cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6851102
title: Using molecular dynamics simulations to identify the key factors responsible for chiral recognition by an amino acid-based molecular micelle

description: Molecular dynamics (MD) simulations were used to investigate the binding of six chiral compounds to the amino acid-based molecular micelle (MM) poly-(sodium undecyl-(L)-leucine-leucine) or poly(SULL). The MM investigated is used as a chiral selector in capillary electrophoresis. The project goal was to characterize the chiral recognition mechanism in these separations and to move toward predictive models to identify the best amino acid-based MM for a given separation. Poly(SULL) was found to contain six binding sites into which chiral compounds could insert. Four sites had similar sizes, shapes, and electrostatic properties. Enantiomers of alprenolol, propranolol, 1,1′-bi-2-naphthyl-2,2′-diyl hydrogen phosphate, 1,1′-bi-2-naphthol, chlorthalidone, or lorazepam were separately docked into each binding pocket and MD simulations with the resulting intermolecular complexes were performed. Solvent-accessible surface area calculations showed the compounds preferentially associated with binding sites where they penetrated into the MM core and shielded their non-polar atoms from solvent. Furthermore, with five of the six compounds the enantiomer with the most favorable free energy of MM association also experienced the most favorable intermolecular hydrogen bonding interactions with the MM. This result suggests that stereoselective intermolecular hydrogen bonds play an important role in chiral discrimination in separations using amino acid-based MMs.GRAPHICAL ABSTRACT
DOI: 10.6084/m9.figshare.6851102.v2
title: Using molecular dynamics simulations to identify the key factors responsible for chiral recognition by an amino acid-based molecular micelle

description: Molecular dynamics (MD) simulations were used to investigate the binding of six chiral compounds to the amino acid-based molecular micelle (MM) poly-(sodium undecyl-(L)-leucine-leucine) or poly(SULL). The MM investigated is used as a chiral selector in capillary electrophoresis. The project goal was to characterize the chiral recognition mechanism in these separations and to move toward predictive models to identify the best amino acid-based MM for a given separation. Poly(SULL) was found to contain six binding sites into which chiral compounds could insert. Four sites had similar sizes, shapes, and electrostatic properties. Enantiomers of alprenolol, propranolol, 1,1′-bi-2-naphthyl-2,2′-diyl hydrogen phosphate, 1,1′-bi-2-naphthol, chlorthalidone, or lorazepam were separately docked into each binding pocket and MD simulations with the resulting intermolecular complexes were performed. Solvent-accessible surface area calculations showed the compounds preferentially associated with binding sites where they penetrated into the MM core and shielded their non-polar atoms from solvent. Furthermore, with five of the six compounds the enantiomer with the most favorable free energy of MM association also experienced the most favorable intermolecular hydrogen bonding interactions with the MM. This result suggests that stereoselective intermolecular hydrogen bonds play an important role in chiral discrimination in separations using amino acid-based MMs.GRAPHICAL ABSTRACT
DOI: 10.6084/m9.figshare.6851078
title: Endocrinology Supplemental Figures and Tables Kanaya-Chen.pdf

description: Endocrinology Supplemental Figures and Tables Kanaya-Chen
DOI: 10.6084/m9.figshare.6851078.v1
title: Endocrinology Supplemental Figures and Tables Kanaya-Chen.pdf

description: Endocrinology Supplemental Figures and Tables Kanaya-Chen
DOI: 10.6084/m9.figshare.6850946
title: COMMSBIO-18-0374B Fig. 6a-d 17C

description: COMMSBIO-18-0374B Fig. 6a-d 17C
DOI: 10.6084/m9.figshare.6850946.v1
title: COMMSBIO-18-0374B Fig. 6 17C

description: COMMSBIO-18-0374B Fig. 6
DOI: 10.6084/m9.figshare.6850883
title: Effects of high-intensity interval training and moderate-intensity continuous training on body adiposity and cardiorespiratory fitness in adolescents with central obesity

description: Data related to the article
DOI: 10.21954/ou.rd.6850865
title: RSVP A Question of Style Corpus 2017

description: A corpus of 85 curated TEI/XML files of articles published in the Edinburgh Review and the Quarterly Review, 1814-1820, produced to support the work of the A Question of Style project.<br>
DOI: 10.6084/m9.figshare.6850883.v1
title: Effects of high-intensity interval training and moderate-intensity continuous training on body adiposity and cardiorespiratory fitness in adolescents with central obesity

description: Data related to the article
DOI: 10.6084/m9.figshare.6850862
title: Microarray analysis of miRNA expression profiles following whole body irradiation in a mouse model

description: <b>Context:</b> Accidental exposure to life-threatening radiation in a nuclear event is a major concern; there is an enormous need for identifying biomarkers for radiation biodosimetry to triage populations and treat critically exposed individuals. <b>Objective:</b> To identify dose-differentiating miRNA signatures from whole blood samples of whole body irradiated mice. <b>Methods:</b> Mice were whole body irradiated with X-rays (2 Gy–15 Gy); blood was collected at various time-points post-exposure; total RNA was isolated; miRNA microarrays were performed; miRNAs differentially expressed in irradiated vs. unirradiated controls were identified; feature extraction and classification models were applied to predict dose-differentiating miRNA signature. <b>Results:</b> We observed a time and dose responsive alteration in the expression levels of miRNAs. Maximum number of miRNAs were altered at 24-h and 48-h time-points post-irradiation. A 23-miRNA signature was identified using feature selection algorithms and classifier models. An inverse correlation in the expression level changes of miR-17 members, and their targets were observed in whole body irradiated mice and non-human primates. <b>Conclusion:</b> Whole blood-based miRNA expression signatures might be used for predicting radiation exposures in a mass casualty nuclear incident.
DOI: 10.6084/m9.figshare.6850862.v1
title: Microarray analysis of miRNA expression profiles following whole body irradiation in a mouse model

description: <b>Context:</b> Accidental exposure to life-threatening radiation in a nuclear event is a major concern; there is an enormous need for identifying biomarkers for radiation biodosimetry to triage populations and treat critically exposed individuals. <b>Objective:</b> To identify dose-differentiating miRNA signatures from whole blood samples of whole body irradiated mice. <b>Methods:</b> Mice were whole body irradiated with X-rays (2 Gy–15 Gy); blood was collected at various time-points post-exposure; total RNA was isolated; miRNA microarrays were performed; miRNAs differentially expressed in irradiated vs. unirradiated controls were identified; feature extraction and classification models were applied to predict dose-differentiating miRNA signature. <b>Results:</b> We observed a time and dose responsive alteration in the expression levels of miRNAs. Maximum number of miRNAs were altered at 24-h and 48-h time-points post-irradiation. A 23-miRNA signature was identified using feature selection algorithms and classifier models. An inverse correlation in the expression level changes of miR-17 members, and their targets were observed in whole body irradiated mice and non-human primates. <b>Conclusion:</b> Whole blood-based miRNA expression signatures might be used for predicting radiation exposures in a mass casualty nuclear incident.
DOI: 10.21954/ou.rd.6850865.v1
title: RSVP A Question of Style Corpus 2017

description: A corpus of 85 curated TEI/XML files of articles published in the Edinburgh Review and the Quarterly Review, 1814-1820, produced to support the work of the A Question of Style project.<br>
DOI: 10.21954/ou.rd.6850865.v3
title: RSVP A Question of Style Corpus 2017

description: A corpus of 85 curated TEI/XML files of articles published in the Edinburgh Review and the Quarterly Review, 1814-1820, produced to support the work of the A Question of Style project.<br>
DOI: 10.21954/ou.rd.6850865.v2
title: RSVP A Question of Style Corpus 2017

description: A corpus of 85 curated TEI/XML files of articles published in the Edinburgh Review and the Quarterly Review, 1814-1820, produced to support the work of the A Question of Style project.<br>
DOI: 10.6084/m9.figshare.6850811
title: Open Access Pathfinder: Cost modelling tools

description: A cost modelling tool developed in 2015 to help establish an internal business case to set up an APC fund for Open Access publishing. It allows users to model different cost projections based on variables such as FTE, number of articles, REF submission targets, and % Green vs Gold OA.<br>There are two Excel files available: one is blank and the other contains sample values to show a worked example. Both files include a Powerpoint Quickstart guide embedded within the home page. This steps you through the workflow and shows how to edit the various variables to customise your model.<br>The tool is a development of initial work undertaken Northumbria University in 2014 which led to the University Executive approving a £100K/annum internal fund for Gold Open Access costs.<br>We anticipate that this will be most useful to institutions which have received a lower/no block grant from RCUK, but there may be other use cases that we have not yet considered.
DOI: 10.6084/m9.figshare.6850793
title: Open Access Pathfinder: institutional case studies

description: Case studies developed in 2015 with the University of Hull, University of Lincoln, Durham University and Teesside University to show different institutional contexts of Open Access.<br>The case studies were developed through semi-structured, multi-disciplinary focus group discussions focusing on five key areas of Open Access implementation: <br>1) Costs2) Structure and workflows3) Institutional policy and strategy4) Advocacy, training and awareness5) Metadata and systems<br>The case studies give an overview of different approaches to dealing creatively with the problems posed by OA policies.
DOI: 10.6084/m9.figshare.6850811.v1
title: Cost modelling tools

description: A cost modelling tool developed in 2015 to help establish an internal business case to set up an APC fund for Open Access publishing. It allows users to model different cost projections based on variables such as FTE, number of articles, REF submission targets, and % Green vs Gold OA.<br>There are two Excel files available: one is blank and the other contains sample values to show a worked example. Both files include a Powerpoint Quickstart guide embedded within the home page. This steps you through the workflow and shows how to edit the various variables to customise your model.<br>The tool is a development of initial work undertaken Northumbria University in 2014 which led to the University Executive approving a £100K/annum internal fund for Gold Open Access costs.<br>We anticipate that this will be most useful to institutions which have received a lower/no block grant from RCUK, but there may be other use cases that we have not yet considered.
DOI: 10.6084/m9.figshare.6850793.v1
title: Institutional Open Access case studies

description: Case studies developed in 2015 with the University of Hull, University of Lincoln, Durham University and Teesside University to show different institutional contexts of Open Access.<br>The case studies were developed through semi-structured, multi-disciplinary focus group discussions focusing on five key areas of Open Access implementation: <br>1) Costs2) Structure and workflows3) Institutional policy and strategy4) Advocacy, training and awareness5) Metadata and systems<br>The case studies give an overview of different approaches to dealing creatively with the problems posed by OA policies.
DOI: 10.6084/m9.figshare.6850748
title: Dataset of "Riparian evapotranspiration is essential to simulate streamflow dynamics and water budgets in a Mediterranean catchment"

description: This dataset includes all the raw data used for the paper "Riparian evapotranspiration is essential to simulate streamflow dynamics and water budgets in a Mediterranean catchment", published in Hydrol. Earth Syst. Sci., in 2018. For more detailed description of the dataset, contact the authors.<br><br>
DOI: 10.6084/m9.figshare.6850748.v1
title: Dataset of "Riparian evapotranspiration is essential to simulate streamflow dynamics and water budgets in a Mediterranean catchment"

description: This dataset includes all the raw data used for the paper "Riparian evapotranspiration is essential to simulate streamflow dynamics and water budgets in a Mediterranean catchment", published in Hydrol. Earth Syst. Sci., in 2018. For more detailed description of the dataset, contact the authors.<br><br>
DOI: 10.6084/m9.figshare.6850739
title: Effect of <i>Porphyromonas gingivalis</i> infection in the placenta and umbilical cord in pregnant mice with low birth weight

description: <b>Objective:</b> Growing evidence indicates an association between periodontitis and delivery outcome; however, the mechanism is unclear. This study aimed to investigate the influence of <i>Porphyromonas gingivalis</i> (<i>Pg</i>) infection on delivery outcome in mice. <b>Materials and methods:</b> Bacteremia was induced in pregnant Slc:ICR mice (8 weeks old) by intravenous injection of <i>Pg.</i> Mice were randomly divided into a control group (CO), and those receiving <i>Pg</i> injection at gestational day 1 (GD1), gestational day 15 (GD15) or every day (ED). Delivery outcome, <i>Pg</i> infection, and gene expression in the placenta and umbilical cord were evaluated. <b>Results:</b> Birth weight was lower in the ED and GD15 groups than in the CO group. A remarkable increase in anti-<i>Pg</i> IgG antibody was observed in the ED and GD1 groups, although <i>Pg</i> was not detected in the placenta or umbilical cord. mRNA expression of <i>Tnfα</i> and <i>Il6</i> in the placenta, and <i>Hif1α</i> in the umbilical cord, was significantly increased in the ED group. Microarray analysis of the umbilical cord revealed increased expression of several genes including <i>Orm1</i>, <i>Mgl2</i>, <i>Rps6ka3</i> and <i>Trim15</i> in the ED group. <b>Conclusions:</b><i>Pg</i> infection during the third trimester caused low birth weight and inflammation in the placenta and umbilical cord.
DOI: 10.6084/m9.figshare.6850724
title: Morpho-molecular diversity and phylogeny of <i>Bysmatrum</i> (Dinophyceae) from the South China Sea and France

description: The dinoflagellate genus <i>Bysmatrum</i> encompasses five epibenthic or tide-pool species and has been characterized by separated anterior intercalary plates. In the present study, we obtained six strains of <i>Bysmatrum</i> from the South China Sea and French Atlantic coast by isolating single cells/cysts from plankton and sediment samples. All strains were examined with light microscopy and scanning electron microscopy. Based on morphological observations, three strains were identified as <i>Bysmatrum subsalsum</i>, characterized by the elongated and rectangular first and a hexagonal second anterior intercalary plate. They differ from each other in the number of sulcal lists and the configuration of the first anterior intercalary plate. One strain was identified as <i>Bysmatrum gregarium</i> and the other two as <i>Bysmatrum granulosum</i>. The cyst-theca relationship of <i>B. subsalsum</i> from the French Atlantic was established by incubation of the cyst, and the geochemical composition of the cyst wall was measured through micro-Fourier transform infrared spectroscopy. <i>Bysmatrum subsalsum</i> from Malaysia shows a bright red stigma in the sulcal area under light microscopy, which was confirmed with transmission electron microscopy: it was identified as a type B eyespot. Small subunit ribosomal DNA (SSU rDNA), partial large subunit ribosomal DNA (LSU rDNA) and internal transcribed spacer (ITS) sequences were obtained from all six strains. The maximum likelihood and Bayesian inference analysis based on concatenated SSU, ITS and LSU sequences revealed that <i>Bysmatrum</i> is monophyletic and nested within Peridiniales. Our strains of <i>B. subsalsum</i> form a new ribotype in the molecular phylogeny (designated as ribotype B). The genetic distance based on ITS sequences among <i>Bysmatrum</i> species ranged from 0.34 to 0.47 and those genetic distances at the intraspecific level of <i>B. subsalsum</i> could reach 0.41, supporting the possibility of hidden crypticity within <i>B. subsalsum</i>.
DOI: 10.6084/m9.figshare.6850739.v1
title: Effect of <i>Porphyromonas gingivalis</i> infection in the placenta and umbilical cord in pregnant mice with low birth weight

description: <b>Objective:</b> Growing evidence indicates an association between periodontitis and delivery outcome; however, the mechanism is unclear. This study aimed to investigate the influence of <i>Porphyromonas gingivalis</i> (<i>Pg</i>) infection on delivery outcome in mice. <b>Materials and methods:</b> Bacteremia was induced in pregnant Slc:ICR mice (8 weeks old) by intravenous injection of <i>Pg.</i> Mice were randomly divided into a control group (CO), and those receiving <i>Pg</i> injection at gestational day 1 (GD1), gestational day 15 (GD15) or every day (ED). Delivery outcome, <i>Pg</i> infection, and gene expression in the placenta and umbilical cord were evaluated. <b>Results:</b> Birth weight was lower in the ED and GD15 groups than in the CO group. A remarkable increase in anti-<i>Pg</i> IgG antibody was observed in the ED and GD1 groups, although <i>Pg</i> was not detected in the placenta or umbilical cord. mRNA expression of <i>Tnfα</i> and <i>Il6</i> in the placenta, and <i>Hif1α</i> in the umbilical cord, was significantly increased in the ED group. Microarray analysis of the umbilical cord revealed increased expression of several genes including <i>Orm1</i>, <i>Mgl2</i>, <i>Rps6ka3</i> and <i>Trim15</i> in the ED group. <b>Conclusions:</b><i>Pg</i> infection during the third trimester caused low birth weight and inflammation in the placenta and umbilical cord.
DOI: 10.6084/m9.figshare.6850724.v1
title: Morpho-molecular diversity and phylogeny of <i>Bysmatrum</i> (Dinophyceae) from the South China Sea and France

description: The dinoflagellate genus <i>Bysmatrum</i> encompasses five epibenthic or tide-pool species and has been characterized by separated anterior intercalary plates. In the present study, we obtained six strains of <i>Bysmatrum</i> from the South China Sea and French Atlantic coast by isolating single cells/cysts from plankton and sediment samples. All strains were examined with light microscopy and scanning electron microscopy. Based on morphological observations, three strains were identified as <i>Bysmatrum subsalsum</i>, characterized by the elongated and rectangular first and a hexagonal second anterior intercalary plate. They differ from each other in the number of sulcal lists and the configuration of the first anterior intercalary plate. One strain was identified as <i>Bysmatrum gregarium</i> and the other two as <i>Bysmatrum granulosum</i>. The cyst-theca relationship of <i>B. subsalsum</i> from the French Atlantic was established by incubation of the cyst, and the geochemical composition of the cyst wall was measured through micro-Fourier transform infrared spectroscopy. <i>Bysmatrum subsalsum</i> from Malaysia shows a bright red stigma in the sulcal area under light microscopy, which was confirmed with transmission electron microscopy: it was identified as a type B eyespot. Small subunit ribosomal DNA (SSU rDNA), partial large subunit ribosomal DNA (LSU rDNA) and internal transcribed spacer (ITS) sequences were obtained from all six strains. The maximum likelihood and Bayesian inference analysis based on concatenated SSU, ITS and LSU sequences revealed that <i>Bysmatrum</i> is monophyletic and nested within Peridiniales. Our strains of <i>B. subsalsum</i> form a new ribotype in the molecular phylogeny (designated as ribotype B). The genetic distance based on ITS sequences among <i>Bysmatrum</i> species ranged from 0.34 to 0.47 and those genetic distances at the intraspecific level of <i>B. subsalsum</i> could reach 0.41, supporting the possibility of hidden crypticity within <i>B. subsalsum</i>.
DOI: 10.6084/m9.figshare.6850691
title: Mis-splicing and breast cancer: systematic analysis of splicing variants of BRCA2 exons 2-9 by minigene assays

description: Paper minigene BRCA2 exons 2-9"Mis-splicing in breast cancer: identification of pathogenic BRCA2 variants by systematic minigene assays"<b>Abstract </b><br>Splicing disruption is a common mechanism of gene inactivation associated with germline variants of susceptibility genes. To study the role of BRCA2 mis-splicing in hereditary breast/ovarian cancer (HBOC), we performed a comprehensive analysis of variants from BRCA2 exons 2 to 9, as well as the initial characterization of the regulatory mechanisms of such exons. A pSAD-based minigene with exons 2-9 was constructed and validated in MCF-7 cells, producing the expected transcript (1,016-nt/V1-BRCA2_exons_2-9-V2). DNA variants from mutational databases were analyzed by NNSplice and Human Splicing Finder softwares. To refine ESE-variant prediction, we mapped the regulatory regions through a functional strategy whereby 26 exonic microdeletions were introduced into the minigene and tested in MCF-7 cells. Thus, we identified nine spliceogenic ESE-rich intervals where ESE-variants may be located. Combining bioinformatics and microdeletion assays, 83 variants were selected and genetically engineered in the minigene. Fifty-three changes impaired splicing: 28 variants disrupted the canonical sites, four created new ones, 10 abrogated enhancers, eight created silencers and three caused a double-effect. Notably, nine spliceogenic-ESE variants were located within ESE-containing intervals. Capillary electrophoresis and sequencing revealed more than 23 aberrant transcripts, where exon skipping was the most common event. Interestingly, variant c.67G&gt;A triggered the usage of a non-canonical GC-donor 4-nt upstream. Thirty-six variants that induced severe anomalies (&gt;60% aberrant transcripts) were analyzed according to the ACMG guidelines. Thus, 28 variants were classified as pathogenic, five as likely pathogenic and three as variants of uncertain significance. Interestingly, 13 VUS were reclassified as pathogenic or likely pathogenic variants.<br>In conclusion, a large fraction of BRCA2 variants (~64%) provoked splicing anomalies lending further support to the high prevalence of this disease-mechanism. The low accuracy of ESE-prediction algorithms may be circumvented by functional ESE-mapping that represents an optimal strategy to identify spliceogenic ESE-variants. Finally, systematic functional assays by minigenes depict a valuable tool for the initial characterization of splicing anomalies and the clinical interpretation of variants.<br><br>