bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combinatorial action of transcription factors in open chromatin contributes to early cellular heterogeneity and organizer mesendoderm specification
Authors: Bright Ann Rose , van Genesen Siebe , Li Qingqing , van Heeringen Simon J. , Grasso Alexia , Veenstra Gert Jan C. 
Published: February 2020

ABSTRACTDuring gastrulation, mesoderm is induced in pluripotent cells, concomitant with dorsal-ventral patterning and establishing of the dorsal axis. How transcription factors operate within the constraints of chromatin accessibility to mediate these processes is not well-understood. We applied chromatin accessibility and single cell transcriptome analyses to explore the emergence of heterogeneity and underlying gene-regulatory mechanisms during early gastrulation inXenopus. ATAC-sequencing of pluripotent animal cap cells revealed a state of open chromatin of transcriptionally inactive lineage-restricted genes, whereas chromatin accessibility in dorsal marginal zone cells more closely reflected the transcriptional activity of genes. We characterized single cell trajectories in animal cap and dorsal marginal zone in early gastrula embryos, and inferred the activity of transcription factors in single cell clusters by integrating chromatin accessibility and single cell RNA-sequencing. We tested the activity of organizer-expressed transcription factors in mesoderm-competent animal cap cells and found combinatorial effects of these factors on organizer gene expression. In particular the combination of Foxb1 and Eomes induced a gene expression profile that mimicked those observed in head and trunk organizer single cell clusters. In addition, genes induced by Eomes, Otx2 or the Irx3-Otx2 combination, were enriched for promoters with maternally regulated H3K4me3 modifications, whereas promoters selectively induced by Lhx8 were marked more frequently by zygotically controlled H3K4me3. Our results show that combinatorial activity of zygotically expressed transcription factors acts on maternally-regulated accessible chromatin to induce organizer gene expression.
Autotaxin impedes anti-tumor immunity by suppressing chemotaxis and tumor infiltration of CD8+T cells
Authors: Matas-Rico Elisa , Frijlink Elselien , van der Haar Àvila Irene , Menegakis Apostolos , van Zon Maaike , Morris Andrew J. , Koster Jan , Salgado-Polo Fernando , de Kivit Sander , Lança Telma , Mazzocca Antonio , Johnson Zoë , Haanen John , Schumacher Ton N. , Perrakis Anastassis , Verbrugge Inge , van den Berg Joost , Borst Jannie , Moolenaar Wouter H. 
Published: February 2020

SummaryAutotaxin (ATX) is secreted by diverse cell types to produce lysophosphatidic acid (LPA) that regulates multiple biological functions via G protein-coupled receptors LPAR1-6. ATX/LPA promotes tumor cell migration and metastasis mainly via LPAR1; however, its actions in the tumor immune microenvironment remain unclear. Here, we show that ATX secreted by melanoma cells is chemorepulsive for tumor-infiltrating lymphocytes and circulating CD8+T cellsex vivo, with ATX functioning as an LPA-producing chaperone. Mechanistically, T-cell repulsion predominantly involves Gα12/13-coupled LPAR6. Upon anti-cancer vaccination of tumor-bearing mice, ATX does not affect the induction of systemic T-cell responses but suppresses tumor infiltration of cytotoxic CD8+T cells and thereby impairs tumor regression. Moreover, single-cell data from patient samples are consistent with intra-tumor ATX acting as a T-cell repellent. These studies highlight an unexpected role for the pro-metastatic ATX-LPAR axis in suppressing CD8+T-cell infiltration to impede anti-tumor immunity, suggesting new therapeutic opportunities.
Nucleosomal embedding reshapes the dynamics of abasic sites
Authors: Bignon Emmanuelle , Claerbout Victor , Jiang Tao , Morell Christophe , Gillet Natacha , Dumont Elise 
Published: February 2020

ABSTRACTApurinic/apyrimidinic (AP) sites are the most common DNA lesions, which benefit from a most efficient repair by the base excision pathway. The impact of losing a nucleobase on the conformation and dynamics of B-DNA is well characterized. Yet AP sites seem to present an entirely different chemistry in nucleosomal DNA, with lifetimes reduced up to 100-fold, and the much increased formation of covalent DNA-protein cross-links, refractory to repair. We report microsecond range, all-atom molecular dynamics simulations that capture the conformational dynamics of AP sites and their tetrahydrofuran analogs at two symmetrical positions within a nucleosome core particle, starting from a recent crystal structure. Different behaviours between the deoxyribo-based and tetrahydrofuran-type abasic sites are evidenced. The two solvent-exposed lesion sites present contrasted extrahelicities, revealing the crucial role of the position of a defect around the histone core. Our all-atom simulations also identify and quantify the occurrence of several spontaneous, non-covalent interactions between AP and positively-charged residues from the histones H2A and H2B tails that prefigure DNA-protein cross-links. This study paves the way towards an in silico mapping of DNA-protein cross-links.
Actin filament oxidation by MICAL1 suppresses protections from cofilin-induced disassembly
Authors: Wioland Hugo , Frémont Stéphane , Guichard Bérengère , Echard Arnaud , Jégou Antoine , Romet-Lemonne Guillaume 
Published: February 2020

ABSTRACTProteins of the ADF/cofilin family play a central role in the disassembly of actin filaments, and their activity must be tightly regulated in cells. Recently, the oxidation of actin filaments by the enzyme MICAL1 was found to amplify the severing action of cofilin through unclear mechanisms. Two essential factors normally prevent filament disassembly: the inactivation of cofilin by phosphorylation, and the protection of filaments by tropomyosins, but whether actin oxidation might interfere with these safeguard mechanisms is unknown. Using single filament experimentsin vitro, we found that actin filament oxidation by MICAL1 increases, by several orders of magnitude, both cofilin binding and severing rates, explaining the dramatic synergy between oxidation and cofilin for filament disassembly. Remarkably, we found that actin oxidation bypasses the need for cofilin activation by dephosphorylation. Indeed, non-activated, phosphomimetic S3D-cofilin binds and severs oxidized actin filaments rapidly, in conditions where non-oxidized filaments are unaffected. Finally, tropomyosin Tpm1.8 loses its ability to protect filaments from cofilin severing activity when actin is oxidized by MICAL1. Together, our results show that MICAL1-induced oxidation of actin filaments suppresses their physiological protection from the action of cofilin. We propose that in cells, direct post-translational modification of actin filaments by oxidation is a way to trigger their severing, in spite of being decorated by tropomyosin, and without requiring the activation of cofilin.
Building a Reference Transcriptome for the Hexaploid Hard Fescue Turfgrass (Festuca brevipila) Using a Combination of PacBio Iso-Seq and Illumina Sequencing
Authors: Qiu Yinjie , Yang Ya , Hirsch Cory D. , Watkins Eric 
Published: February 2020

AbstractBackgroundHard fescue (Festuca brevipilaTracey, 2n=6x=42) is a cool season turfgrass with a fine leaf texture that performs well under low-input management. Breeding and genetics studies ofF. brevipilahave been limited due to the complexity of its hexaploid genome. To advance our knowledge ofF. brevipilagenomics, we used PacBio isoform sequencing to develop a reference transcriptome for this species.ResultsHere, we report theF. brevipilareference transcriptome generated from root, crown, leaf, and inflorescence tissues. We obtained 59,510 full-length transcripts, of which 38,556 were non-redundant full-length transcripts. The longest and shortest transcripts were 11,487 and 58 bp, respectively. Distribution of synonymous distances among paralogs withinF. brevipilasuggested highly similar subgenomes that are difficult to distinguish from sequencing errors. To evaluate the phylogenetic relationships amongF. brevipilaand close relatives, we sequenced three additional transcriptomes using closely related species on an Illumina platform. The results of our phylotranscriptomic analysis supported the close relationships amongF. brevipila(6x),Festuca ovina(4x),Festuca ovinasubsp.ovina(2x), andFestuca valesiaca(2x), with high levels of discordance among gene trees.ConclusionsOverall, theF. brevipilaPacBio Isoseq reference transcriptome provided the foundation for transcriptome studies and allowed breeders a resource for gene discovery in this important turfgrass species.
Gut Microbiome Profiling of a Rural and Urban South African Cohort Reveals Biomarkers of a Population in Lifestyle Transition
Authors: Oduaran OH. , Tamburini FB. , Sahibdeen V. , Brewster R. , Gómez-Olivé FX. , Kahn K. , Norris SA. , Tollman SM. , Twine R. , Wade AN. , Wagner RG. , Lombard Z. , Bhatt AS. , Hazelhurst S. 
Published: February 2020

AbstractBackgroundComparisons of traditional hunter-gatherers and pre-agricultural communities in Africa with urban and suburban Western North American and European cohorts have clearly shown that diet, lifestyle and environment are associated with gut microbiome composition. Yet, little is known about the gut microbiome composition of most African adults. South Africa comprises a richly diverse ethnolinguistic population that is experiencing an ongoing epidemiological transition and concurrent spike in the prevalence of obesity, largely attributed to a shift towards more Westernized diets and increasingly inactive lifestyle practices. To better characterize the microbiome of African adults living in more mainstream lifestyle settings and to investigate associations between the microbiome and obesity, we conducted a pilot study in two South African cohorts that are representative of urban and rural populations. The study was designed collaboratively with community leaders. As the rate of overweight and obesity is particularly high in women, we collected single time-point stool samples from 170 HIV-negative women (51 at Soweto; 119 at Bushbuckridge), performed 16S rRNA gene sequencing on these samples and compared the data to concurrently collected anthropometric data.ResultsWe found the overall gut microbiome of our cohorts to be reflective of their ongoing epidemiological transition. Specifically, our results show a relatively higher than expected abundance of Western gut-associated taxa such as Barnesiella and the presence of Bifidobacteria and Bacteroides together with the more traditionally non-Western gut-associated Prevotella, Treponema and Succinivibrio. Interestingly, we observed a relatively higher abundance of the Melainabacteria, Vampirovibrio, a predatory bacterium, in the rural cohort. We also found Prevotella, despite its generally high prevalence relative to all taxa present in the cohort, to be associated with obesity.ConclusionsAltogether, this work identifies putative microbial features associated with host health in a historically understudied community. Furthermore, we note the crucial role of community engagement to the success of a study in an African setting, the importance of more population-specific studies to inform targeted interventions as well as present a basic foundation for future research in this regard.
Paired high-throughput, in-situ imaging and high-throughput sequencing illuminate acantharian abundance and vertical distribution
Authors: Mars Brisbin Margaret , Brunner Otis Davey , Grossmann Mary Matilda , Mitarai Satoshi 
Published: February 2020

AbstractAcantharians are important contributors to surface primary production and to carbon flux to the deep sea, but are often underestimated because their delicate structures are destroyed by plankton nets or dissolved by preservatives. As a result, relatively little is known about acantharian biology, especially regarding their life cycles. Here, we take a paired approach, bringing together high-throughput, in-situ imaging and high-throughput sequencing, to investigate acantharian abundance, vertical distribution, and life-history in the western North Pacific. Observed concentrations of acantharian cells correlated well with sequence abundances from acantharians with known, recognizable morphologies, but not to sequences from those without known morphology (basal environmental clades). These results suggest basal clades may lack characteristic star-shaped skeletons or are much smaller than known acantharians. The decreased size-range of acantharians imaged at depth supports current hypotheses regarding asymbiotic acantharian life cycles: cysts or vegetative cells release reproductive swarmer cells at depth and juvenile cells grow as they ascend towards the surface. Moreover, sequencing data present the possibility that photosymbiotic acantharians also reproduce at depth, like their asymbiotic, encysting relatives, which is counter to previous hypotheses. Finally, in-situ imaging captured a new acantharian behavior that may be a previously undescribed predation strategy.
Simultaneous auditory agnosia: Systematic description of a new type of auditory segregation deficit following a right hemisphere lesion
Authors: Holmes Emma , Utoomprurkporn Nattawan , Hoskote Chandrashekar , Warren Jason D. , Bamiou Doris-Eva , Griffiths Timothy D. 
Published: February 2020

AbstractWe investigated auditory processing in a young patient who experienced a single embolus causing an infarct in the right middle cerebral artery territory. This lead to damage to auditory cortex including planum temporale that spared medial Heschl’s gyrus, and included damage to the posterior insula and inferior parietal lobule. She first reported difficulty hearing all sounds, which fully recovered within days, but she subsequently reported chronic difficulties with segregating speech from noise and segregating elements of music. Clinical tests showed no evidence for abnormal cochlear function. Follow-up tests confirmed difficulties with auditory segregation in her left ear that spanned multiple domains, including speech-in-noise and music streaming. Testing with a stochastic figure-ground task—a way of estimating generic acoustic foreground and background segregation—demonstrated that this was also abnormal. This is the first demonstration of an acquired deficit in the segregation of complex acoustic patterns due to cortical damage, which we argue is a causal explanation for the symptomatic deficits in the segregation of speech and music. These symptoms are analogous to the visual symptom of simultaneous agnosia. Consistent with functional imaging studies on normal listeners, the work implicates non-primary auditory cortex. Further, the work demonstrates a (partial) lateralisation of the necessary anatomical substrate for segregation that has not been previously highlighted.HighlightsRare case of auditory agnosia in a young patient with a right-hemisphere infarctDamage affecting non-primary auditory cortex, but sparing primary auditory cortexGeneralised auditory segregation deficit, revealed by auditory figure-ground taskThis explains segregation deficits for speech-in-noise and music streamingThe deficit affects stimuli presented on the left
Diversity and Distribution of a Novel Genus of HyperthermophilicAquificaeViruses Encoding a Proof-reading Family-A DNA Polymerase
Authors: Palmer Marike , Hedlund Brian P. , Roux Simon , Tsourkas Philippos K. , Doss Ryan K. , Stamereilers Casey , Mehta Astha , Dodsworth Jeremy A. , Lodes Michael , Monsma Scott , del Rio Tijana Glavina , Schoenfeld Thomas W. , Eloe-Fadrosh Emiley A. , Mead David A. 
Published: February 2020

ABSTRACTDespite the high abundance ofAquificaein many geothermal systems, these bacteria are difficult to culture and no viruses infecting members of this phylum have been isolated. Here, we describe the complete, circular dsDNA Uncultivated Virus Genome (UViG) ofThermocrinisOctopus Spring virus (TOSV), derived from metagenomic data, along with eight related UViGs representing three additional species,ThermocrinisGreat Boiling Spring virus (TGBSV),AquificaeJoseph’s Coat Spring Virus (AJCSV), andAquificaeConch Spring Virus (ACSV). Four near-complete UViGs, ranged from 37,256 bp to 41,208 bp and encoded 48 to 53 open reading frames. Despite low overall similarity between viruses from different hot springs, the genomes shared a high degree of synteny, and encoded numerous genes for nucleotide metabolism, including a polyprotein PolA-type polymerase with likely accessory functions, a DNA Pol III beta subunit (sliding clamp), a thymidylate kinase, a DNA gyrase, a helicase, and a DNA methylase. Also present were conserved genes predicted to code for phage capsids, large and small terminases, portal protein, holin, and lytic transglycosylase, all consistent with a distant relatedness to cultivatedCaudovirales. TOSV and TGBSV had the highest coverage in their respective metagenomes and are predicted to infectThermocrinis ruberandThermocrinis jamiesonii, respectively, as multiple CRISPR spacers matching the viral genomes were identified withinThermocrinis ruberOC1/4TandThermocrinis jamiesoniiGBS1T. Based on the predicted, unusual bi-directional replication strategy, low sequence similarity to known viral genomes, and a unique position in gene-sharing networks, we propose a new putative genus, Pyrovirus, in the orderCaudovirales.
Autism in black, Asian and minority ethnic communities: a report on the first Autism Voice UK Symposium
Authors: Kandeh Mariama Seray , Kandeh Mariama Korrca , Martin Nicola , Krupa Joanna 
Published: February 2020

Purpose
Little is known about the way autism is interpreted and accepted among the black, Asian and minority ethnic (BAME) populations in the UK. This report summarises a Symposium on autism in the UK-BAME community in 2018, organised by Autism Voice UK, Participatory Autism Research Collective and the Critical Autism and Disabilities Studies Research Group at London South Bank University.

Design/methodology/approach
The stance a family or community takes about a condition such as autism is influenced by their cultural background. The aims of the Symposium were to highlight different perspectives about autism in BAME communities and to preserve the cultural dignity of the community in supporting autistic members. Beliefs about autism, its diagnosis and acceptance of and support for autistic people from a specific cultural perspective of BAME communities must be cautiously interpreted by autism professionals because beliefs vary among different cultural groups.

Findings
Thematic analysis of feedback from participants yielded the following foci. Firstly, cultural, ethnic and religious sensitivities were important to participants who felt that these were often ignored by non-BAME professionals. Secondly, the need for collaboration to improve autism awareness within the community and understanding by professionals of the intersectionality between autism and identity in BAME families was prioritised. Thirdly, issues around feelings of stigma were common, but delegates felt that these were not well understood beyond people identifying as BAME.

Originality/value
An action plan was created which highlighted raising public awareness through community engagement, improvement of access to information for parents and culturally aware autism education for professionals and BAME communities.
An analysis of technical information for mechatronics research
Authors: Osorio Nestor L. , Osorio Gabriel E. 
Published: February 2020

Purpose
Mechatronics is a very important area of research in industrial applications. The purpose of this study is to find some of the most important components of the literature on this subject.

Design/methodology/approach
The analysis is based on the use of the database Compendex; it was searched in the broadest way for documents related to mechatronics. In addition, subject guides from libraries of universities with mechatronics programs were studied to find resources available in those areas.

Findings
The literature of mechatronics is extensive and multidisciplinary. Based on the results from Compendex, the following data were found: most productive authors, list of leading journals and conference proceedings, publishers and grant organizations, authors’ affiliations and other minor details. Based on the analysis of subject guides, the following types of resources were found: research databases, reference books and ebook collections.

Research limitations/implications
Part of the analysis is based on a search performed in one technical database, Compendex; it was the database that generated the largest number of citations as compared to Inspec and the Web of Science. The results have a strong English language focus. It is possible that by using the results from multiple data bases, some additional sources could be obtained.

Practical implications
Mechatronics is a relatively new technological field comprising a number of scientific and engineering areas. The results obtained summarized a significant amount of bibliographic information.

Originality/value
The work is original; to the best of the authors’ knowledge, no other study has analyzed the literature on this subject.
Exploring role of gratitude in developing teacher leadership in Indian universities
Authors: Garg Naval 
Published: February 2020

PurposeThe benefits of teacher leadership have attracted the attention of policymakers, practitioners and researchers. It is increasingly advocated as one of the most crucial and indispensable components of the school, college and university administration. The present study tends to investigate the role of gratitude in developing teacher leadership through examining sufficiency and necessity of thankfulness for educational leadership.Design/methodology/approachThe study explores sufficiency and necessity of gratitude for seven dimensions of educational leadership with the help of correlation, regression and necessary condition analysis.FindingsThe paper concludes that gratitude is both sufficient and necessary condition for overall teacher leadership and its seven dimensions.Originality/valueThe paper is based on original data.
Review of the Delphi method in library and information science research
Authors: Lund Brady D. 
Published: February 2020

PurposeThis article presents an introduction to the Delphi method and review of Delphi studies published in the literature of library and information science (LIS).Design/methodology/approachA review of Delphi studies published between the years of 1971 and 2019 is performed, using studies retrieved from the Library and Information Science Source database. A total of 122 articles were retrieved and evaluated based on the population studied, means of identifying experts, number of participants for each study round, type of Delphi, and type of findings.FindingsGeneral librarians (any type), academic librarians, and information science researchers are the most common populations in LIS Delphi studies. On average (middle 50 percent of studies), 14–36 experts are used in the first round of LIS Delphi studies (mediann = 23). Employment in a specific role and publications in scholarly journals are the most common means of identifying experts. Variants of the e-Delphi (online survey/email) method are increasingly common, particularly in LIS Delphi studies that focus on general information science, rather than library, topics. Though LIS Delphi studies are relatively few in number, they have a consistent record of being published in some of the most prestigious LIS journals.Originality/valueThis paper provides an introduction to the Delphi method for LIS research and presents an overview of existing literature in LIS that utilizes the research method. No overview of this extent exists in the LIS literature, and, thus, this paper may serve as an important information source about the method for LIS researchers.