bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loter: A software package to infer local ancestry for a wide range of species
Authors: Dias-Alves Thomas , Mairal Julien , Blum Michael G.B. 
Published: November 2017

AbstractAdmixture between populations provides opportunity to study biological adaptation and phenotypic variation. Admixture studies rely on local ancestry inference for admixed individuals, which consists of computing at each locus the number of copies that originate from ancestral source populations. Existing software packages for local ancestry inference are tuned to provide accurate results on human data and recent admixture events. Here, we introduce Loter, an open-source software package that does not require any biological parameter besides haplotype data in order to make local ancestry inference available for a wide range of species. Using simulations, we compare the performance of Loter to HAPMIX, LAMP-LD, and RFMix. HAPMIX is the only software severely impacted by imperfect haplotype reconstruction. Loter is the less impacted software by increasing admixture time when considering simulated and admixed human genotypes. For simulations of admixed Populus genotypes, Loter and LAMP-LD are robust to increasing admixture times by contrast to RFMix. When comparing length of reconstructed and true ancestry tracts, Loter and LAMP-LD provide results whose accuracy is again more robust than RFMix to increasing admixture times. We apply Loter to individuals resulting from admixture betweenPopulus trichocarpaandPopulus balsamiferaand lengths of ancestry tracts indicate that admixture took place around 100 generations ago. We expect that providing a rapid and parameter-free software for local ancestry inference will make more accessible genomic studies about admixture processes.
Sensitivity to sequencing depth in single-cell cancer genomics
Authors: Alves João M. , Posada David 
Published: November 2017

AbstractBackgroundQuerying cancer genomes at single-cell resolution is expected to provide a powerful framework to understand in detail the dynamics of cancer evolution. However, given the high costs currently associated with single-cell sequencing, together with the inevitable technical noise arising from single-cell genome amplification, cost-effective strategies that maximize the quality of single-cell data are critically needed. Taking advantage of five published single-cell whole-genome and whole-exome cancer datasets, we studied the impact of sequencing depth and sampling effort towards single-cell variant detection, including structural and driver mutations, genotyping accuracy, clonal inference and phylogenetic reconstruction, using recent tools specifically designed for single-cell data.ResultsAltogether, our results suggest that, for relatively large sample sizes (25 or more cells), sequencing single tumor cells at depths >5x does not drastically improve somatic variant discovery, the characterization of clonal genotypes or the estimation of phylogenies from single tumor cells.ConclusionsWe demonstrate that sequencing many individual tumor cells at a modest depth represents an effective alternative to explore the mutational landscape and clonal evolutionary patterns of cancer genomes, without the excessively high costs associated with high-coverage genome sequencing.
Technology-independent estimation of cell type composition using differentially methylated regions
Authors: Hicks Stephanie C. , Irizarry Rafael A. 
Published: November 2017

AbstractBackgroundHigh-resolution genome-wide measurement of DNA methylation (DNAm) has become a widely used assay in biomedical research. A major challenge in measuring DNAm is variability introduced from intra-sample cellular heterogeneity, which is a convolution of DNAm profiles across cell types. When this source of variability is confounded with an outcome of interest, if unaccounted for, false positives ensue. This is particularly problematic in epigenome-wide association studies for human disease performed on whole blood, a heterogeneous tissue. To account for this source of variability, a first step is to determine the actual cell proportions of each sample. Currently, the most effective approach is based on fitting a linear model in which one assumes the DNAm profiles of the representative cell types are known. However, we can only make this assumption when a dedicated experiment is performed to provide a plug-in estimate for these profiles. Although this method works well in practice, technology-specific biases lead to platform-dependent plug-in profiles. As a result, to apply the current methods across technologies we are required to repeat these costly experiments for each platform.ResultsHere, we present a method that accurately estimates cell proportions agnostic to platform by first using experimental data to identify regions in which each cell type is clearly methylated or unmethlyated and model these as latent states. While the continuous measurements used in the linear model approaches are affected by platform-specific biases, the latent states are biologically driven and therefore technology independent, implying that experimental data only needs to be collected once. We demonstrate that our method accurately estimates the cell composition from whole blood samples and is applicable across multiple platforms, including microarray and sequencing platforms.
Coherent olfactory bulb gamma oscillations arise from coupling independent columnar oscillators
Authors: Peace Shane T. , Johnson Benjamin C. , Werth Jesse C. , Li Guoshi , Kaiser Martin E. , Fukunaga Izumi , Schaefer Andreas T. , Molnar Alyosha C. , Cleland Thomas A. 
Published: November 2017

AbstractSpike timing-based representations of sensory information depend on embedded dynamical frameworks within neuronal networks that establish the rules of local computation and interareal communication. Here, we investigated the dynamical properties of olfactory bulb circuitry in mice of both sexes using microelectrode array recordings from slice andin vivopreparations. Neurochemical activation or optogenetic stimulation of sensory afferents evoked persistent gamma oscillations in the local field potential. These oscillations arose from slower, GABA(A) receptor-independent intracolumnar oscillators coupled by GABA(A)-ergic synapses into a faster, broadly coherent network oscillation. Consistent with the theoretical properties of coupled-oscillator networks, the spatial extent of zero-phase coherence was bounded in slices by the reduced density of lateral interactions. The intactin vivonetwork, however, exhibited long-range lateral interactions that suffice in simulation to enable zero-phase gamma coherence across the olfactory bulb. The timing of action potentials in a subset of principal neurons was phase-constrained with respect to evoked gamma oscillations. Coupled-oscillator dynamics in olfactory bulb thereby enable a common clock, robust to biological heterogeneities, that is capable of supporting gamma-band spike synchronization and phase coding across the ensemble of activated principal neurons.New & NoteworthyOdor stimulation evokes rhythmic gamma oscillations in the field potential of the olfactory bulb, but the dynamical mechanisms governing these oscillations have remained unclear. Establishing these mechanisms is important, as they determine the biophysical capacities of the bulbar circuit to, for example, maintain zero-phase coherence across a spatially extended network, or coordinate the timing of action potentials in principal neurons. These properties in turn constrain and suggest hypotheses of sensory coding.
Toyota Hilux: how South Africa’s top pickup battled market challenges
Authors: Pheko Samenthea , Bick Geoff , Barnardo Claire 
Published: November 2017

Subject area
The Toyota Hilux case has been designed to show the complexities associated with managerial decision-making in a highly competitive vehicle market in South Africa. The case centres on the challenges the Toyota Hilux faced in sustaining its market leadership position amid intense competition from its rivals and changing customer preferences.

Study level/applicability
The case is suited to marketing and strategy students who are eager to demonstrate their critical thinking and managerial decision-making skills as part of their Masters of Business Administration (MBA) and Executive MBA academic programmes, and delegates on Executive Education programmes.

Case overview
The teaching case focuses on the Toyota Hilux brand and the various business dilemmas that Calvyn Williams, sales and marketing manager, and his team experience prior to the launch of the next Hilux: the fierce competition from other brands and the various marketing strategies used.

Expected learning outcomes
The objective of this teaching case is to afford students a “hands-on” understanding and appreciation of the challenges faced by market leaders in sustaining their dominance and selecting the most appropriate strategies for market leaders to adopt in extremely competitive environments such as the South African vehicle market.

Supplementary materials
Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code
CSS 8: Marketing.
High Carbon Stock forests provide co‐benefits for tropical biodiversity
Authors: Deere Nicolas J. , Guillera‐Arroita Gurutzeta , Baking Esther L. , Bernard Henry , Pfeifer Marion , Reynolds Glen , Wearn Oliver R. , Davies Zoe G. , Struebig Matthew J. 
Published: November 2017

Abstract

Carbon‐based policies provide powerful opportunities to unite tropical forest conservation with climate change mitigation. However, their effectiveness in delivering biodiversity co‐benefits is dependent on high levels of biodiversity being found in high carbon areas. Previous studies have focussed solely on the co‐benefits associated with Reducing Emissions from Deforestation and forest Degradation (REDD+) over large spatial scales, with few empirically testing carbon‐biodiversity correlations at management unit scales appropriate to decision‐makers. Yet, in development frontiers, where most biodiversity and carbon loss occurs, carbon‐based policies are increasingly driven by commodity certification schemes, which are applied at the concession level.

Working in a typical human‐modified landscape in Southeast Asia, we examined the biodiversity value of land prioritised via application of REDD+ or the High Carbon Stock (HCS) approach, the emerging land‐use planning tool for oil palm certification. Carbon stocks were estimated via low‐ and high‐resolution datasets derived from global or local‐level biomass. Mammalian species richness was predicted using hierarchical Bayesian multispecies occupancy models of camera‐trap data from forest and oil palm habitats.

At the community level, HCS forest supported comparable mammal diversity to control sites in continuous forest, while lower carbon strata exhibited reduced species occupancy.

No association was found between species richness and carbon when the latter was estimated using coarse‐resolution data. However, when using high‐resolution, locally validated biomass data, diversity demonstrated positive relationships with carbon for threatened and disturbance‐sensitive species, suggesting sensitivity of co‐benefits to carbon data sources and the species considered.

Policy implications. Our work confirms the potential for environmental certification and Reducing Emissions from Deforestation and forest Degradation to work in tandem with conservation to mitigate agricultural impacts on tropical forest carbon stocks and biodiversity. Successful implementation of both approaches could be used to direct development to low carbon, low biodiversity areas in tropical countries.
The role of bryophytes for tree seedling responses to winter climate change: Implications for the stress gradient hypothesis
Authors: Lett Signe , Wardle David A. , Nilsson Marie‐Charlotte , Teuber Laurenz M. , Dorrepaal Ellen 
Published: November 2017

AbstractWhen tree seedlings establish beyond the current tree line due to climate warming, they encounter existing vegetation, such as bryophytes that often dominate in arctic and alpine tundra. The stress gradient hypothesis (SGH) predicts that plant interactions in tundra become increasingly negative as climate warms and conditions become less harsh. However, for seedlings, climate warming might not result in lower winter stress, if insulating snow cover is reduced.We aimed to understand if bryophytes facilitate seedling survival in a changing winter climate and if these effects of bryophytes on tree seedlings comply with theSGHalong elevational gradients under contrasting snow conditions.In the Swedish subarctic, we transplanted intact bryophyte cores covered by each of three bryophyte species and bryophyte‐free control soil from above the tree line to two field common garden sites, representing current and future tree line air temperature conditions (i.e. current tree line elevation and a lower, warmer, elevation below the tree line). We planted seedlings ofBetula pubescensandPinus sylvestrisinto these cores and subjected them to experimental manipulation of snow cover during one winter.In agreement with theSGH, milder conditions caused by increased snow cover enhanced the generally negative or neutral effects of bryophytes on seedlings immediately after winter. Furthermore, survival ofP. sylvestrisseedlings after one full year was higher at lower elevation, especially when snow cover was thinner. However, in contrast with theSGH, impacts of bryophytes on over‐winter survival of seedlings did not differ between elevations, and impacts on survival ofB. pubescensseedlings after 1 year was more negative at lower elevation. Bryophyte species differed in their effect on seedling survival after winter, but these differences were not related to their insulating capacity.Synthesis. Our study demonstrates that interactions from bryophytes can modify the impacts of winter climate change on tree seedlings, andvice versa. These responses do not always comply withSGH, but could ultimately have consequences for large‐scale ecological processes such as tree line shifts. These new insights need to be taken into account in predictions of plant species responses to climate change.
Simulated caribou browsing limits the effect of nutrient addition on the growth of Betula glandulosa, an expanding shrub species in Eastern Canada
Authors: Morrissette‐Boileau Clara , Boudreau Stéphane , Tremblay Jean‐Pierre , Côté Steeve D. 
Published: November 2017

Abstract

Warmer summer temperatures and enhanced soil fertility increase shrub growth in tundra ecosystems, and these factors have likely contributed to shrub expansion at the circumpolar scale over the last decades. Conversely, large herbivores have the potential to counteract the positive impacts of climate change on shrub growth. Indeed, by stripping the leaves, herbivores have the potential to control the growth of shrub species and, consequently, limit their expansion.

To disentangle the impacts of climate change and herbivory on Betula glandulosa Michx., we conducted a 5‐year factorial experiment near Deception Bay, Nunavik, Canada, in which we simulated warmer temperatures, increased nitrogen availability and three caribou browsing intensities during the growing season. At the end of the experiment, we harvested the above‐ground biomass of B. glandulosa and conducted dendrochronological analyses on stems.

Fertilised plots under ambient temperature had 34% greater shrub biomass than plots assigned to the combined treatment of nitrogen addition and warmer temperatures. Browsing intensity had no effect on final biomass. Nitrogen addition increased radial growth (18%–33%; 3 years out of 5). Overall, browsing had a cumulative negative impact on B. glandulosa radial growth during the 5‐year experiment. While browsing had no effect in the first year of the experiment, moderate browsing (leaves stripped on 25% of available shoots) decreased radial growth by 27% at year 2, 32% at year 4 and 27% at year 5. Heavy browsing (leaves stripped on 75% of available shoots annually) decreased radial growth by c. 27% at year 2, 37% at year 3, 50% at year 4 and 48% at year 5. We did not observe significant interactions between browsing, temperature and nitrogen availability.

Synthesis. Our results clearly showed that caribou browsing may limit the growth of B. glandulosa, and thus can potentially limit its expansion. Herbivory should thus be considered when predicting tundra vegetation changes in the Arctic, at least in areas with high herbivore densities.
Comparing Statewide and Single‐center Data to Predict High‐frequency Emergency Department Utilization Among Patients With Asthma Exacerbation
Authors: Samuels‐Kalow Margaret E. , Faridi Mohammad K. , Espinola Janice A. , Klig Jean E. , Camargo Carlos A. 
Published: November 2017

AbstractBackgroundPrevious studies examining high‐frequency emergency department (ED) utilization have primarily used single‐center data, potentially leading to ascertainment bias if patients visit multiple centers. The goals of this study were 1) to create a predictive model to prospectively identify patients at risk of high‐frequency ED utilization for asthma and 2) to examine how that model differed using statewide versus single‐center data.MethodsTo track ED visits within a state, we analyzed 2011 to 2013 data from the New York State Healthcare Cost and Utilization Project State Emergency Department Databases. The first year of data (2011) was used to determine prior utilization, 2012 was used to identify index ED visits for asthma and for demographics, and 2013 was used for outcome ascertainment. High‐frequency utilization was defined as 4+ ED visits for asthma within 1 year after the index visit. We performed analyses separately for children (age < 21 years) and adults and constructed two models: one included all statewide (multicenter) visits and the other was restricted to index hospital (single‐center) visits. Multivariable logistic regression models were developed from potential predictors selected a priori. The final model was chosen by evaluating model performance using Akaike's Information Criterion scores, 10‐fold cross‐validation, and receiver operating characteristic curves.ResultsAmong children, high‐frequency ED utilization for asthma was observed in 2,417 of 94,258 (2.56%) using all statewide visits, compared to 1,853 of 94,258 (1.97%) for index hospital visits only. Among adults, the corresponding results were 7,779 of 159,874 (4.87%) and 5,053 of 159,874 (3.16%), respectively. In the multicenter visit model, the area under the curve (AUC) from 10‐fold cross‐validation for children was 0.70 (95% confidence interval [CI] = 0.69–0.72), compared to 0.71 (95% CI = 0.69–0.72) in the single‐center visit model. The corresponding AUC results for adults were 0.76 (95% CI = 0.76–0.77) and 0.76 (95% CI = 0.75–0.77), respectively.ConclusionData available at the index ED visit can predict subsequent high‐frequency utilization for asthma with AUC ranging from 0.70 to 0.76. Model accuracy was similar regardless of whether outcome ascertainment included all statewide visits (multicenter) or was limited to the index hospital (single‐center).
Rheumatic heart disease in pregnancy: How can health services adapt to the needs of Indigenous women? A qualitative study
Authors: Belton Suzanne , Kruske Sue , Jackson Pulver Lisa , Sherwood Juanita , Tune Kylie , Carapetis Jonathan , Vaughan Geraldine , Peek Michael , McLintock Claire , Sullivan Elizabeth 
Published: November 2017

ObjectivesTo study rheumatic heart disease health literacy and its impact on pregnancy, and to identify how health services could more effectively meet the needs of pregnant women with rheumatic heart disease.Materials and methodsResearchers observed and interviewed a small number of Aboriginal women and their families during pregnancy, childbirth and postpartum as they interacted with the health system. An Aboriginal Yarning method of relationship building over time, participant observations and interviews with Aboriginal women were used in the study. The settings were urban, island and remote communities across the Northern Territory. Women were followed interstate if they were transferred during pregnancy. The participants were pregnant women and their families. We relied on participants’ abilities to tell their own experiences so that researchers could interpret their understanding and perspective of rheumatic heart disease.ResultsAboriginal women and their families rarely had rheumatic heart disease explained appropriately by health staff and therefore lacked understanding of the severity of their illness and its implications for childbearing. Health directives in written and spoken English with assumed biomedical knowledge were confusing and of limited use when delivered without interpreters or culturally appropriate health supports.ConclusionsDespite previous studies documenting poor communication and culturally inadequate care, health systems did not meet the needs of pregnant Aboriginal women with rheumatic heart disease. Language‐appropriate health education that promotes a shared understanding should be relevant to the gender, life‐stage and social context of women with rheumatic heart disease.
Influenza burden, prevention, and treatment in asthma‐A scoping review by the EAACI Influenza in asthma task force
Authors: Schwarze J. , Openshaw P. , Jha A. , del Giacco S. R. , Firinu D. , Tsilochristou O. , Roberts G. , Selby A. , Akdis C. , Agache I. , Custovic A. , Heffler E. , Pinna G. , Khaitov M. , Nikonova A. , Papadopoulos N. , Akhlaq A. , Nurmatov U. , Renz H. , Sheikh A. , Skevaki C. 
Published: November 2017

AbstractTo address uncertainties in the prevention and management of influenza in people with asthma, we performed a scoping review of the published literature on influenza burden; current vaccine recommendations; vaccination coverage; immunogenicity, efficacy, effectiveness, and safety of influenza vaccines; and the benefits of antiviral drugs in people with asthma. We found significant variation in the reported rates of influenza detection in individuals with acute asthma exacerbations making it unclear to what degree influenza causes exacerbations of underlying asthma. The strongest evidence of an association was seen in studies of children. Countries in the European Union currently recommend influenza vaccination of adults with asthma; however, coverage varied between regions. Coverage was lower among children with asthma. Limited data suggest that good seroprotection and seroconversion can be achieved in both children and adults with asthma and that vaccination confers a degree of protection against influenza illness and asthma‐related morbidity to children with asthma. There were insufficient data to determine efficacy in adults. Overall, influenza vaccines appeared to be safe for people with asthma. We identify knowledge gaps and make recommendations on future research needs in relation to influenza in patients with asthma.