bluuebunny/crossref_metadata_2025_split huggingface dataset:
Divided Allegiance
Authors: Joseph John E. 
Published: December 2016

SummaryRead outside its immediate historical context,Languages in Contact(1953) by Uriel Weinreich (1926–1967), most particularly its Preface by André Martinet (1908–1999), contains statements that can seem contradictory and mystifying. Describing his student Weinreich’s book, Martinet characterises bilingualism as “divided linguistic allegiance”, and uses the metaphor of a battlefield to describe the feelings of language variation experienced by bilinguals – but also by monolinguals, suggesting that the mainstream doctrine of languages as self-contained and unified is nothing more than a useful abstraction. Martinet’s own allegiances were divided between loyalty to his student and to his profession, since his own best-known work tended in the direction of the abstraction. All this was taking place in a febrile atmosphere at Columbia University, as “loyalty investigations” were being implemented by the Dean of Students to root out suspected communists – people thought to have allegiances divided between the two sides of the Iron Curtain. This paper tries to make the curious statements in the Preface and the book proper comprehensible by reading them within these professional and political contexts. It considers too how Martinet and Weinreich conceive of the bilingual brain on the model of two nations within a single state.
Distinct, shared and complementary: gendered agroecological knowledge in review.
Authors: Elias M. 
Published: December 2016

Abstract
The gendered nature of local agroecological knowledge remains poorly recognized. Gender biases in research and practice result in policies, programmes and interventions that are based on an incomplete understanding of local knowledge systems, and particularly of women's knowledge. This review of over 250 articles, books and chapters explores the complex, culturally specific and dynamic relationship between gender and agroecological knowledge, and underscores the central role both rural men and women play in managing biologically diverse, anthropogenic landscapes. Gender relations and norms, including the gender division of rights and responsibilities spatially, temporally and taskwise critically influence the acquisition and adaptation of local agroecological knowledge. Local knowledge varies across not only genders, but also other axes of social differentiation such as age and ethnicity, which intersect to shape the ways individuals, households and communities interact with their environment. Women and men may have different knowledge about the same or different things, and different ways of organizing and transmitting their knowledge. Although gendered spheres of knowledge are distinct, they are also shared, interwoven and complementary; and are neither fixed nor separable. Understanding local knowledge systems requires recognizing the distinctiveness, overlaps and interdependence of gendered knowledge repertoires. Current socio-economic trends are causing rapid shifts in local agroecological knowledge systems and resource management practices, and interrupting inter-generational knowledge transfers. Recognizing and valuing both women's and men's agroeocological knowledge(s) is crucial to preserve this (adaptive and evolving) body of knowledge, the cultures in which it is embedded and the agroecosystems it contributes to sustaining.
Self-selection Policing and the Disqualified Driver
Authors: Roach Jason 
Published: December 2016

AbstractPrevious research has identified those who commit serious driving offences, such as driving while over the legal limit for alcohol, dangerous and reckless driving, and driving while legally disqualified, as more likely to engage in other types of criminality, including serious offences, than their non-serious driving offender counterparts. Furthermore, those who continue to drive while disqualified have been singled out as the most likely group of serious driving offenders to be involved in a wide array of different types of offending and at rates more consistent with mainstream criminals than those who simply commit other driving-related offences. The present study builds on previous findings by focusing explicitly on the offending versatility of a sample of 50 disqualified drivers, the different categories of crime they commit, and the recency of other offences relative to the driving whilst disqualifying offence. With an overwhelming percentage of the sample found to have convictions for other types of offences, the study concludes with the suggestion that although driving while disqualified should be considered a trigger offence in self-selection policing, several anticipated obstacles to implementation must first be removed before it can be firmly integrated into current police practice.
Mandibular Actinomyces osteomyelitis mimicking osteosarcoma
Authors: Lau Lawrence , Darraj Majid , Keynan Yoav 
Published: December 2016

Introduction:

Actinomyces is a relatively uncommon cause of infection of the head and neck. However, its presentation is usually atypical and can be difficult to recognize. In this case report, we present the diagnostic and therapeutic challenges that can arise from cervicofacial actinomycosis.

Case presentation:
A 26-year-old woman from Northern Manitoba in her second trimester of pregnancy presented to the emergency department with a 2-month history of progressive pain and swelling of her right mandible. Imaging revealed lytic lesions involving the angle and ramus of the right mandible with possibility of osteosarcoma, and she was taken for hemimandibulectomy. Intraoperative specimens revealed Actinomyces odontolyticus. She was subsequently started on piperacillin–tazobactam that was later stepped down to amoxicillin–clavulanate with radiographic and clinical improvement of her osteomyelitis.

Conclusion:
Cervicofacial actinomycosis may mimic several neoplastic, granulomatous and infectious conditions, and often require tissue culture for diagnosis. Therapy often necessitates a combination of surgical resection and prolonged medical therapy, which is tailored to the burden of disease in the individual patient.
Single-cell transcriptomes of fluorescent, ubiquitination-based cell cycle indicator cells
Authors: Böttcher Michael , Kouno Tsukasa , Madissoon Elo , Motakis Efthymios , Abugessaisa Imad , Kato Sachi , Suzuki Harukazu , Hayashizaki Yoshihide , Kasukawa Takeya , Carninci Piero , Lassmann Timo , Shin Jay W. , Plessy Charles 
Published: December 2016

AbstractWe used a transgenic HeLa cell line that reports cell cycle phases through fluorescent, ubiquitination-based cell cycle indicators (Fucci), to produce a reference dataset of more than 270 curated single cells. Microscopic images were taken from each cell followed by RNA-sequencing, so that single-cell expression data is associated to the fluorescence intensity of the Fucci probes in the same cell. We developed an open data management and quality control workflow that enables users to replicate the processing of the sequence and microscopic image data that we deposited in public repositories. The workflow outputs a table with metadata, that is the starting point for further studies on these data. Beyond its use for cell cycle studies, We also expect that our workflow can be adapted to other single-cell projects using a similar combination of sequencing data and fluorescence measurements.
MECAT: an ultra-fast mapping, error correction andde novoassembly tool for single-molecule sequencing reads
Authors: Xiao Chuan-Le , Chen Ying , Xie Shang-qian , Chen Kai-Ning , Wang Yan , Luo Feng , Xie Zhi 
Published: December 2016

ABSTRACTThe high computational cost of current assembly methods for the long, noisy single molecular sequencing (SMS) reads has prevented them from assembling large genomes. We introduce an ultra-fast alignment method based on a novel global alignment score. For large human SMS data, our method is 7X faster than MHAP for pairwise alignment and 15X faster than BLASR for reference mapping. We develop a Mapping, Error Correction and de novo Assembly Tool (MECAT) by integrating our new alignment and error correction methods, with the Celera Assembler. MECAT is capable of producing high qualityde novoassembly of large genome from SMS reads with low computational cost. MECAT produces reference-quality assemblies ofSaccharomyces cerevisiae,Arabidopsis thaliana,Drosophila melanogasterand reconstructs the human CHM1 genome with 15% longer NG50 in only 7600 CPU core hours using 54X SMS reads and a Chinese Han genome in 19200 CPU core hours using 102X SMS reads.
Shared Nearest Neighbor clustering in a Locality Sensitive Hashing framework
Authors: Kanj Sawsan , Brüls Thomas , Gazut Stéphane 
Published: December 2016

AbstractWe present a new algorithm to cluster high dimensional sequence data, and its application to the field of metagenomics, which aims to reconstruct individual genomes from a mixture of genomes sampled from an environ-mental site, without any prior knowledge of reference data (genomes) or the shape of clusters. Such problems typically cannot be solved directly with classical approaches seeking to estimate the density of clusters, e.g., using the shared nearest neighbors rule, due to the prohibitive size of contemporary sequence datasets. We explore here a new method based on combining the shared nearest neighbor (SNN) rule with the concept of Locality Sensitive Hashing (LSH). The proposed method, called LSH-SNN, works by randomly splitting the input data into smaller-sized subsets (buckets) and, employing the shared nearest neighbor rule on each of these buckets. Links can be created among neighbors sharing a sufficient number of elements, hence allowing clusters to be grown from linked elements. LSH-SNN can scale up to larger datasets consisting of millions of sequences, while achieving high accuracy across a variety of sample sizes and complexities.
Dynamic flexibility in striatal-cortical circuits supports reinforcement learning
Authors: Gerraty Raphael T. , Davidow Juliet Y. , Foerde Karin , Galvan Adriana , Bassett Danielle S. , Shohamy Daphna 
Published: December 2016

AbstractComplex learned behaviors must involve the integrated action of distributed brain circuits. While the contributions of individual regions to learning have been extensively investigated, understanding how distributed brain networks orchestrate their activity over the course of learning remains elusive. To address this gap, we used fMRI combined with tools from dynamic network neuroscience to obtain time-resolved descriptions of network coordination during reinforcement learning. We found that learning to associate visual cues with reward involves dynamic changes in network coupling between the striatum and distributed brain regions, including visual, orbitofrontal, and ventromedial prefrontal cortex. Moreover, we found that flexibility in striatal network dynamics correlates with participants’ learning rate and inverse temperature, two parameters derived from reinforcement learning models. Finally, we found that not all forms of learning relate to this circuit: episodic memory, measured in the same participants at the same time, was related to dynamic connectivity in distinct brain networks. These results suggest that dynamic changes in striatal-centered networks provide a mechanism for information integration during reinforcement learning.Significance StatementLearning from the outcomes of actions–referred to asreinforcement learning–is an essential part of life. The roles of individual brain regions in reinforcement learning have been well characterized in terms of the updating of values for actions or sensory stimuli. Missing from this account, however, is a description of the manner in which different brain areas interact during learning to integrate sensory and value information. Here we characterize flexible striatal-cortical network dynamics that relate to reinforcement learning behavior.
Patterns of temporal and enemy niche use by a community of leaf cone moths (Caloptilia) coexisting on maples (Acer) as revealed by metabarcoding
Authors: Nakadai Ryosuke , Kawakita Atsushi 
Published: December 2016

AbstractThe diversity of herbivorous insects is often considered a function of host plant diversity. However, recent research has uncovered many examples of closely related herbivores using the same host plant(s), suggesting that partitioning of host plants is not the only mechanism generating diversity. Herbivores sharing hosts may utilize different parts of the same plant, but such resource partitioning is often not apparent; hence, the factors that allow closely related herbivores to coexist are still largely undetermined. We examined whether partitioning of phenology or natural enemies may explain the coexistence of leaf cone moths (Caloptilia; Gracillariidae) associated with maples(Acer;Sapindaceae). Larval activity of 10 sympatricCaloptiliaspecies found on nine maple species was monitored every 2–3 weeks for a total of 13 sampling events, and an exhaustive search for internal parasitoid wasps was conducted using high-throughput sequencing. Blocking primers were used to facilitate the detection of wasp larvae inside moth tissue. We found considerable phenological overlap amongCaloptiliaspecies, with two clear peaks in July and September–October. CoexistingCaloptiliaspecies also had largely overlapping parasitoid communities; a total of 13 wasp species belonging to four families attackedCaloptiliain a non-specific fashion at an overall parasitism rate of 46.4%. Although coexistence may be facilitated by factors not accounted for in this study, it appears that niche partitioning is not necessary for closely related herbivores to stably coexist on shared hosts. Co-occurrence without resource partitioning may provide an additional axis along which herbivorous insects attain increased species richness.
A coarse-graining, ultrametric approach to resolve the phylogeny of prokaryotic strains with frequent homologous recombination
Authors: Pang Tin Yau 
Published: December 2016

ABSTRACTA frequent event in the evolution of prokaryotic genomes is homologous recombination, where a foreign DNA stretch replaces a genomic region similar in sequence. Recombination can affect the relative position of two genomes in a phylogenetic reconstruction in two different ways: (i) one genome can recombine with a DNA stretch that is similar to the other genome, thereby reducing their pairwise sequence divergence; (ii) one genome can recombine with a DNA stretch from an outgroup genome, increasing the pairwise divergence. While several recombination-aware phylogenetic algorithms exist, many of these cannot account for both types of recombination; some algorithms can, but do so inefficiently. Moreover, many existing algorithms require that a substantial portion of each genome has not been affected by recombination, a sometimes unrealistic assumption. Here, we propose a novel coarse-graining approach for phylogenetic reconstruction (CGP), which is recombination-aware, applicable even if all genomic regions have experienced substantial amounts of recombination, and can be used on both nucleotide and amino acid sequences. CGP considers the local density of substitutions along pairwise genome alignments, fitting a model to the empirical distribution of substitution density to infer the pairwise coalescent time. Given all pairwise coalescent times, CGP reconstructs an ultrametric tree representing vertical inheritance. Based on simulations, we show that the proposed approach can reconstruct ultrametric trees with accurate topology, branch lengths, and root positioning. Applied to a set ofE. colistrains, the reconstructed trees are most consistent with gene distributions when inferred from amino acid sequences, a data type that cannot be utilized by many alternative approaches.AUTHOR SUMMARYIn homologous recombination, segments of foreign DNA overwrite similar segments of a prokaryotic genome. A single recombination event can simultaneously introduce many DNA substitutions. This disturbs phylogenetic signals, making it difficult to reconstruct prokaryotic family trees. While a handful of recombination-aware phylogenetic algorithms have been proposed, most do not take all effects of recombination into account; others rely on the frequently unrealistic assumption that a substantial part of a genome has not been affected by recombination at all. Here, we introduce a novel approach to phylogenetic reconstruction, which estimates the age of the most recent common ancestor of two strains from the density distribution of DNA or amino acid substitutions between their genomes. The proposed phylogenetic tree is the tree most compatible with these age estimates. Based on nucleotide or amino acid sequences, our approach accurately predicts the topology, branch lengths, and root positioning of prokaryotic family trees.
Co-occurring eQTLs and mQTLs: detecting shared causal variants and shared biological mechanisms
Authors: Pierce Brandon L. , Tong Lin , Argos Maria , Jasmine Farzana , Rakibuz-Zaman Muhammad , Sarwar Golam , Islam Md. Tariqul , Shahriar Hasan , Islam Tariqul , Rahman Mahfuzar , Yunus Md. , Kibriya Muhammad G. , Chen Lin S. , Ahsan Habibul 
Published: December 2016

AbstractInherited genetic variation impacts local gene expression and DNA methylation in humans. Expression and methylation quantitative trait loci (cis-eQTLs and cis-mQTLs) often occur at the same genomic location, suggesting a common causal variant and shared mechanism. Using DNA and RNA from peripheral blood of Bangladeshi individuals, we use “co-localization” methods to identify 3,695 eQTL-mQTL pairs that are likely to share a causal variant. Using partial correlation analysis and mediation analysis, we identify >500 pairs with evidence of a causal relationships between expression and methylation (i.e., shared mechanism) with many additional pairs that we are underpowered to detect. These co-localized pairs are enriched for SNPs showing opposite effects on expression and methylation, although a many affect multiple CpGs in opposite directions. Evidence of shared SNP-age interaction also supports shared mechanisms for two eQTL-mQTL pairs. This work demonstrates the pervasiveness of co-regulated expression and methylation traits in the human genome. This approach can be applied to other types of molecular QTLs to enhance our understanding of regulatory mechanisms.
X-ray grating interferometer for in situ and at-wavelength wavefront metrology
Authors: Kayser Yves , David Christian , Flechsig Uwe , Krempasky Juraj , Schlott Volker , Abela Rafael 
Published: December 2016

A wavefront metrology setup based on the X-ray grating interferometry technique for spatially resolved, quantitative, in situ and at-wavelength measurements of the wavefront at synchrotron radiation and hard X-ray free-electron laser beamlines is reported. Indeed, the ever-increasing demands on the optical components to preserve the wavefront shape and the coherence of the delivered X-ray beam call for more and more sensitive diagnostic instruments. Thanks to its angular sensitivity, X-ray grating interferometry has been established in recent years as an adequate wavefront-sensing technique for quantitatively assessing the quality of the X-ray wavefront under working conditions and hence for the in situ investigation of X-ray optical elements. In order to characterize the optical elements at any given beamline by measuring the aberrations introduced in the wavefront, a transportable X-ray grating interferometry setup was realised at the Swiss Light Source (SLS). The instrument, which is expected to be a valuable tool for investigating the quality of the X-ray beam delivered at an endstation, will be described hereafter in terms of the hardware setup and the related data analysis procedure. Several exemplary experiments performed at the X05DA Optics beamline of the SLS will be presented.
Study of the structural and electrical behavior of Bi(Mg,Ti)O3 modified (Ba,Ca)TiO3 ceramics
Authors: Shamim Md. Kashif , Sharma Seema , Singh Arpana , Rai Radheshyam , Rani Rashmi 
Published: December 2016

The ability of BaTiO3 to form solid solutions with different dopants (both iso- and aliovalent) makes it versatile for various applications. In the present study, (Ba,Ca)TiO3 (BCT) is modified with Bi(MgTi)O3 (BMT) in search for new lead-free ferroelectric material and improve their properties. For this purpose, BCT acts as a main base material and BMT acts as a modifier to fabricate a multifunctional material. In this study, we report the structural and electrical properties of lead free piezo-ceramics ([Formula: see text])(Ba[Formula: see text]Ca[Formula: see text])TiO3–[Formula: see text]Bi(Mg[Formula: see text]Ti[Formula: see text])O3 with [Formula: see text], 0.4, 0.5 prepared by solid-state sintering technique. Single perovskite phase with tetragonal structure is obtained for all the compositions, which is reconfirmed by the Raman Spectroscopic study. Dielectric study confirm the temperature stable behavior of the dielectric permittivity values above 300[Formula: see text]C. The dielectric constant value decreases with increase in BMT doping content. Impedance Spectroscopic study confirms non-Debye type dielectric relaxation in the specimen. The Nyquist plot and conductivity studies show the negative temperature coefficient of resistance behavior (NTCR) of the samples.
The interaction of estrogen and CSE/H2S pathway in the development of atherosclerosis
Authors: Li Hongzhu , Mani Sarathi , Wu Lingyun , Fu Ming , Shuang Tian , Xu Changqing , Wang Rui 
Published: December 2016

Both estrogen and hydrogen sulfide (H2S) have been shown to inhibit the development of atherosclerosis. We previously reported that cystathionine γ-lyase knockout (CSE-KO) male mice develop atherosclerosis earlier than male wild-type (WT) mice. The present study investigated the interaction of CSE/H2S pathway and estrogen on the development of atherosclerosis in female mice. Plasma estrogen levels were significantly lower in female CSE-KO mice than in female WT mice. NaHS treatment had no effect on plasma estrogen levels in both WT and CSE-KO female mice. After CSE-KO and WT female mice were fed with atherogenic diet for 12 wk, plasma lipid levels were significantly increased and triglyceride levels decreased compared with those of control diet-fed mice. Atherogenic diet induced more atherosclerotic lesion, oxidative stress, intracellular adhesion molecule-1 (ICAM-1), and NF-κB in CSE-KO mice than in WT mice. Estrogen treatment of atherogenic diet-fed WT mice attenuated hypercholesterolemia, oxidative stress, ICAM-1 expression, and NF-κB in WT mice but not in atherogenic diet-fed CSE-KO mice. Furthermore, H2S production in both the liver and vascular tissues was enhanced by estrogen in WT mice but not in CSE-KO mice. It is concluded that the antiatherosclerotic effect of estrogen is mediated by CSE-generated H2S. This study provides new insights into the interaction of H2S and estrogen signaling pathways on the regulation of cardiovascular functions. NEW & NOTEWORTHY Female cystathionine γ-lyase (CSE)-knockout mice have significantly lower plasma estrogen levels and more severe early atherosclerotic lesion than female wild-type mice. H2S production in liver and vascular tissues is enhanced by estrogen via its stimulatory effect on CSE activity. The antiatherosclerotic effect of estrogen is mediated by CSE-generated H2S.