductor.org/packages/IMMAN,http://profiles.bs.ipm.ir/softwares/IMMAN/.Contactmirzie@ipm.ir,mjafari@ipm.ir,asafari@sfu.caSupplementary informationSupplementary data are available online.
CAMSA: a Tool for Comparative Analysis and Merging of Scaffold Assemblies
Authors: Aganezov Sergey S. , Alekseyev Max A. 
Published: August 2016

MotivationDespite the recent progress in genome sequencing and assembly, many of the currently available assembled genomes come in a draft form. Such draft genomes consist of a large number of genomic fragments (scaffolds), whose positions and orientations along the genome are unknown. While there exists a number of methods for reconstruction of the genome from its scaffolds, utilizing various computational and wet-lab techniques, they often can produce only partial error-prone scaffold assemblies. It therefore becomes important to compare and merge scaffold assemblies produced by different methods, thus combining their advantages and highlighting present conflicts for further investigation. These tasks may be labor intensive if performed manually.ResultsWe present CAMSA—a tool for comparative analysis and merging of two or more given scaffold assemblies. The tool (i) creates an extensive report with several comparative quality metrics; (ii) constructs the most confident merged scaffold assembly; and (iii) provides an interactive framework for a visual comparative analysis of the given assemblies. Among the CAMSA features, only scaffold merging can be evaluated in comparison to existing methods. Namely, it resembles the functionality of assembly reconciliation tools, although their primary targets are somewhat different. Our evaluations show that CAMSA produces merged assemblies of comparable or better quality than existing assembly reconciliation tools while being the fastest in terms of the total running time.AvailabilityCAMSA is distributed under the MIT license and is available athttp://cblab.org/camsa/.
Thermal niche evolution across replicatedAnolislizard adaptive radiations
Authors: Gunderson Alex R. , Mahler D. Luke , Leal Manuel 
Published: August 2016

AbstractElucidating how ecological and evolutionary mechanisms interact to produce and maintain biodiversity is a fundamental problem in evolutionary ecology. We investigate this issue by focusing on how physiological evolution affects performance and species coexistence along the thermal niche axis in replicated radiations ofAnolislizards, groups best known for resource partitioning based on morphological divergence. We find repeated divergence in thermal physiology within these radiations, and that this divergence significantly affects performance within natural thermal environments. Morphologically similar species that co-occur invariably differ in their thermal physiology, providing evidence that physiological divergence facilitates species co-existence within anole communities. Despite repeated divergence in traits of demonstrable ecological importance, phylogenetic comparative analyses indicate that physiological traits have evolved more slowly than key morphological traits related to the structural niche. Phylogenetic analyses also reveal that physiological divergence is correlated with divergence in broad-scale habitat climatic features commonly used to estimate thermal niche evolution, but that the latter incompletely predicts variation in the former. We provide comprehensive evidence for repeated adaptive evolution of physiological divergence withinAnolisadaptive radiations, including the complementary roles of physiological and morphological divergence in promoting community-level diversity. We recommend greater integration of performance-based traits into analyses of climatic niche evolution, as they facilitate a more complete understanding of the phenotypic and ecological consequences of climatic divergence.
Clinical Utility of Expanded Carrier Screening: Reproductive Behaviors of At-Risk Couples
Authors: Ghiossi Caroline , Goldberg James D. , Haque Imran S. , Lazarin Gabriel A. , Wong Kenny K. 
Published: August 2016

ABSTRACTPurposeExpanded carrier screening (ECS) analyzes dozens or hundreds of recessive genes for determining reproductive risk. Data on clinical utility of screening conditions beyond professional guidelines is scarce.MethodsIndividuals underwent ECS for up to 110 genes. 537 at-risk couples (ARC), those in which both partners carry the same recessive disease, were invited to a retrospective IRB-approved survey of their reproductive decision making after receiving ECS results.Results64 eligible ARC completed the survey. Of 45 respondents screened preconceptionally, 62% (n=28) planned IVF with PGD or prenatal diagnosis (PNDx) in future pregnancies. 29% (n=13) were not planning to alter reproductive decisions. The remaining 9% (n=4) of responses were unclear.Of 19 pregnant respondents, 42% (n=8) elected PNDx, 11% (n=2) planned amniocentesis but miscarried, and 47% (n=9) considered the condition insufficiently severe to warrant invasive testing. Of the 8 pregnancies that underwent PNDx, 5 were unaffected and 3 were affected. 2 of 3 affected pregnancies were terminated.Disease severity was found to have significant association (p=0.000145) with changes in decision making, whereas guideline status of diseases, controlled for severity, was not (p=0.284).ConclusionMost ARC altered reproductive planning, demonstrating the clinical utility of ECS. Severity of conditions factored into decision making.
Love is all around us in the workplace
Authors: Wheatcroft John 
Published: August 2016

Purpose
The paper examines relationships in the workplace. It considers issues such as employee engagement, decisions to be in a relationship with a co-worker and its effects on commitment certainty in a sample of adults. They all said they were currently working with their romantic partner.

Design/methodology/approach
Bearing in mind that workplace romance can be a taboo topic, the researchers recruited participants anonymously from online social media websites.

Findings
Some participants said that they were motivated to be in a romantic relationship with a co-worker to increase status. They tended to report lower levels of engagement. However, when relationships hit a tricky patch and/or they felt uncertainty about the relationship, these participants tended to commit themselves more, rather than less to their work.

Originality/value
This is the first study to examine the influence of workplace romantic relationships in the context of employee engagement. It also documents links between workplace relationships and performance variables.
The mediating effect of management accounting system on the relationship between competition and managerial performance
Authors: Ghasemi Reza , Azmi Mohamad Noor , Karami Meisam , Hafiz Bajuri Norkhairul , Asgharizade Ezzatollah 
Published: August 2016

Purpose
This study aims to examine the effect of interaction between market competition and management accounting system (MAS) characteristics on managerial performance. Scope of the study is concentrated on Iranian financial organizations and managers of these organizations were identified as respondents for the questionnaire survey.

Design/methodology/approach
This study used the SmartPLS to analyze the data, and the model of the study was estimated with structural equation modeling (SEM). It follows the recommended two-stage analytical procedures of SEM: assessing confirmatory measurement models (factor analysis) and confirmatory structural models (path analysis).

Findings
The study uncovered the existence of direct relationships between competition and MAS, and between MAS and managerial performance. The study also confirmed that the relationship between competition and managerial performance is mediated by MAS.

Research limitations/implications
The findings provide valuable insights to guide managers in financial organizations to improve their performance through suitable MAS by considering internal and environmental factors. Recommendations on how to improve MAS and managerial performance are provided accordingly.

Originality/value
Prior researches confirm that there is no unique and universal MAS for all organizations, as this depends on internal firm characteristics and environmental features. However, there has been a lack of empirical evidence on MAS researches in the service organizations.
IFRS and accounting quality: legal origin, regional, and disclosure impacts
Authors: Dayanandan Ajit , Donker Han , Ivanof Mike , Karahan Gökhan 
Published: August 2016

Purpose
The purpose of this study is to examine whether the quality of financial reporting has improved after the adoption of International Financial Reporting Standards (IFRS) in Europe and across the world. The study investigates the impact of IFRS on income smoothing and earnings management in different geographic regions under different legal origins and disclosure environments.

Design/methodology/approach
To measure income smoothing in the pre- and post-IFRS periods, the authors use the coefficient of variation and the panel unit root model proposed by Im et al. (2003) for testing whether net income is stationary throughout the sample period. The study uses a dynamic panel estimation framework, as it captures the dynamics of IFRS on discretionary accruals efficiently. Discretionary accruals are used to measure earnings management.

Findings
The results suggest that the adoption of high quality standards, such as IFRS, reduces income smoothing and earnings management. In addition, the study finds that earnings management has decreased in the post-IFRS period, in particular, for French and Scandinavian civil law countries, but not for German civil law countries and common law countries. The latter can be explained by the fact that common law countries have strong investor protection laws, strict law enforcement and high disclosure levels of financial information. The study also finds empirical evidence that the adoption of IFRS reduces earnings management in countries with high levels of financial disclosure. Overall, the study shows that the adoption of IFRS improved the quality of financial reporting.

Originality/value
This study is useful for accounting standard setters across the world, including those countries that have not yet decided to adopt IFRS. The study contributes to the literature by examining the adoption of IFRS in income smoothing and earnings management under different legal regimes and disclosure environments by using advanced empirical methodologies.
Fluctuating capacity and impulsiveness in acquired brain injury: the dilemma of “unwise” decisions under the Mental Capacity Act
Authors: Lennard Chris 
Published: August 2016

Purpose
– The purpose of this paper is to examine the dilemma at the heart of nursing care – the striving for empowerment of people in nurses’ care with the responsibility to protect vulnerable adults from harm. In doing so, it argues that in difficult and borderline cases, capacity assessment is complex and ultimately based on a judgment involving interpretation, and welcomes the views of clinicians who have challenged the procedural test of capacity in the Mental Capacity Act (MCA).

Design/methodology/approach
– It presents an illustrative study of a person with acquired brain injury (ABI) resident in a nursing home, who had been assessed under the MCA and judged to have capacity regarding health and welfare decisions, who subsequently displayed a persistent and impulsive desire to leave the unit without thought of risk and vulnerability to herself, prompting safeguarding concerns, and a reassessment of her capacity.

Findings
– The paper asserts that supporting people with ABI during capacity assessments, as the MCA decrees, in a very structured way can create a false sense of “capacity”. It maintains that executive impairments in ABI, being difficult to assess in formal settings, are best undertaken over time, in real-life settings, with evidence from third parties. It welcomes the MCA’s desire to protect individual autonomy and avoid undue paternalism, through ensuring people are not deemed to lack capacity simply because they make an unwise decision.

Originality/value
– But it goes on to argue that in ABI it is often the fact of unwise decision making that is the prominent factor and main concern, particularly in regard to impulsive decision making. If nurses have to make a judgment as to how unwise decisions made with decision-making capacity are to be distinguished from unwise decisions made without it in people with ABI, then, the author concludes, a major area of difficulty for nurses is ascertaining when the presumption of capacity should be challenged, an area that an updated code of practice needs to clarify.
Social value change, embeddedness and social entrepreneurship
Authors: Velvin Jan , Bjørnstad Kristian , Krogh Erling 
Published: August 2016

PurposeThis study aims to explore the shift in social and cultural values in the wake of ongoing change; specifically, the degree of embeddedness of these values among farm-based entrepreneurs. The authors examine how this value-change-embeddedness continuum can further the development of theories in the field of social entrepreneurship.Design/methodology/approachThe authors use an exploratory and a descriptive approach when interviewing eight farmers and members of their respective households. The sample encompasses almost all the providers of farm-based tourism in this particular area of rural Norway. The empirical materials form the basis for selecting our theoretical approach, one of which is a structural life-mode analysis.FindingsThe findings show that the social value of self-reliance, when taken to extremes, can hinder the growth of deeper commercial cooperation between farmers. This constitutes a challenge to efficiency and effectiveness on a larger scale, given a need for both independence and interdependence together with flexible entrepreneurial network cooperation in social entrepreneurship. The findings also indicate that social entrepreneurship does not necessarily have to include a cognitive shift in values and roles for the exclusion of a productive entrepreneurial identity.Originality/valueBy focusing on value changes in social entrepreneurship, this paper addresses a significant gap in the entrepreneurship literature relating to the process of value creation. By using the structural life-mode analysis, this study identifies the underlying value changes that are fundamental to entrepreneurial processes, allowing that process to unfold and take hold to the betterment of affected farm-based communities.