bluuebunny/crossref_metadata_2025_split huggingface dataset:
GWAS of QRS Duration Identifies New Loci Specific to Hispanic/Latino Populations Swenson Hispanic/Latino QRS GWAS
Authors: Swenson Brenton R. , Louie Tin , Lin Henry J. , MéndezGiráldez Raú , Below Jennifer E , Laurie Cathy C. , Kerr Kathleen F. , Highland Heather , Thornton Timothy A. , Ryckman Kelli K. , Kooperberg Charles , Soliman Elsayed Z. , Seyerle Amanda A. , Guo Xiuqing , Taylor Kent D. , Yao Jie , Heckbert Susan R. , Darbar Dawood , Petty Lauren E. , McKnight Barbara , Cheng Susan , Bello Natalie A. , Whitsel Eric A. , Hanis Craig L. , Nalls Mike A. , Evans Daniel S. , Rotter Jerome I. , Sofer Tamar , Avery Christy , Sotoodehnia Nona 
Published: July 2018

ABSTRACTBackgroundThe electrocardiographically quantified QRS duration measures ventricular depolarization and conduction. QRS prolongation has been associated with poor heart failure prognosis and cardiovascular mortality, including sudden death. While previous genome-wide association studies (GWAS) have identified 32 QRS SNPs across 26 loci among European, African, and Asian-descent populations, the genetics of QRS among Hispanics/Latinos has not been previously explored.MethodsWe performed a GWAS of QRS duration among Hispanic/Latino ancestry populations (n=15,124) from four studies using 1000 Genomes imputed genotype data (adjusted for age, sex, global ancestry, clinical and study-specific covariates). Study-specific results were combined using fixed-effects, inverse variance-weighted meta-analysis.ResultsWe identified six loci associated with QRS (P<5×10−8), including two novel loci:MYOCD, a nuclear protein expressed in the heart, andSYT1, an integral membrane protein. The top association in theMYOCDlocus, intronic SNP rs16946539, was found in Hispanics/Latinos with a minor allele frequency (MAF) of 0.04, but is monomorphic in European and African descent populations. The most significant QRS duration association was for intronic SNP rs3922344 (P= 8.56×10−26) inSCN5A/SCN10A. Three additional previously identified loci,CDKN1A,VTI1A, andHAND1, also exceeded the GWAS significance threshold among Hispanics/Latinos. A total of 27 of 32 previously identified QRS duration SNPs were shown to generalize in Hispanics/Latinos.ConclusionsOur QRS duration GWAS, the first in Hispanic/Latino populations, identified two new loci, underscoring the utility of extending large scale genomic studies to currently under-examined populations.
New tools for diet analysis: nanopore sequencing of metagenomic DNA from rat stomach contents to quantify diet
Authors: Freed Nikki E. , Pearman William S. , Smith Adam N. H. , Breckell Georgia , Dale James , Silander Olin K. 
Published: July 2018

AbstractBackgroundUsing metagenomics to determine animal diet offers a new and promising alternative to current methods. Here we show that rapid and inexpensive diet quantification is possible through metagenomic sequencing with the portable Oxford Nanopore Technologies (ONT) MinION. Using an amplification-free approach, we profiled the stomach contents from wild-caught rats.ResultsWe conservatively identified diet items from over 50 taxonomic orders, ranging across nine phyla that include plants, vertebrates, invertebrates, and fungi. This highlights the wide range of taxa that can be identified using this simple approach. We calibrate the accuracy of this method by comparing the characteristics of reads matching the ground-truth host genome (rat) to those matching diet items, and show that at the family-level, false positive taxon assignments are approximately 97.5% accurate. We also suggest a way to mitigate for database biases in metagenomic approaches. Finally, we implement a constrained ordination analysis and show that we can identify the sampling location of an individual rat within tens of kilometres based on diet content alone.ConclusionsThis work establishes proof-of-principle for long-read metagenomic methods in quantitative diet analysis. We show that diet content can be quantified even with limited expertise, using a simple, amplification free workflow and a relatively inexpensive and accessible next generation sequencing method. Continued increases in the accuracy and throughput of ONT sequencing, along with improved genomic databases, suggests that a metagenomic approach to quantification of animal diets will become an important method in the future.
Integrating genomic resources to present full gene and promoter capture probe sets for bread wheat
Authors: Gardiner Laura-jayne , Brabbs Thomas , Akhunova Alina , Jordan Katherine , Budak Hikmet , Richmond Todd , Singh Sukwinder , Catchpole Leah , Akhunov Eduard , Hall Anthony 
Published: July 2018

AbstractBackgroundWhole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits.ResultsWe present and validate two gold standard capture probe sets for hexaploid bread wheat, a gene and a promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high confidence genes and promoters that were identified in the genome alongside a large proportion of the low confidence genes and promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for SNP calling while significantly reducing cost per sample for gene and promoter capture.ConclusionsWe show that a capture design employing an ‘island strategy’ can enable analysis of the large gene/promoter space of wheat with only 2×160 Mb probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations.
Energetic substrate availability regulates synchronous activity in an excitatory neural network
Authors: Tourigny David S. , Kaiser Abdul Karim Muhammad , Echeveste Rodrigo , Kotter Mark R. N. , O’Neill John S. 
Published: July 2018

AbstractNeural networks are required to meet significant metabolic demands associated with performing sophisticated computational tasks in the brain. The necessity for efficient transmission of information imposes stringent constraints on the metabolic pathways that can be used for energy generation at the synapse, and thus low availability of energetic substrates can reduce the efficacy of synaptic function. Here we study the effects of energetic substrate availability on global neural network behavior and find that glucose alone can sustain excitatory neurotransmission required to generate high-frequency synchronous bursting that emerges in culture. In contrast, obligatory oxidative energetic substrates such as lactate and pyruvate are unable to substitute for glucose, indicating that processes involving glucose metabolism form the primary energy-generating pathways supporting coordinated network activity. Our experimental results are discussed in the context of the role that metabolism plays in supporting the performance of individual synapses, including the relative contributions from postsynaptic responses, astrocytes, and presynaptic vesicle cycling. We propose a simple computational model for our excitatory cultures that accurately captures the inability of metabolically compromised synapses to sustain synchronous bursting when extracellular glucose is depleted.
Short-term radiofrequency exposure from new generation mobile phones reduces EEG alpha power with no effects on cognitive performance
Authors: Vecsei Zsuzsanna , Knakker Balázs , Juhász Péter , Thuróczy György , Trunk Attila , Hernádi István 
Published: July 2018

AbstractAlthough mobile phone (MP) use has been steadily increasing in the last decades and similar positive trends are expected for the near future, systematic investigations on neurophysiological and cognitive effects caused by recently developed technological standards for MPs are scarcely available. Here, we investigated the effects of radiofrequency (RF) fields emitted by new-generation mobile technologies, specifically, Universal Mobile Telecommunications System (UMTS) and Long-Term Evolution (LTE), on intrinsic scalp EEG activity in the alpha band (8–12 Hz) and cognitive performance in the Stroop test. The study involved 60 healthy, young-adult university students (34 for UMTS and 26 for LTE) with double-blind administration of Real and Sham exposure in separate sessions. EEG was recorded before, during and after RF exposure, and Stroop performance was assessed before and after EEG recording. Both RF exposure types caused a notable decrease in the alpha power over the whole scalp that persisted even after the cessation of the exposure, whereas no effects were found on any aspects of performance in the Stroop test. The results imply that the brain networks underlying global alpha oscillations might require minor reconfiguration to adapt to the local biophysical changes caused by focal RF exposure mimicking MP use.
DrosophilaHox genes induce melanised pseudo-tumours when misexpressed in hemocytes
Authors: Ponrathnam Titus , Mishra Rakesh K 
Published: July 2018

AbstractHomeotic genes are the key early determinants of cell identity along the anterior-posterior body axis across bilaterians. More recently, however, several late non-homeotic functions of hox genes have emerged in a variety of organogenesis processes, including in mammals. Being crucial factors in determining cell identity and organogenesis, the misregulation of hox genes is likely to be associated with defects in these processes. Several studies have reported misexpression of hox genes in a variety of malignancies including acute myeloid leukaemia. Considering thatDrosophilais a well-established model for the study of haematopoiesis, we ectopically expressed the hox genes,Dfd,Ubx,abd-AandAbd-B, to ask if and how it will alter the process of haematopoiesis. We observed black melanised spots circulating in the viscera of the larvae and extensive lethality at during the pupal stage in these conditions. Such abnormalities are the hallmark of dysregulated haematopoiesis. We also observed an increase in blood cell number as well as their enhanced differentiation into lamellocytes. Our study opens a new possibility of addressing the function hox genes in normal and leukemogenic hematopoiesis with potential implications in downstream targets for diagnostic markers and therapy.SummaryDrosophilaHox genes, when expressed in blood cells, are leukemogenic, induce cell autonomous proliferation and differentiation. This reinforces previous studies in vertebrates and allows for Hox induced leukaemia to be studied inDrosophila.
Genome-wide maps of distal gene regulatory regions active in the human placenta
Authors: Zhang Joanna , Simonti Corinne N. , Capra John A. 
Published: July 2018

ABSTRACTPlacental dysfunction is implicated in many pregnancy complications, including preeclampsia and preterm birth (PTB). While both these syndromes are influenced by environmental risk factors, they also have a substantial genetic component that is not well understood. Precisely controlled gene expression during development is crucial to proper placental function and often mediated through gene regulatory enhancers. However, we lack accurate maps of placental enhancer activity due to the challenges of assaying the placenta and the difficulty of comprehensively identifying enhancers. To address the gap in our knowledge of gene regulatory elements in the placenta, we used a two-step machine learning pipeline to synthesize existing functional genomics studies, transcription factor (TF) binding patterns, and evolutionary information to predict placental enhancers. The trained classifiers accurately distinguish enhancers from the genomic background and placental enhancers from enhancers active in other tissues. Genomic features collected from tissues and cell lines involved in pregnancy are the most predictive of placental regulatory activity. Applying the classifiers genome-wide enabled us to create a map of 33,010 predicted placental enhancers, including 4,562 high-confidence enhancer predictions. The genome-wide placental enhancers are significantly enriched nearby genes associated with placental development and birth disorders and for SNPs associated with gestational age. These genome-wide predicted placental enhancers provide candidate regions for further testing in vitro, will assist in guiding future studies of genetic associations with pregnancy phenotypes, and aid interpretation of potential mechanisms of action for variants found through genetic studies.
Evidence for a Recombinant Origin of HIV-1 group M from Genomic Variation
Authors: Olabode Abayomi S , Avino Mariano , Ng Tammy , Abu-Sardanah Faisal , Dick David W , Poon Art FY 
Published: July 2018

AbstractReconstructing the early dynamics of the HIV-1 pandemic can provide crucial insights into the socioeconomic drivers of emerging infectious diseases in human populations, including the roles of urbanization and transportation networks. Current evidence indicates that the global pandemic comprising almost entirely of HIV-1/M originated around the 1920s in central Africa. However, these estimates are based on molecular clock estimates that are assumed to apply uniformly across the virus genome. There is growing evidence that recombination has played a significant role in the early history of the HIV-1 pandemic, such that different regions of the HIV-1 genome have different evolutionary histories. In this study, we have conducted a dated-tip analysis of all near full-length HIV-1/M genome sequences that were published in the GenBank database. We used a sliding window approach similar to the ‘bootscanning’ method for detecting breakpoints in intersubtype recombinant sequences. We found evidence of substantial variation in estimated root dates among windows, with an estimated mean time to the most recent common ancestor (tMRCA) of 1922. Estimates were significantly autocorrelated, which was more consistent with an early recombination event than with stochastic error variation in phylogenetic reconstruction and dating analyses. A piecewise regression analysis supported the existence of at least one recombination breakpoint in the HIV-1/M genome with interval-specific means around 1929 and 1913, respectively. This analysis demonstrates that a sliding window approach can accommodate early recombination events outside the established nomenclature of HIV-1/M subtypes, although it is difficult to incorporate the earliest available samples due to their limited genome coverage.
Covariation analysis with improved parameters reveals conservation in lncRNA structures
Authors: Tavares Rafael C A , Pyle Anna Marie , Somarowthu Srinivas 
Published: July 2018

AbstractThe existence of phylogenetic covariation in base-pairing is strong evidence for functional elements of RNA structure, although available tools for identifying covariation are limited. R-scape is a recently developed program for prediction of covariation from sequence alignments, but it has limited utility on long RNAs, especially those of eukaryotic origin. Here we show that R-scape can be adapted for powerful prediction of covariation in long RNA molecules, including mammalian lncRNAs.
Strategies to manage hail risk in apple production
Authors: Porsch Annkatrin , Gandorfer Markus , Bitsch Vera 
Published: July 2018

Purpose
Hail risk management is essential for successful farm management in German fruit production, particularly because hail events and associated losses have increased in recent years. The purpose of this paper is to conduct a detailed risk analysis comparing different strategies to manage hail risk, taking into account farmers’ risk aversion and farm-specific conditions.

Design/methodology/approach
Within an expected utility framework, two different strategies for managing hail risk are compared: one belonging to the group of financial instruments (hail insurance) and the other to the group of technical instruments (anti-hail net). A unique data set comprising a ten-year time series of orchard-specific hail damage and hail insurance data is used.

Findings
For orchards with low local hail risk and low yield potential, not using hail risk mitigation is most efficient. For orchards with high local hail risk and high yield potential, anti-hail nets provide the highest certainty equivalents. For orchards with high local risk, but low yield potential, hail insurance is most efficient. For orchards, with low local risk, but high yield potential, the certainty equivalents are higher for anti-hail net, when the farmer is risk neutral or slightly risk-averse. With increasing risk aversion, hail insurance is most efficient, which can be explained by the greater degree of the instrument’s flexibility.

Originality/value
The novelty of the study lies in the direct comparison of the risk effects of anti-hail nets and hail insurance in fruit production.
Linking protean and boundaryless career with organizational commitment
Authors: Alonderienė Raimonda , Šimkevičiūtė Indrė 
Published: July 2018

PurposeDue to the changes in the market, the shift to proactive and self-developed career management is evident. It results in the emergence of contemporary career attitudes, namely, protean and boundaryless ones. Individuals with protean career (PC) and boundaryless career (BC) attitudes may be more inclined to switch jobs, which affect decreased organizational commitment. The purpose of this paper is to analyze whether PC and BC attitudes affect organizational commitment of young adults in finance sector.Design/methodology/approachThe data of 177 young Lithuanian adults from finance sector were collected in quantitative research.FindingsThe research results indicate that young adults in finance sector have contemporary career attitudes significantly expressed. The regression analysis findings show that affective commitment is positively predicted by self-directed career management and boundaryless mindset, and negatively predicted by values-driven career orientation and organizational mobility preference. Continuance commitment is negatively predicted by self-directed career management and organizational mobility preference.Originality/valueThis research is valuable as few if any studies cover contemporary career attitudes and organizational commitment of already working young adults in finance sector in a European country, namely, Lithuania.
Takeover defense, collective action and the top management team
Authors: Tribbitt Mark A. , Yang Yi 
Published: July 2018

PurposeThe purpose of the study is to examine the interaction between the structure of the top management team, takeover defense mechanisms and firms rate of collective actions.Design/methodology/approachThe study uses elements of agency theory, prospect theory and competitive dynamics research to develop a model for examining heterogeneity in the rate of collective actions among firms in the technology sector. A sample of 299 firm-year observations arrayed into panel regression analyses is used.FindingsThe findings from this study show a positive relationship between the size of the top management team and the count of collective actions when takeover defense mechanisms are present. Further this study finds a negative relationship between top management team ownership and collective actions when these same takeover defense mechanisms are present. Additionally, the female ratio of the top management team is negatively related to collective actions.Research limitations/implicationsThis study was conducted using a sample of technological firms. These relationships may not be generalizable to firms in other contexts. Further, other elements of the firm’s governance structure (i.e. board of directors or shareholders) may play an important role in the strategic decision-making process.Originality/valueThis study expands on existing research by linking several blocks of literature, top management team literature, competitive dynamics literature and corporate governance literature, into a model to examine firm structural characteristics on the heterogeneity in the propensity to formulate collective actions among firms.
Older people’s travel and mobility needs: a reflection of a hierarchical model 10 years on
Authors: Musselwhite Charles , Haddad Hebba 
Published: July 2018

Purpose
In 2010, the authors published a model of older people’s travel and mobility needs in the Quality of Ageing and Older Adults journal (Musselwhite and Haddad, 2010b). The model comprises three levels, practical (the need to get from A to B as quickly, cheaply and efficiently as possible), psychosocial (the need for independence, control and status) and aesthetic needs (the need for travel for its own sake), all which need to be fulfilled to achieve wellbeing and quality of life. Since then, the model has been translated into different languages and been cited 119 times across different formats. The paper aims to discuss this issue.

Design/methodology/approach
Using ten years of analysing feedback that includes articles that cited the model, discussions with academics, policy makers and practitioners as well as from older people themselves, this paper reflects on the original model.

Findings
Five key themes are generated from the re-examination: the validity of the model; the utility and usefulness of needs in understanding travel behaviour and turning them into policy or practice; application of the model to different contexts; understanding the relationship between travel needs and health and wellbeing; and fitting the model to future changes in transport and social policy.

Originality/value
This reflection on this well-cited and well-used model allows a re-adjustment of the model, updating it to be used in conjunction with policy and practice, especially highlighting the need to further distinguish mobility for aesthetic needs.
Impact of contract farming on yield, costs and profitability in low‐value crop: evidence from a low‐income country
Authors: Mishra Ashok K. , Kumar Anjani , Joshi Pramod K. , D'Souza Alwin 
Published: July 2018

Lentils, a low‐value and highly nutritious crop, are Nepal's largest pulse cash crop. However, the majority of the nation's smallholders produce lentils on very small plots of land. The large gap in lentil yields between Nepal and other lentil‐producing countries underscores the importance of improving yields and income of smallholders. When it comes to the financial viability of small farms, particularly in developing countries, and globalisation, contract farming (CF) may prove useful in achieving efficiency and profitability in smallholder lentil farms in Nepal. This study employs the propensity score matching approach to examine the effects of the adoption of CF on yields, profitability and costs of smallholder lentil farms in Nepal. Findings from this study reveal that contrary to popular belief, CF adoption by lentil producers in Nepal has a positive and significant effect on per‐hectare revenues, profits and yield and a negative impact on variable and transportation costs. The study finds that only very smallholder lentil farms (0.01‐0.05 ha) benefit from CF.