bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ethnolinguistic Orientation and Language Variation: Measuring and Archiving Ethnolinguistic Vitality, Attitudes, and Identity
Authors: Noels Kimberly A. , Kil Hali , Fang Yang 
Published: November 2014

AbstractSociolinguists and social psychologists have long been interested in how language variation is associated with social psychological variables, including people's beliefs about and attitudes toward languages and their speakers, as well as their feelings of affiliation with ethnolinguistic groups, and there is a growing interest in archiving such information along with sociolinguistic data for subsequent research. With this end in mind, we suggest some brief, quantitative indices that might be appropriate and useful for documenting social psychological variables for contemporary and future purposes. The first construct considered is ethnolinguistic vitality, which refers to those characteristics that make a language group likely to behave as an active collective entity in language contact situations. The second is language attitudes, which refer to the feelings and beliefs that people hold with regard to their own and others' languages and the associated language community/ies. The third is ethnolinguistic identity, which refers to the manner and extent to which individuals define themselves as members of an ethnolinguistic group. Although we maintain that more extensive, detailed coding should be included in sociolinguistic archives, we suggest that these three sets of indices should be minimally included in a battery to assess a speaker's ethnolinguistic orientation.
Sharing of Data as It Relates to Human Subjects Issues and Data Management Plans
Authors: Warner Natasha 
Published: November 2014

AbstractResearchers often wish to make knowledge publicly available, especially through publication, but may not wish to share their raw data. Human Subjects offices (IRBs) sometimes wish to keep all information private or even to have raw data destroyed. Funding agencies may hope for the data they finance collection of to be made publicly available to increase its impact. These motivations often conflict. This paper discusses how current Human Subjects regulations impact sharing of corpus data among researchers, how funding agencies influence this, and how researchers react to these forces. The paper also discusses potential future changes to the current outcomes, through changes to Human Subjects Protection regulations and changes to funding agency requirements on data sharing.
Archiving and Managing Sociolinguistic Data: The Problems of Portability, Access and Security, and Discoverability and Relevance
Authors: Kendall Tyler 
Published: November 2014

AbstractIn recent years, sociolinguists have become increasingly focused on and more explicit about ensuring the preservation, and accessibility, of their data. This increased focus on our data has involved new lines of work explicitly on data management and, in turn, has led to important (re)considerations of the nature of sociolinguistic data and the metadata of importance for sociolinguist research. While many of the papers in this special issue focus on issues having to do with specific metadata, in this paper, I consider archiving and sharing data more generally. I attend to three specific problem areas, portability access and security, and discoverability and relevance, providing advice as well as some ‘food for thought’ discussions for each.
The Role of Metadata in the Infrastructure for Archival Interoperation
Authors: Simons Gary F. 
Published: November 2014

AbstractSociolinguists want to be able to share and compare datasets, and they want to do so now and far into the future. Achieving this dream will require that sociolinguistic corpora are archived in a sustainable way and that those corpora are encoded in such a way that interoperation among them is possible. This paper first sets the stage by describing broadly the requirements for sustainable archiving. It then focuses on the role of metadata in constructing an infrastructure that will support the kind of interoperation that is envisioned – both corpus‐level metadata for facilitating the discovery of relevant corpora and observation‐level metadata for facilitating the comparison of observations that are comparable.
The Problem with Binaries: Coding for Gender and Sexuality
Authors: Eckert Penelope 
Published: November 2014

AbstractGender has emerged as the primary social constraint in variation, but the complexities of correlations with a gender binary make it clear that gender must be examined as it interacts with other social constraints (e.g. class). Recent interest in sexuality as a social variable has emerged similarly to that found in studies of gender, with a problematic focus on a binary based on gender choice of sexual partner. This paper examines the problems with the binary treatment of gender and sexuality in variation studies, and considers the consequences and options for the coding and use of large corpora.
Baculovirus‐induced tree‐top disease: how extended is the role ofegtas a gene for the extended phenotype?
Authors: Ros Vera I. D. , van Houte Stineke , Hemerik Lia , van Oers Monique M. 
Published: November 2014

AbstractMany parasites alter host behaviour to enhance their chance of transmission. Recently, the ecdysteroidUDP‐glucosyl transferase (egt) gene from the baculovirusLymantria disparmultiple nucleopolyhedrovirus (LdMNPV) was identified to induce tree‐top disease inL. disparlarvae. Infected gypsy moth larvae died at elevated positions (hence the term tree‐top disease), which is thought to promote dissemination of the virus to lower foliage. It is, however, unknown whetheregthas a conserved role among baculoviruses in inducing tree‐top disease. Here, we studied tree‐top disease induced by the baculovirusAutographa californicamultiple nucleopolyhedrovirus (AcMNPV) in two different host insects,Trichoplusia niandSpodoptera exigua, and we investigated the role of the viralegtgene therein. AcMNPVinduced tree‐top disease in bothT. niandS. exigualarvae, although inS. exiguaa moulting‐dependent effect was seen. ThoseS. exigualarvae undergoing a larval moult during the infection process died at elevated positions, while larvae that did not moult after infection died at low positions. For bothT. niandS. exigua, infection with a mutant AcMNPVlackingegtdid not change the position where the larvae died. We conclude thategthas no highly conserved role in inducing tree‐top disease in lepidopteran larvae. The conclusion thategtis a ‘gene for an extended phenotype’ is therefore not generally applicable for all baculovirus–host interactions. We hypothesize that in some baculovirus–host systems (including LdMNPVinL. dispar), an effect ofegton tree‐top disease can be observed through indirect effects ofegton moulting‐related climbing behaviour.
Population genomics of natural and experimental populations of guppies (Poecilia reticulata)
Authors: Fraser Bonnie A. , Künstner Axel , Reznick David N. , Dreyer Christine , Weigel Detlef 
Published: November 2014

AbstractConvergent evolution represents one of the best lines of evidence for adaptation, but few cases of phenotypic convergence are understood at the genetic level. Guppies inhabiting the Northern Mountain Range of Trinidad provide a classic example of phenotypic convergent evolution, where adaptation to low or high predation environments has been found for a variety of traits. A major advantage of this system is the possibility of long‐term experimental studies in nature, including transplantation from high to low predation sites. We used genome scans of guppies from three natural high and low predation populations and from two experimentally established populations and their sources to examine whether phenotypic convergent evolution leaves footprints at the genome level. We used population‐genetic modelling approaches to reconstruct the demographic history and migration among sampled populations. Naturally colonized low predation populations had signatures of increased effective population size since colonization, while introduction populations had signatures of decreased effective population size. Only a small number of regions across the genome had signatures of selection in all natural populations. However, the two experimental populations shared many genomic regions under apparent selection, more than expected by chance. This overlap coupled with a population decrease since introduction provides evidence for convergent selection occurring in the two introduced populations. The lack of genetic convergence in the natural populations suggests that convergent evolution is lacking in these populations or that the effects of selection become difficult to detect after a long‐time period.
The iron‐binding CyaY and IscX proteins assist the ISC‐catalyzed Fe‐S biogenesis in Escherichia coli
Authors: Roche Béatrice , Huguenot Allison , Barras Frédéric , Py Béatrice 
Published: November 2014

SummaryIn eukaryotes, frataxin deficiency (FXN) causes severe phenotypes including loss of iron‐sulfur (Fe‐S) cluster protein activity, accumulation of mitochondrial iron and leads to the neurodegenerative disease Friedreich's ataxia. In contrast, in prokaryotes, deficiency in the FXN homolog, CyaY, was reported not to cause any significant phenotype, questioning both its importance and its actual contribution to Fe‐S cluster biogenesis. Because FXN is conserved between eukaryotes and prokaryotes, this surprising discrepancy prompted us to reinvestigate the role of CyaY in Escherichia coli. We report that CyaY (i) potentiates E. coli fitness, (ii) belongs to the ISC pathway catalyzing the maturation of Fe‐S cluster‐containing proteins and (iii) requires iron‐rich conditions for its contribution to be significant. A genetic interaction was discovered between cyaY and iscX, the last gene of the isc operon. Deletion of both genes showed an additive effect on Fe‐S cluster protein maturation, which led, among others, to increased resistance to aminoglycosides and increased sensitivity to lambda phage infection. Together, these in vivo results establish the importance of CyaY as a member of the ISC‐mediated Fe‐S cluster biogenesis pathway in E. coli, like it does in eukaryotes, and validate IscX as a new bona fide Fe‐S cluster biogenesis factor.
The metabolic regulator CodY links Listeria monocytogenes metabolism to virulence by directly activating the virulence regulatory gene prfA
Authors: Lobel Lior , Sigal Nadejda , Borovok Ilya , Belitsky Boris R. , Sonenshein Abraham L. , Herskovits Anat A. 
Published: November 2014

SummaryMetabolic adaptations are critical to the ability of bacterial pathogens to grow within host cells and are normally preceded by sensing of host‐specific metabolic signals, which in turn can influence the pathogen's virulence state. Previously, we reported that the intracellular bacterial pathogen Listeria monocytogenes responds to low availability of branched‐chain amino acids (BCAAs) within mammalian cells by up‐regulating both BCAA biosynthesis and virulence genes. The induction of virulence genes required the BCAA‐responsive transcription regulator, CodY, but the molecular mechanism governing this mode of regulation was unclear. In this report, we demonstrate that CodY directly binds the coding sequence of the L. monocytogenes master virulence activator gene, prfA, 15 nt downstream of its start codon, and that this binding results in up‐regulation of prfA transcription specifically under low concentrations of BCAA. Mutating this site abolished CodY binding and reduced prfA transcription in macrophages, and attenuated bacterial virulence in mice. Notably, the mutated binding site did not alter prfA transcription or PrfA activity under other conditions that are known to activate PrfA, such as during growth in the presence of glucose‐1‐phosphate. This study highlights the tight crosstalk between L. monocytogenes metabolism and virulence, while revealing novel features of CodY‐mediated regulation.
Enterococcus faecalis pCF10‐encoded surface proteins PrgA, PrgB (aggregation substance) and PrgC contribute to plasmid transfer, biofilm formation and virulence
Authors: Bhatty Minny , Cruz Melissa R. , Frank Kristi L. , Laverde Gomez Jenny A. , Andrade Fernando , Garsin Danielle A. , Dunny Gary M. , Kaplan Heidi B. , Christie Peter J. 
Published: November 2014

SummaryEnterococcus faecalis pCF10 transfers at high frequencies upon pheromone induction of the prgQ transfer operon. This operon codes for three cell wall‐anchored proteins – PrgA, PrgB (aggregation substance) and PrgC – and a type IV secretion system through which the plasmid is delivered to recipient cells. Here, we defined the contributions of the Prg surface proteins to plasmid transfer, biofilm formation and virulence using the Caenorhabditis elegans infection model. We report that a combination of PrgB and extracellular DNA (eDNA), but not PrgA or PrgC, was required for extensive cellular aggregation and pCF10 transfer at wild‐type frequencies. In addition to PrgB and eDNA, production of PrgA was necessary for extensive binding of enterococci to abiotic surfaces and development of robust biofilms. However, although PrgB is a known virulence factor in mammalian infection models, we determined that PrgA and PrgC, but not PrgB, were required for efficient killing in the worm infection model. We propose that the pheromone‐responsive, conjugative plasmids of E. faecalis have retained Prg‐like surface functions over evolutionary time for attachment, colonization and robust biofilm development. In natural settings, these biofilms are polymicrobial in composition and constitute optimal environments for signal exchange, mating pair formation and widespread lateral gene transfer.
Rice stripe tenuivirus p2 may recruit or manipulate nucleolar functions through an interaction with fibrillarin to promote virus systemic movement
Authors: Zheng Luping , Du Zhenguo , Lin Chen , Mao Qianzhuo , Wu Kangcheng , Wu Jianguo , Wei Taiyun , Wu Zujian , Xie Lianhui 
Published: November 2014

SummaryRice stripe virus (RSV) is the type species of the genus Tenuivirus and represents a major viral pathogen affecting rice production in East Asia. In this study, RSV p2 was fused to yellow fluorescent protein (p2‐YFP) and expressed in epidermal cells of Nicotiana benthamiana. p2‐YFP fluorescence was found to move to the nucleolus initially, but to leave the nucleolus for the cytoplasm forming numerous distinct bright spots there at later time points. A bimolecular fluorescence complementation (BiFC) assay showed that p2 interacted with fibrillarin and that the interaction occurred in the nucleus. Both the nucleolar localization and cytoplasmic distribution of p2‐YFP fluorescence were affected in fibrillarin‐silenced N. benthamiana. Fibrillarin depletion abolished the systemic movement of RSV, but not that of Tobacco mosaic virus (TMV) and Potato virus X (PVX). A Tobacco rattle virus (TRV)‐based virus‐induced gene silencing (VIGS) method was used to diminish RSV NS2 (encoding p2) or NS3 (encoding p3) during RSV infection. Silencing of NS3 alleviated symptom severity and reduced RSV accumulation, but had no obvious effects on virus movement and the timing of symptom development. However, silencing of NS2 abolished the systemic movement of RSV. The possibility that RSV p2 may recruit or manipulate nucleolar functions to promote virus systemic infection is discussed.
Homologous recombination and retention of a single form of most genes shape the highly chimeric mitochondrial genome of a cybrid plant
Authors: Sanchez‐Puerta M. Virginia , Zubko Mikhajlo K. , Palmer Jeffrey D. 
Published: November 2014

Summary

The structure and evolution of angiosperm mitochondrial genomes are driven by extremely high rates of recombination and rearrangement. An excellent experimental system for studying these events is offered by cybrid plants, in which parental mitochondria usually fuse and their genomes recombine. Little is known about the extent, nature and consequences of mitochondrial recombination in these plants.

We conducted the first study in which the organellar genomes of a cybrid – between Nicotiana tabacum and Hyoscyamus niger – were sequenced and compared to those of its parents.

This cybrid mitochondrial genome is highly recombinant, reflecting at least 30 crossovers and five gene conversions between its parental genomes. It is also surprisingly large (41% and 64% larger than the parental genomes), yet contains single alleles for 90% of mitochondrial genes.

Recombination produced a remarkably chimeric cybrid mitochondrial genome and occurred entirely via homologous mechanisms involving the double‐strand break repair and/or break‐induced replication pathways. Retention of a single form of most genes could be advantageous to minimize intracellular incompatibilities and/or reflect neutral forces that preferentially eliminate duplicated regions. We discuss the relevance of these findings to the surprisingly frequent occurrence of horizontal gene – and genome – transfer in angiosperm mitochondrial DNAs.
Novel ITGB6 mutation in autosomal recessive amelogenesis imperfecta
Authors: Seymen F , Lee K‐E , Koruyucu M , Gencay K , Bayram M , Tuna EB , Lee ZH , Kim J‐W 
Published: November 2014

ObjectiveHereditary defects in tooth enamel formation, amelogenesis imperfecta (AI), can be non‐syndromic or syndromic phenotype. Integrins are signaling proteins that mediate cell–cell and cell–extracellular matrix communication, and their involvement in tooth development is well known. The purposes of this study were to identify genetic cause of an AI family and molecular pathogenesis underlying defective enamel formation.Materials and MethodsWe recruited a Turkish family with isolated AI and performed mutational analyses to clarify the underlying molecular genetic etiology.ResultsAutozygosity mapping and exome sequencing identified a novel homozygous ITGB6 transversion mutation in exon 4 (c.517G>C, p.Gly173Arg). The glycine at this position in the middle of the βI‐domain is conserved among a wide range of vertebrate orthologs and human paralogs. Clinically, the enamel was generally thin and pitted with pigmentation. Thicker enamel was noted at the cervical area of the molars.ConclusionsIn this study, we identified a novel homozygous ITGB6 mutation causing isolated AI, and this advances the understanding of normal and pathologic enamel development.
Flying with diverse passengers: greater richness of parasitic nematodes in migratory birds
Authors: Koprivnikar Janet , Leung Tommy L. F. 
Published: November 2014

Environmental changes are simultaneously affecting parasitic diseases and animal migrations, making it important to understand the disease dynamics of migratory species, including their range of infections and investment into defences. There is an urgent need for such knowledge because migratory animals, especially birds, are important for pathogen transmission and also particularly sensitive to environmental changes. Here we compare the nematode species richness and relative immune investment (via relative spleen size) of almost 200 migratory and non‐migratory species within three diverse groups of birds (Anseriformes, Accipitriformes and Turdidae) with worldwide distributions and varied ecology. Our results provide the first large‐scale demonstration that migratory birds face greater challenge from macroparasites as they have significantly dissimilar nematode fauna and higher nematode species richness compared to non‐migratory species. Even though birds with relatively large spleens had more nematode species, there was no difference in relative spleen size between migratory and non‐migratory bird species. The physiological stress of migration can be exacerbated by the potential range of pathologies induced by their richer nematode communities, particularly in combination with environmental perturbations. Altered migration stemming from global changes can also have important consequences for nematode transmission.SynthesisMost studies on parasites of migratory birds versus non‐migratory birds focus upon blood parasites; here we compared the diversity of another important parasite group – nematodes (roundworms) in three orders of birds. We found for any given order, migratory species and species with proportionally larger spleens generally have a wider range of nematodes. It is unclear why migratory species harbour more nematode species. Global climate change is expected to influence both bird migration patterns and infectious diseases, which may increase host susceptibility to parasitism and also introduce diverse nematodes to new areas and potential hosts.
Synovial cyst of the temporomandibular joint: a case report with surgical management and long‐term follow‐up
Authors: Verma S. , Chambers I. 
Published: November 2014

AbstractSynovial cysts of the temporomandibular joint (TMJ) are rare, with only 10 cases reported in the literature. They may present with pain, swelling or trismus and can be a diagnostic dilemma for the clinician. With reference to the literature, this case report describes the presentation, investigation and management of a rare synovial cyst of the TMJ, presenting as a painful preauricular swelling in a 33‐year‐old woman. The long‐term follow‐up of this patient is discussed. We explore different modes of imaging of such disorders, as well as the histological features and the reported treatment modalities of temporomandibular synovial cysts.
Corrections of Lower Limb Deformities in Patients with Diastrophic Dysplasia
Authors: Al Kaissi Ali , Kenis Vladimir , Melchenko Eugeniy , Chehida Farid Ben , Ganger Rudolf , Klaushofer Klaus , Grill Franz 
Published: November 2014

ObjectiveAccurate understanding of the cause of the underlying pathology in children with diastrophic dysplasia would help in designing targeted management of their locomotion.MethodsDiastrophic dysplasia was diagnosed in twelve patients (nine girls and three boys; age range 1–14 years), all of whom presented with small stature and apparent short extremities. Club foot (mostly talipes equinovarus) was the most frequent and consistent abnormality. Concomitant abnormalities such as hip flexion contracture, flexion contractures of the knees with excessive valgus deformity and lateral patellar subluxation, were also encountered. Muscle ultrasound and muscle magnetic resonance imaging imaging showed no myopathic changes and muscle biopsies and the respiratory chain were normal. Serum choline kinase and plasma lactate concentrations were normal.ResultsSurgical correction of the foot and ankle in patients with diastrophic dysplasia is extremely difficult because of the markedly distorted anatomy. In all of these children, plantigrade foot was achieved along with the improved function of the locomotor system. Mutations of the diastrophic dysplasia sulfate transporter (also known as solute carrier family 26 member 2) were encountered.ConclusionArthrogryposis multiplex is the usual terminology used to describe the abnormality in infants with multiple contractures. Diligent orthopaedic care should be provided based on an accurate understanding of the associated syndromes in such children.
RNAi‐based GM plants: food for thought for risk assessors
Authors: Ramon Matthew , Devos Yann , Lanzoni Anna , Liu Yi , Gomes Ana , Gennaro Andrea , Waigmann Elisabeth 
Published: November 2014

SummaryRNA interference (RNAi) is an emerging technology that offers new opportunities for the generation of new traits in genetically modified (GM) plants. Potential risks associated with RNAi‐based GM plants and issues specific to their risk assessment were discussed during an international scientific workshop (June 2014) organized by the European Food Safety Authority (EFSA). Selected key outcomes of the workshop are reported here.