bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimate of disease heritability using 7.4 million familial relationships inferred from electronic health records
Authors: Polubriaginof Fernanda , Vanguri Rami , Quinnies Kayla , Belbin Gillian M. , Yahi Alexandre , Salmasian Hojjat , Lorberbaum Tal , Nwankwo Victor , Li Li , Shervey Mark , Glowe Patricia , Ionita-Laza Iuliana , Simmerling Mary , Hripcsak George , Bakken Suzanne , Goldstein David , Kiryluk Krzysztof , Kenny Eimear E. , Dudley Joel , Vawdrey David K. , Tatonetti Nicholas P. 
Published: July 2016

AbstractHeritability is essential for understanding the biological causes of disease, but requires laborious patient recruitment and phenotype ascertainment. Electronic health records (EHR) passively capture a wide range of clinically relevant data and provide a novel resource for studying the heritability of traits that are not typically accessible. EHRs contain next-of-kin information collected via patient emergency contact forms, but until now, these data have gone unused in research. We mined emergency contact data at three academic medical centers and identified millions of familial relationships while maintaining patient privacy. Identified relationships were consistent with genetically-derived relatedness. We used EHR data to compute heritability estimates for 500 disease phenotypes. Overall, estimates were consistent with literature and between sites. Inconsistencies were indicative of limitations and opportunities unique to EHR research. These analyses provide a novel validation of the use of EHRs for genetics and disease research.One Sentence SummaryWe demonstrate that next-of-kin information can be used to identify familial relationships in the EHR, providing unique opportunities for precision medicine studies.
Each cell needs long double-stranded RNA for silencing by feeding RNAi inC. elegans
Authors: Raman Pravrutha , Zaghab Soriayah M , Traver Edward C , Jose Antony M 
Published: July 2016

ABSTRACTLong double-stranded RNA (dsRNA) can silence genes of matching sequence upon ingestion in many invertebrates and is therefore being developed as a pesticide. Such feeding RNA interference (RNAi) is best understood in the wormC. elegans, where it is thought that derivatives of ingested dsRNA, including short dsRNAs, move between cells and cause systemic silencing. Movement of short dsRNAs has been inferred using tissue-specific rescue of the long dsRNA-binding protein RDE-4 by expressing it from repetitive transgenes. We found that the use of repetitive transgenes for the tissue-specific rescue of a gene could inhibit RNAi within that tissue and could result in misexpression of the gene in other tissues. Both inhibition and misexpression were not detectable when a single-copy transgene was used for tissue-specific rescue. In animals with single-copy rescue of RDE-4, RNAi was restricted to the tissue with RDE-4 expression. Thus, unlike previous observations using repetitive transgenes, these results suggest that binding of long dsRNA by RDE-4 in each silenced cell is required for systemic RNAi. Taken together with the requirement for long dsRNA to trigger RNAi in insects, these results suggest that the entry of long dsRNA is a necessary first step for feeding RNAi in animal cells.
Projected spread of Zika virus in the Americas
Authors: Zhang Qian , Sun Kaiyuan , Chinazzi Matteo , Pastore-Piontti Ana , Dean Natalie E. , Rojas Diana Patricia , Merler Stefano , Mistry Dina , Poletti Piero , Rossi Luca , Bray Margaret , Halloran M. Elizabeth , Longini Ira M. , Vespignani Alessandro 
Published: July 2016

AbstractWe use a data-driven global stochastic epidemic model to project past and future spread of the Zika virus (ZIKV) in the Americas. The model has high spatial and temporal resolution, and integrates real-world demographic, human mobility, socioeconomic, temperature, and vector density data. We estimate that the first introduction of ZIKV to Brazil likely occurred between August 2013 and April 2014 (90% credible interval). We provide simulated epidemic profiles of incident ZIKV infections for several countries in the Americas through February 2017. The ZIKV epidemic is characterized by slow growth and high spatial and seasonal heterogeneity, attributable to the dynamics of the mosquito vector and to the characteristics and mobility of the human populations. We project the expected timing and number of pregnancies infected with ZIKV during the first trimester, and provide estimates of microcephaly cases assuming different levels of risk as reported in empirical retrospective studies. Our approach represents an early modeling effort aimed at projecting the potential magnitude and timing of the ZIKV epidemic that might be refined as new and more accurate data from the region become available.
de novoassembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer
Authors: Istace Benjamin , Friedrich Anne , d’Agata Léo , Faye Sébastien , Payen Emilie , Beluche Odette , Caradec Claudia , Davidas Sabrina , Cruaud Corinne , Liti Gianni , Lemainque Arnaud , Engelen Stefan , Engelen Stefan , Wincker Patrick , Schacherer Joseph , Aury Jean-Marc 
Published: July 2016

AbstractOxford Nanopore Technologies Ltd (Oxford, UK) have recently commercialized MinION, a small and low-cost single-molecule nanopore sequencer, that offers the possibility of sequencing long DNA fragments. The Oxford Nanopore technology is truly disruptive and can sequence small genomes in a matter of seconds. It has the potential to revolutionize genomic applications due to its portability, low-cost, and ease of use compared with existing long reads sequencing technologies. The MinION sequencer enables the rapid sequencing of small eukaryotic genomes, such as the yeast genome. Combined with existing assembler algorithms, near complete genome assemblies can be generated and comprehensive population genomic analyses can be performed. Here, we resequenced the genome of theSaccharomyces cerevisiaeS288C strain to evaluate the performance of nanopore-only assemblers. Then wede novosequenced and assembled the genomes of 21 isolates representative of theS. cerevisiaegenetic diversity using the MinION platform. The contiguity of our assemblies was 14 times higher than the Illumina-only assemblies and we obtained one or two long contigs for 65% of the chromosomes. This high continuity allowed us to accurately detect large structural variations across the 21 studied genomes. Moreover, because of the high completeness of the nanopore assemblies, we were able to produce a complete cartography of transposable elements insertions and inspect structural variants that are generally missed using a short-read sequencing strategy.
A single double-strand break system reveals repair dynamics and mechanisms in heterochromatin and euchromatin
Authors: Janssen Aniek , Breuer Gregory A. , Brinkman Eva K. , van der Meulen Annelot I. , Borden Sean V. , van Steensel Bas , Bindra Ranjit S. , LaRocque Jeannine R. , Karpen Gary H. 
Published: July 2016

Repair of DNA double-strand breaks (DSBs) must be properly orchestrated in diverse chromatin regions to maintain genome stability. The choice between two main DSB repair pathways, nonhomologous end-joining (NHEJ) and homologous recombination (HR), is regulated by the cell cycle as well as chromatin context.Pericentromeric heterochromatin forms a distinct nuclear domain that is enriched for repetitive DNA sequences that pose significant challenges for genome stability. Heterochromatic DSBs display specialized temporal and spatial dynamics that differ from euchromatic DSBs. Although HR is thought to be the main pathway used to repair heterochromatic DSBs, direct tests of this hypothesis are lacking. Here, we developed an in vivo single DSB system for both heterochromatic and euchromatic loci in Drosophila melanogaster. Live imaging of single DSBs in larval imaginal discs recapitulates the spatio–temporal dynamics observed for irradiation (IR)-induced breaks in cell culture. Importantly, live imaging and sequence analysis of repair products reveal that DSBs in euchromatin and heterochromatin are repaired with similar kinetics, employ both NHEJ and HR, and can use homologous chromosomes as an HR template. This direct analysis reveals important insights into heterochromatin DSB repair in animal tissues and provides a foundation for further explorations of repair mechanisms in different chromatin domains.
What are the sources of capability dynamism? Reconceptualizing dynamic capabilities from the perspective of organizational change
Authors: Andreeva Tatiana , Ritala Paavo 
Published: July 2016

Purpose– The concept of dynamic capabilities emerged from strategic management theory, the aim being to determine how organizations can achieve and sustain competitive advantage in a continuously changing environment. It is widely accepted in the literature that this concept, although extremely popular and potentially powerful, still needs clarification and elaboration. The main criticisms are centered on the lack of understanding of where these capabilities originate and how their dynamism can be sustained in the long run. The purpose of this paper is to bring some novel insights into these issues in bridging the theories of strategic management and change management.Design/methodology/approach– This paper is based on extensive literature review and bridges dynamic capabilities and change management literatures.Findings– The paper proposes a distinction between domain-specific and generic dynamic capabilities and puts forward the concept of “organizational change capability” as representing a generic dynamic capability. The nature of such capability is discussed using the insights from organizational change theory.Originality/value– This paper provides a novel way to examine the sources of capability dynamism both conceptually and empirically by integrating insights from organizational change and dynamic capabilities literatures.
A comparative framework for culturally differentiated digital game-based learning
Authors: Park Jae , Wen Run 
Published: July 2016

Purpose
– The purpose of this paper is to explore culture as the unit of analysis in comparative education in the context of technology-mediated learning known as digital game-based learning (DGBL).

Design/methodology/approach
– Two digital games for Chinese language learning were purposefully designed and produced following existing studies in cross-cultural psychology, learning theories and second language acquisition. To corroborate the assumption that culture affects user’s preference of DGBL learning interface, the two newly developed instructional tools were evaluated with eastern and western learners to find out their perceptions and choices through direct observation, pre-/post-assessments and a group interview.

Findings
– The evaluation indicates the validity of the key assumptions in the theoretical framework: eastern learners were fond of the type of digital game that involves social cues and situational factors, whereas, western learners preferred a simple design and goal-oriented learning game in which they had the power of control.

Originality/value
– This paper suggests a theoretical and technical framework to design, and produce culturally sensitive DGBL learning tools. Extant studies on the relationship between culture and DGBL are usually on how digital games generate unique learning experiences and culture. Looking at the same phenomenon but in a reverse direction, this study reports on how learners’ culture determines their preferences in DGBL.
Influences of customer participation and customer brand engagement on brand loyalty
Authors: Apenes Solem Birgit Andrine 
Published: July 2016

Purpose
Value co-creation assumes that customers take active roles and create value together with firms. This paper aims to investigate the short- and long-term effects of customer participation on brand loyalty, through brand satisfaction. Participation effects were also examined among social media-using customers with the additional explanatory factor of brand engagement.

Design/methodology/approach
Two studies were conducted among insurance customers: a cross-sectional study using a nationwide sample (N = 954) and a subsample of social media users (N = 145) to examine short-term effects, and a longitudinal study using data from three assessment timepoints (N = 376) to enable empirical long-term testing.

Findings
The cross-sectional study showed positive short-term effects of customer participation on brand loyalty, mediated by satisfaction. Among customers using social media, positive participation effects gained from brand engagement strengthened brand satisfaction. The longitudinal study did not show similar positive long-term effects of customer participation.

Practical implications
These findings help deepen service marketers’ understanding of the possible short-term effects of customer participation and customer brand engagement, and caution them to not expect that customer participation will have long-term positive satisfaction and loyalty effects.

Originality/value
This research provides interesting short- and long-term findings, due to the complementary cross-sectional and longitudinal study designs.
Money meanings among French and American adolescents
Authors: Rose Gregory M. , Bakir Aysen , Gentina Elodie 
Published: July 2016

Purpose
This paper examines adolescent’ money attitudes in the USA and France. It introduces and validates an 18-item scale for assessing adolescent money attitudes, explores the symbolic values that American and French teens attach to money, identifies the major segments of teens based on their attitudes toward money and assesses the importance that these groups place on price, novelty and brand name.

Design/methodology/approach
Twenty-eight in-depth interviews were initially conducted to explore adolescent’ money attitudes, assist in the development of measures and provide a context for interpreting subsequent results. Exploratory factor analysis (among 90 French and 70 American adolescents), followed by confirmatory factor analysis (among 332 French and 273 American adolescents) indicated that six dimensions captured money meanings. These dimensions were used in a subsequent cluster analysis to group teens into segments.

Findings
Six dimensions (worry, achievement, status, security, budget and evil) captured teenage money attitudes among French and American adolescents. A cluster analysis based on these dimensions yielded three groups: no worries, success and security. These three groups varied in their attitudes toward money and the importance that they placed on price, brand and novelty in purchasing.

Practical implications
This study provides measures for assessing adolescent money meanings and presents a preliminary segmentation of USA and French adolescents based on their attitudes toward money.

Originality/value
The results explore the impact of money attitudes on adolescent consumption preferences, demonstrate the utility of measuring adolescent’ money attitudes and segmenting adolescents based on these attitudes and emphasize the importance of both cultural and individual differences.
Co-creation of brand identities: consumer and industry influence and motivations
Authors: Kennedy Eric , Guzmán Francisco 
Published: July 2016

Purpose
This paper aims to develop an understanding of the phenomena of co-creation and how this practice is used in shaping brand identities. This research provides answers to questions on both the consumer and industry sides of co-creation.

Design/methodology/approach
Two studies are developed. First, a qualitative study is used to gain insight from key decision-makers with responsibility for a brand. Second, a study of millennial consumers is used to develop the antecedents of consumer motivations of co-creation of brand identities.

Findings
When combined, the outcomes of these studies create a comprehensive framework that encompasses two models of brand identity co-creation. The qualitative study leads to the emergence of two major constructs, which, combined with the consumer study, lead to the development of two models that represent the antecedents of co-creation from a managerial and consumer perspective.

Research limitations/implications
For Study one, a larger pool of respondents or different data collection method might have led to additional managerial insights. The study two sample was limited to millennials. Although this group of consumers is identified as highly engaged with brands, the study could have benefited from a more general consumer sample.

Practical implications
The organization framework could help managers gain a deeper understanding for effectively co-creating their brand identities with all stakeholders, in particular consumers.

Originality/value
This research contributes to theory and practice by analyzing the process of stakeholder brand identity co-creation.
Effects of the environment on illegal cartel activity
Authors: Kunsch David W. , Schnarr Karin , Rowe W. Glenn 
Published: July 2016

Purpose– Using resource dependency theory, the purpose of this paper is to examine what elements in the business environment may be associated with the formation and continuance of cartels.Design/methodology/approach– The authors employ a unique data set of 148 cartel data points from the 1970s to 2008 which have at least one American company involved to quantitatively test causal relationships. The authors also interview key class action anti-trust attorneys for their views and opinions on the impact of these environmental factors on cartel formation and continuance.Findings– The authors find statistically significant relationships between the pursuit and maintenance of industry profits and the dynamism in the industry, and illegal behavior as represented through price fixing by business cartels. The authors find that in the attorneys’ opinion, it is also the pursuit of individual corporate profits and munificence that are associated with these cartels.Practical implications– This research furthers the understanding of organizational deviance which is critical given its impact on organizations, individuals, regulators, law enforcement, and the general public.Originality/value– This research is a first step in considering cartel activity in a way that encompasses external influences in a new and innovative manner and as a tool to help researchers and practitioners better understand how organizational deviance, as manifested through illegal corporate activity, can be anticipated, identified, and prevented.
Firm-specific risk, managerial certainty and optimism
Authors: Jancenelle Vivien E. , Storrud-Barnes Susan F. , Iaquinto Anthony L , Buccieri Dominic 
Published: July 2016

Purpose– The purpose of this paper is to focus on investor reactions to unanticipated changes in income, and whether those reactions can be mitigated by managerial discussion. The authors investigate how top-management team certainty and optimism during post-earnings announcement conference calls can serve as corrective actions and add back firm value in times of unexpected changes in firm-specific risk.Design/methodology/approach– The research question is tested empirically in the context of large, publicly traded, US firms’ quarterly earnings announcements, and their subsequent post-earnings announcement conference calls. The authors use the advanced content analysis software DICTION to measure the levels of managerial certainty and optimism displayed during post-earnings announcement conference calls, and event-study methodology to measure investors’ reactions.Findings– Results indicate that earnings surprises are negatively associated with firm value, but that this relationship is mitigated positively by displays of managerial certainty and optimism during post-earnings announcement conference calls.Originality/value– This work uses an innovative research design to study top-management team rhetoric in post-earnings announcement conference calls, and how specific discussions mitigate investors’ negative reactions to increases in firm-specific risk. The study highlights the importance of top-management team certainty and optimism for value creation in times of change in firm-specific risk, and the importance of rhetoric as a tool for corrective action.
Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons
Authors: Habib Naomi , Li Yinqing , Heidenreich Matthias , Swiech Lukasz , Avraham-Davidi Inbal , Trombetta John J. , Hession Cynthia , Zhang Feng , Regev Aviv 
Published: July 2016

Visualizing gene expression in nucleiGene expression can vary greatly within a single cell. Using techniques that they developed for sequencing single nuclei and labeling proliferating cells in vivo, Habibet al.performed RNA sequencing of 1402 single nuclei from the adult mouse hippocampus. Combining this approach with a clustering algorithm for single-cell and -nucleus RNA sequencing data delineated specific cell types during cell differentiation and development. By providing polyadenylated RNA from nuclei alone, as opposed to cytoplasmic RNA, these methods open the application of single-cell transcriptomics to tissues in which individual cells are difficult to isolate.Science, this issue p.925
Genome Sequence of a
Proteus mirabilis
Strain Isolated from the Salivary Glands of Larval
Lucilia sericata
Authors: Yuan Ye , Zhang Yu , Fu Shuhua , Crippen Tawni L. , Visi David K. , Benbow M. Eric , Allen Michael S. , Tomberlin Jeffery K. , Sze Sing-Hoi , Tarone Aaron M. 
Published: July 2016

ABSTRACT

We announce a draft genome sequence of a
Proteus mirabilis
strain derived from
Lucilia sericata
salivary glands. This strain is demonstrated to attract and induce oviposition by
L. sericata
, a common blow fly important to medicine, agriculture, and forensics. The genome sequence will help dissect interkingdom communication between the species.
Draft Genome Sequence of the Plant Growth-PromotingCupriavidus gilardiiStrain JZ4 Isolated from the Desert PlantTribulus terrestris
Authors: Lafi Feras F. , Bokhari Ameerah , Alam Intikhab , Bajic Vladimir B. , Hirt Heribert , Saad Maged M. 
Published: July 2016

ABSTRACTWe isolated the plant endophytic bacteriumCupriavidus gilardiistrain JZ4 from the roots of the desert plantTribulus terrestris, collected from the Jizan region, Saudi Arabia. We report here the draft genome sequence of JZ4, together with several enzymes related to plant growth-promoting activity, environmental adaption, and antifungal activity.
A
Narnavirus
in the Trypanosomatid Protist Plant Pathogen
Phytomonas serpens
Authors: Akopyants Natalia S. , Lye Lon-Fye , Dobson Deborah E. , Lukeš Julius , Beverley Stephen M. 
Published: July 2016

ABSTRACT

We describe here a new RNA virus (PserNV1) from the plant protist parasite
Phytomonas serpens
(family
Trypanosomatidae
,
Kinetoplastida
, supergroup
Excavata
). The properties of PserNV1 permit assignment to the genus
Narnavirus
(
Narnaviridae
), the first reported from a host other than fungi or oomycetes.
Complete Genome Sequences of Two Methicillin-Sensitive
Staphylococcus aureus
Isolates Representing a Population Subset Highly Prevalent in Human Colonization
Authors: Weber Robert E. , Layer Franziska , Fuchs Stephan , Bender Jennifer K. , Fiedler Stefan , Werner Guido , Strommenger Birgit 
Published: July 2016

ABSTRACT

Here, we report the high-quality draft genome sequences of two methicillin-susceptible
Staphylococcus aureus
isolates, 08-02119 and 08-02300. Belonging to sequence type 582 (ST582) and ST7, both isolates are representatives of clonal lineages often associated with asymptomatic colonization of humans.
First Complete Genome Sequence of
Suakwa aphid-borne yellows virus
from East Timor
Authors: Maina Solomon , Edwards Owain R. , de Almeida Luis , Ximenes Abel , Jones Roger A. C. 
Published: July 2016

ABSTRACT

We present here the first complete genomic RNA sequence of the polerovirus
Suakwa aphid-borne yellows virus
(SABYV), from East Timor. The isolate sequenced came from a virus-infected pumpkin plant. The East Timorese genome had a nucleotide identity of 86.5% with the only other SABYV genome available, which is from Taiwan.