bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population level mitogenomics of the long-lived Greater Mouse-eared bat,Myotis myotis, reveals dynamic heteroplasmy and challenges the Free Radical Theory of Ageing
Authors: Jebb David , Foley Nicole M. , Whelan Conor V. , Touzalin Frédéric , Puechmaille Sebastien J. , Teeling Emma C. 
Published: November 2017

AbstractBackgroundBats are the only mammals capable of true, powered flight, which drives an extremely high metabolic rate. The “Free Radical Theory of Ageing” (FTRA) posits that a high metabolic rate leads to mitochondrial heteroplasmy and the progressive ageing phenotype. Contrary to this, bats are the longest lived order of mammals despite their small size and high metabolic rate. To investigate if bats exhibit increased mitochondrial heteroplasmy with age as predicted by the FRTA, we performed targeted, deep sequencing of mitogenomes and measured point heteroplasmy in wild, long livedMyotis myotisas they age.ResultsIn total, blood was sampled from 195 individuals, aged between <1 and at 6+ years old, and whole mitochondria were sequenced, with a subset sampled over multiple years. The majority of heteroplasmies, 77.6%, were at a frequency below 5%. Oxidative mutations were not the primary source of heteroplasmies and present in only a small number of individuals, likely representing local oxidative stress events. There was a significant positive correlation between age and heteroplasmy, with a rate of increase of 0.13 sites per year. Longitudinal data from recaptured individuals show heteroplasmy is dynamic, and does not increase uniformly over time.ConclusionsWe show that bats do not suffer from the predicted, inevitable increase in heteroplasmy which underscores the FRTA. Most heteroplasmies were at low frequency and are primarily transitions. Heteroplasmy increased with age, however how this contributes to ageing is unclear, as heteroplasmy was dynamic, questioning its presumed role as a primary driver of ageing.
VarExp: Estimating variance explained by Genome-Wide GxE summary statistics
Authors: Laville Vincent , Bentley Amy R. , Privé Florian , Zhu Xiafoeng , Gauderman Jim , Winkler Thomas W , Province Mike , Rao DC , Aschard Hugues ,   on behalf of the CHARGE Gene-Lifestyle Interactions Working Group
Published: November 2017

AbstractMany genomic analyses, such as genome-wide association studies (GWAS) or genome-wide screening for Gene-Environment (GxE) interactions have been performed to elucidate the underlying mechanisms of human traits and diseases. When the analyzed outcome is quantitative, the overall contribution of identified genetic variants to the outcome is often expressed as the percentage of phenotypic variance explained. In practice, this is commonly estimated using individual genotype data. However, using individual-level data faces practical and ethical challenges when the GWAS results are derived in large consortia through meta-analysis of results from multiple cohorts. In this work, we present a R package, “VarExp”, that allows for the estimation of the percentage of phenotypic variance explained by variants of interest using summary statistics only. Our package allows for a range of models to be evaluated, including marginal genetic effects, GxE interaction effects, and main genetic and interaction effects jointly. Its implementation integrates all recent methodological developments on the topic and does not need external data to be uploaded by users.The R source code, tutorial and associated example are available at https://gitlab.pasteur.fr/statistical-genetics/VarExp.git.
Determinants of Transcription Initiation Directionality in Metazoans
Authors: Ibrahim Mahmoud M. , Karabacak Aslihan , Glahs Alexander , Kolundzic Ena , Hirsekorn Antje , Carda Alexa , Tursun Baris , Zinzen Robert P. , Lacadie Scott A. , Ohler Uwe 
Published: November 2017

AbstractDivergent transcription from promoters and enhancers is pervasive in many species, but it remains unclear if it is a general and passive feature of all eukaryotic cis regulatory elements. To address this, we define promoters and enhancers in C. elegans, D. melanogaster and H. sapiens using ATAC-Seq and investigate the determinants of their transcription initiation directionalities by analyzing genome-wide nascent, cap-selected, polymerase run-on assays. All three species initiate divergent transcription from separate core promoter sequences. Sequence asymmetry downstream of forward and reverse initiation sites, known to be important for termination and stability in H. sapiens, is unique in each species. Chromatin states of divergent promoters are not entirely conserved, but in all three species, the levels of histone modifications on the +1 nucleosome are independent from those on the -1 nucleosome, arguing for independent initiation events. This is supported by an integrative model of H3K4me3 levels and core promoter sequence that is highly predictive of promoter directionality and of two types of promoters: those with balanced initiation directionality and those with skewed directionality. Lastly, D. melanogaster enhancers display variation in chromatin architecture depending on enhancer location, and D. melanogaster promoter regions with dual enhancer/promoter potential are enriched for divergent transcription. Our results point to a high degree of variation in regulatory element transcription initiation directionality within and between metazoans, and to non-passive regulatory mechanisms of transcription initiation directionality in those species.
Paleocene origin of the Neotropical lineage of cleptoparasitc bees Ericrocidini-Rhathymini (Hymenoptera, Apidae)
Authors: Martins Aline C. , Luz David R. , Melo Gabriel A. R. 
Published: November 2017

AbstractCleptoparasitic bees abandoned the pollen collecting for their offspring and lay their eggs on other bees’ provisioned nests. Also known as cuckoo bees they belong to several lineages, especially diverse in Apinae. We focused on a lineage of Apinae cleptoparasitic bees, the clade Ericrocidini+Rhathymini, which attack nests of the oil-collecting bees. We sequenced five genes for a broad sampling in this clade plus a large outgroup and reconstruct phylogeny and divergence times. We confirmed the monophyly of the clade Ericrocidini+Rhathymini and its position inside the ericrocidine line, together with the tribes Protepeolini, Isepeolini and Coelioxoidini. Our results corroborate the current taxonomic classification.Ericrocisis the basal most lineage in Ericrocidini and the position ofAcanthopusand the most diverse genusMesopliawere inconclusive. Ericrocidini+Rhathymini diverged fromParepeolus aterrimus74 mya in the Cretaceous. Considering the robust molecular evidence of their sister relationships, the striking differences on the first instar larvae morphology of the two groups are probably adaptations to the distinct nesting biology of their hosts. As other parasites in the ericrocidine line, both groups possess larvae adapted to kill the immature host and to feed on floral oil provisioned by the host female. The evolution of host specialization in the line Ericrocidini+Rhathymini retroced to the Eocene when they arose synchronously with their hosts,CentrisandEpicharis.
From tree tops to the ground: reversals to terrestrial habit inGaleandraorchids (Epidendroideae: Catasetinae)
Authors: Martins Aline C. , Bochorny Thuane , Pérez-Escobar Oscar A. , Chomicki Guillaume , Monteiro Silvana H. N. , de Camargo Smidt Eric 
Published: November 2017

AbstractThe colonization of the epiphytic niche of tropical forest canopies played an important role in orchid’s extraordinary diversification in the Neotropics. However, reversals to the terrestrial habit occurred sparsely in species of Epidendroideae. To better understand which factors might have been involved in reversals to terrestrial habits in the predominantly epiphytic Epidendroideae, we investigateGaleandradiversification in time and space. We hypothesized that the reversal to the terrestrial habitat is linked to the origin of open vegetation habitats in South America. We generated a time-calibrated phylogeny based on a matrix of 17 out of 20 species ofGaleandraplus outgroups and seven DNA markers. We found thatGaleandraoriginated towards end of the Miocene, about 10 Ma in Amazonia (including the Guiana Shield). The terrestrial clade originated synchronously with the rise of dry vegetation biomes, suggesting that aridification during the last 5 million years dramatically impacted the diversification of epiphytic lineages in the Neotropics. Habit is correlated with floral spur lengths and geographic range size. The longer spurs and narrower ranges are found in epiphytic species: probably adapted to a specialized pollination mode, associated to the long-tongued Euglossini bees, which also prefer forested habits. The terrestrial species presents variable floral spurs and wide distribution ranges, with evidence of self-pollination, suggesting the loss of specialized pollination system and concomitant range expansion.
Sensory cortex is optimised for prediction of future input
Authors: Singer Yosef , Teramoto Yayoi , WiĲmore Ben D. B. , King Andrew J. , Schnupp Jan W. H. , Harper Nicol S. 
Published: November 2017

Neurons in sensory cortex are tuned to diverse features in natural scenes. But what determines which features neurons become selective to? Here we explore the idea that neuronal selectivity is optimised to represent features in the recent past of sensory input that best predict immediate future inputs. We tested this hypothesis using simple feedforward neural networks, which were trained to predict the next few video or audio frames in clips of natural scenes. The networks developed receptive fields that closely matched those of real cortical neurons, including the oriented spatial tuning of primary visual cortex, the frequency selectivity of primary auditory cortex and, most notably, in their temporal tuning properties. Furthermore, the better a network predicted future inputs the more closely its receptive fields tended to resemble those in the brain. This suggests that sensory processing is optimised to extract those features with the most capacity to predict future input.Impact statementPrediction of future input explains diverse neural tuning properties in sensory cortex.
Effect of entrepreneurial and market orientation on consumer engagement and performance of manufacturing SMEs
Authors: Mamun Abdullah Al , Mohiuddin Muhammad , Fazal Syed Ali , Ahmad Ghazali Bin 
Published: November 2017

Purpose
This study aims to examine the effect of entrepreneurial and market orientations on consumer engagement and the performance of manufacturing small- and medium-sized enterprises (SMEs) under the premise of the resource-based view (RBV) theory.

Design/methodology/approach
This study adopts a cross-sectional design, and quantitative data were collected from 360 manufacturing SMEs in Peninsular Malaysia. SMEs were selected using a stratified multi-stage sampling method from a total of 37,861 manufacturing SMEs. The respondents were selected from Selangor, Johor, Penang, Perak, Kelantan and Terengganu, as these states make up the majority (79 per cent) of the manufacturing SMEs in Malaysia.

Findings
Entrepreneurial and market orientations have statistically significant positive effects on consumer engagement. Consumer engagement in turn positively affects the performance of manufacturing SMEs in Peninsular Malaysia. Findings also revealed a partial mediation of consumer engagement between entrepreneurial and market orientations on performance.

Research limitations/implications
A larger sample size may improve the generalizability of the findings. Managers may be able to apply the findings of this paper in developing strategies for their manufacturing SMEs, specifically, by focusing on entrepreneurial and market orientation to raise consumer engagement and to improve the overall performances of their SMEs.

Originality/value
This study focuses on manufacturing SMEs in Malaysia, an emerging country with conditions unique to other industrialized countries. This study aims to demonstrate that integrated entrepreneurial and market orientations have significant effects on SMEs’ performance. This relationship could be mediated by consumer engagement. Specifically, consumer orientation may influence the effect of entrepreneurial and market orientations on overall firm performance..
Aging mechanisms and intervention targets
Authors: Liu Jun‐Ping 
Published: November 2017

SummaryPremature aging occurs frequently to various tissues and organs resulting in the tissue‐specific chronic diseases. The mechanisms of tissue‐specific premature aging are largely unknown. In response to environmental cues, aging may originate from cytoplasm or the nucleus of a cell with cytoplasm aging in association with organelle degeneration in terminally differentiated cells and nuclear aging with dysfunctional telomeres and irreversible cell cycle arrest in stem and cancer cells. Either cytoplasm aging or nuclear aging may cause extracellular senescence‐associated low‐grade inflammation to spread aging. Referring to the recent findings in this special issue of Healthy Aging in CEPP and beyond, we describe the molecular and cellular mechanisms of physiological aging and tissue‐specific pathological aging in chronic diseases.
Active Packaging Applications for Food
Authors: Yildirim Selçuk , Röcker Bettina , Pettersen Marit Kvalvåg , Nilsen‐Nygaard Julie , Ayhan Zehra , Rutkaite Ramune , Radusin Tanja , Suminska Patrycja , Marcos Begonya , Coma Véronique 
Published: November 2017

AbstractThe traditional role of food packaging is continuing to evolve in response to changing market needs. Current drivers such as consumer's demand for safer, “healthier,” and higher‐quality foods, ideally with a long shelf‐life; the demand for convenient and transparent packaging, and the preference for more sustainable packaging materials, have led to the development of new packaging technologies, such as active packaging (AP). As defined in the European regulation (EC) No 450/2009, AP systems are designed to “deliberately incorporate components that would release or absorb substances into or from the packaged food or the environment surrounding the food.” Active packaging materials are thereby “intended to extend the shelf‐life or to maintain or improve the condition of packaged food.” Although extensive research on AP technologies is being undertaken, many of these technologies have not yet been implemented successfully in commercial food packaging systems. Broad communication of their benefits in food product applications will facilitate the successful development and market introduction. In this review, an overview of AP technologies, such as antimicrobial, antioxidant or carbon dioxide‐releasing systems, and systems absorbing oxygen, moisture or ethylene, is provided, and, in particular, scientific publications illustrating the benefits of such technologies for specific food products are reviewed. Furthermore, the challenges in applying such AP technologies to food systems and the anticipated direction of future developments are discussed. This review will provide food and packaging scientists with a thorough understanding of the benefits of AP technologies when applied to specific foods and hence can assist in accelerating commercial adoption.
Prospects on the evolutionary mitogenomics of plants: A case study on the olive family (Oleaceae)
Authors: Van de Paer Céline , Bouchez Olivier , Besnard Guillaume 
Published: November 2017

AbstractThe mitogenome is rarely used to reconstruct the evolutionary history of plants, contrary to nuclear and plastid markers. Here, we evaluate the usefulness of mitochondrial DNA for molecular evolutionary studies in Oleaceae, in which cases of cytoplasmic male sterility (CMS) and of potentially contrasted organelle inheritance are known. We compare the diversity and the evolution of mitochondrial and chloroplast genomes by focusing on the olive complex and related genera. Using high‐throughput techniques, we reconstructed complete mitogenomes (ca. 0.7 Mb) and plastomes (ca. 156 kb) for six olive accessions and one Chionanthus. A highly variable organization of mitogenomes was observed at the species level. In olive, two specific chimeric genes were identified in the mitogenome of lineage E3 and may be involved in CMS. Plastid‐derived regions (mtpt) were observed in all reconstructed mitogenomes. Through phylogenetic reconstruction, we demonstrate that multiple integrations of mtpt regions have occurred in Oleaceae, but mtpt regions shared by all members of the olive complex derive from a common ancestor. We then assembled 52 conserved mitochondrial gene regions and complete plastomes of ten additional accessions belonging to tribes Oleeae, Fontanesieae and Forsythieae. Phylogenetic congruence between topologies based on mitochondrial regions and plastomes suggests a strong disequilibrium linkage between both organellar genomes. Finally, while phylogenetic reconstruction based on plastomes fails to resolve the evolutionary history of maternal olive lineages in the Mediterranean area, their phylogenetic relationships were successfully resolved with complete mitogenomes. Overall, our study demonstrates the great potential of using mitochondrial DNA in plant phylogeographic and metagenomic studies.
Discussion of “Financial Statement Comparability and the Efficiency of Acquisition Decisions”
Authors: Klein April 
Published: November 2017

AbstractChen, Collins, Kravet, and Mergenthaler (CCKM, ) is an empirical investigation of whether, after controlling for other known determinants of an acquirer's abnormal stock returns and expected and realized synergies, financial statement comparability impacts the investment decisions surrounding the acquirer's purchase of another company. The primary result is that higher financial statement comparability, as measured by De Franco, Kothari, and Verdi (DKV, ), yields improvements on outcomes associated with mergers and acquisitions. This discussion presents some criticisms of the DKV measure as applied to this study; the main criticism being whether the DKV measure captures accounting comparability or the risk of the target firm. The empirical results presented in CCKM are consistent with both explanations, thus making it difficult to disentangle CCKM's interpretation from an alternative explanation of their empirical findings.
MicroRNA‐21 Contributes to Reduced Microvascular Function in Binge Drinking Young Adults
Authors: Bian Jing‐Tan , Piano Mariann R. , Kotlo Kumar U. , Mahmoud Abeer M. , Phillips Shane A. 
Published: November 2017

BackgroundBinge drinking is associated with increased risk for cardiovascular (CV) disease. MicroRNA‐21 (miR21) is up‐regulated in the setting of excessive alcohol consumption and CV disease. Therefore, the goal of this study was to examine the vasodilatory responses to flow and acetylcholine (ACh) in the absence and presence of an anti‐miR21 inhibitor in the microcirculation of young adult repeated binge drinkers (BDs).MethodsGluteal subcutaneous adipose tissue biopsies were obtained from young adults (18 to 30 years, n = 35 vessels from BDs and n = 28 vessels from abstainers). Resistance arteries (RAs) were isolated, incubated with anti‐miR21 or a negative control (NC) to miR21 (12 hours; 50 nM), and lumen diameters measured with video microscopy. miR21 of adipose tissues was determined by quantitative polymerase chain reaction.ResultsFlow‐induced dilation and ACh‐induced dilation (AChID) were reduced in BDs as compared to abstainers. The miR21 inhibitor but not the NC abrogated these effects in BDs, but did not affect vasodilation in abstainers. Nitric oxide synthase inhibition with L‐NAME reduced vasodilation in abstainers but not in BDs. In BDs, vasodilation was reduced by L‐NAME in the presence of anti‐miR21 but not the NC. Scavenging the reactive oxygen species, hydrogen peroxide with polyethylene glycol catalase reduced dilation in BDs but did not affect the restored dilation by the miR21 inhibitor. Maximum dilation to papaverine (endothelium independent) was similar between groups and unaffected by pharmacological inhibition. Finally, vascular endogenous miR21 was increased in BDs compared to abstainers.ConclusionsEndogenous miR21 is increased in RAs of young BDs, leading to reduced flow and AChID in the microcirculation.
Communities mobilizing for change on alcohol (CMCA): secondary analyses of a randomized controlled trial showing effects of community organizing on alcohol acquisition by youth in the Cherokee nation
Authors: Wagenaar Alexander C. , Livingston Melvin D. , Pettigrew Dallas W. , Kominsky Terrence K. , Komro Kelli A. 
Published: November 2017

AbstractAimsWe evaluated the effects of a community organizing intervention, Communities Mobilizing for Change on Alcohol (CMCA), on the propensity of retail alcohol outlets to sell alcohol to young buyers without age identification and on alcohol acquisition behaviors of underage youth.DesignRandom assignment of community to treatment (n = 3) or control (n = 2). Student surveys were conducted four times per year for 3 years; the cohort was in 9th and 10th grades in the 2012–13 academic year. Alcohol purchase attempts were conducted every 4 weeks at alcohol retailers in each community (31 repeated waves).SettingThe Cherokee Nation, located in northeastern Oklahoma, USA.ParticipantsA total of 1399 high school students (50% male; 45% American Indian) and 113 stores licensed to sell alcohol across five study communities.InterventionLocal community organizers formed independent citizen action teams to advance policies, procedures and practices of local institutions in ways to reduce youth access to alcohol and foster community norms opposed to teen drinking.MeasurementsPerceptions regarding police enforcement and perceived difficulty of and self‐reported actual acquisition of alcohol from parents, adults, peers and stores.FindingsAlcohol purchases by young‐appearing buyers declined significantly, an 18 [95% confidence interval (CI) = 3, 33] percentage‐point reduction over the intervention period. Student survey results show statistically significant differences in the trajectory of perceived police enforcement, increasing 7 (4, 10) percentage points, alcohol acquisition from parents, decreasing 4 (0.1, 8) percentage points, acquisition from 21+ adults, decreasing 6 (0.04, 11) percentage points, from < 21 peers decreasing 8 (3, 13) percentage points and acquisition from stores decreasing 5 (1, 9) percentage points.ConclusionsA community organizing intervention, Communities Mobilizing for Change on Alcohol (CMCA), is effective in reducing the availability of alcohol to underage youth in the United states. Furthermore, results indicate that the previously reported significant effects of CMCA on teen drinking operate, at least in part, through effects on alcohol access.