cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5203948
title: Reworking of intra-oceanic rocks in a deep sea basin: example from the Bou-Maiza complex (Edough massif, eastern Algeria)

description: Metagabbros and amphibolites exposed in the Bou-Maïza area of the Edough massif (northeast Algeria) are described in detail. Field and petro-structural observations point to the syn-sedimentary emplacement of gabbros as clasts, blocks and lenses of polymictic gabbroic breccias. Associated amphibolites display fine-scale parallel sedimentary bedding and represent mafic epiclastites, litharenites and mafic greywackes. The mafic beds and lenses are intercalated with aluminous pelitic schists of continental origin, quartzite and marble. It is concluded that all mafic rocks from this locality derive from the erosion of an oceanic plutono-volcanic complex of MORB affinity that was reworked in a block matrix mélange and emplaced as turbidites and debris flows during the Mesozoic. We propose a convergent plate margin setting for these formations connected with the subducted Calabrian branch of the Tethyan slab.
DOI: 10.6084/m9.figshare.5203951.v1
title: Plasma protein, haematologic and blood chemistry changes in African grey parrots (<i>Psittacus erithacus</i>) experimentally infected with bornavirus

description: Bornaviruses are considered to be the causative agent of proventricular dilatation disease (PDD) in psittacine birds. In order to detect haematological and blood chemistry changes during the development of PDD and a possible correlation with clinical signs and the virological status, six African grey parrots (<i>Psittacus erithacus</i>) were experimentally infected with parrot bornavirus 4 (PaBV-4) by subcutaneous route. All six parrots developed clinical signs of varying extent and successful infection was confirmed in all the birds by seroconversion or detection of RNA of the PaBV-4 infection strain. Based on population-based and intra-individual reference ranges established during 12 months prior to experimental infection, only minor haematological changes were detected in individual birds after infection. Changes in blood chemistry were restricted to aspartate aminotransferase, creatine kinase, total protein, glucose and uric acid. Plasma protein electrophoresis revealed marked changes starting 10 weeks post infection characterized by an increase in the <i>γ</i>-globulin fraction and a gradual decrease to normal values during weeks 22–34. Indications of an acute-phase reaction at the initial stages of infection were not detected. While three birds suffered from clinical signs of PDD, which included weight loss and neurological disorders and died before development of haematological and plasma protein changes, recovery of clinical disease was paralleled in the remaining birds by an increase in <i>γ</i>-globulins and bornavirus-specific antibody titres.
DOI: 10.6084/m9.figshare.5203948.v1
title: Reworking of intra-oceanic rocks in a deep sea basin: example from the Bou-Maiza complex (Edough massif, eastern Algeria)

description: Metagabbros and amphibolites exposed in the Bou-Maïza area of the Edough massif (northeast Algeria) are described in detail. Field and petro-structural observations point to the syn-sedimentary emplacement of gabbros as clasts, blocks and lenses of polymictic gabbroic breccias. Associated amphibolites display fine-scale parallel sedimentary bedding and represent mafic epiclastites, litharenites and mafic greywackes. The mafic beds and lenses are intercalated with aluminous pelitic schists of continental origin, quartzite and marble. It is concluded that all mafic rocks from this locality derive from the erosion of an oceanic plutono-volcanic complex of MORB affinity that was reworked in a block matrix mélange and emplaced as turbidites and debris flows during the Mesozoic. We propose a convergent plate margin setting for these formations connected with the subducted Calabrian branch of the Tethyan slab.
DOI: 10.6084/m9.figshare.5203897
title: ChrY: SNPs and Genotypes in Sus scrofa (Pig)

description: * Porcine Y-chromosome variation is consistent with the occurrence of paternal gene flow from non-Asian to Asian populations. <br><br>SNPs_chrom_Y.xls is a file where the genotyped regions for the seven loci of Chromosome-Y in the article above (*) are detailed.<br><br>SNP_chromY_individuals.pdf is a pdf file where the genotype for each individual in the article above (*) is detailed.<br><br><br><br><br>
DOI: 10.6084/m9.figshare.5203897.v2
title: ChrY: SNPs and Genotypes in Sus scrofa (Pig)

description: * Porcine Y-chromosome variation is consistent with the occurrence of paternal gene flow from non-Asian to Asian populations. <br><br>SNPs_chrom_Y.xls is a file where the genotyped regions for the seven loci of Chromosome-Y in the article above (*) are detailed.<br><br>SNP_chromY_individuals.pdf is a pdf file where the genotype for each individual in the article above (*) is detailed.<br><br><br><br><br>
DOI: 10.6084/m9.figshare.5203897.v1
title: chromY: SNPs and genotypes in Pig

description: SNPs_chrom_Y.xls is a file where the genotyped regions for the seven loci of Chromosome-Y are detailed.<br><br>SNP_chromY_individuals.pdf is a odf file where the genotype for each individual is detailed.<br><br><br><br><br>
DOI: 10.6084/m9.figshare.5203798
title: Supplementary Material for: Cerebral and Renal Oxygen Saturation Are Not Compromised in the Presence of Retrograde Blood Flow in either the Ascending or Descending Aorta in Term or Near-Term Infants with Left-Sided Obstructive Lesions

description: <b><i>Background:</i></b> In infants with left-sided obstructive lesions (LSOL), the presence of retrograde blood flow in either the ascending or descending aorta may lead to diminished cerebral and renal blood flow, respectively. <b><i>Objectives:</i></b> Our aim was to compare cerebral and renal tissue oxygen saturation (rSO<sub>2</sub>) between infants with LSOL with antegrade and retrograde blood flow in the ascending aorta and with and without diastolic backflow in the descending aorta. <b><i>Methods:</i></b> Based on 2 echocardiograms, the study group was categorized according to the direction of blood flow in the ascending and descending aorta. We measured cerebral and renal rSO<sub>2</sub> using near-infrared spectroscopy and calculated fractional tissue oxygen extraction (FTOE). <b><i>Results:</i></b> Nineteen infants with LSOL, admitted to the NICU between 0 and 28 days after birth, were included. Infants with antegrade blood flow (<i>n </i>= 12) and infants with retrograde blood flow in the ascending aorta (<i>n</i> = 7) had similar cerebral rSO<sub>2</sub> and FTOE during both echocardiograms. Only during the first echocardiogram, infants with retrograde blood flow in the ascending aorta had lower renal FTOE (0.14 vs. 0.32,<i> p</i> = 0.04) and tended to have higher renal rSO<sub>2</sub> (80 vs. 65%,<i> p</i> = 0.09). The presence of diastolic backflow in the descending aorta was not associated with cerebral or renal rSO<sub>2</sub> and FTOE during the first (<i>n</i> = 8) as well as the second echocardiogram (<i>n</i> = 10). <b><i>Conclusions:</i></b> Retrograde blood flow in the ascending aorta was not associated with cerebral oxygenation, while diastolic backflow in the descending aorta was not associated with renal oxygenation in infants with LSOL.
DOI: 10.6084/m9.figshare.5203771
title: Supplementary Material for: Outcome of Preterm Neonates with a Birth Weight &lt;1,500 g with Severe Hypoxemic Respiratory Failure Rescued by Inhaled Nitric Oxide Therapy and High-Frequency Oscillatory Ventilation

description: <b><i>Background:</i></b> Despite being an experimental therapy in preterm neonates, inhaled nitric oxide (iNO) is used as a rescue therapy when high-frequency oscillatory ventilation (HFOV) and other conventional therapies fail. <b><i>Objective:</i></b> We aimed to determine the outcomes of very-low-birth-weight (VLBW) neonates with hypoxemic respiratory failure (HRF) who had received iNO after maximal conventional therapies. <b><i>Methods:</i></b> We retrospectively reviewed preterm neonates (&lt;33 weeks of gestation with a birth weight &lt;1,500 g) who had all received HFOV and then iNO from March 1, 2009 to April 1, 2014 at the Royal Alexandra Hospital. We collected demographic and clinical parameters, doses, duration and response to iNO, survival to neonatal intensive care unit (NICU) discharge, major complications, and neurodevelopmental outcome at 18-24 months of corrected age. <b><i>Results:</i></b> During the study period, 1,168 eligible preterm neonates were admitted; 155 (13%) had HRF treated with HFOV, of whom 47 (30%) received iNO. The baseline characteristics between the 24 survivors and 23 nonsurvivors were not different. Survivors had a greater decrease in oxygenation index than nonsurvivors (61 vs. 33%) after 6 h of iNO (<i>p</i> = 0.003). The causes of death were refractory hypoxemia (8), multi-organ failure (7), treatment withdrawal (6), and others (2). During the NICU stay, 23 survivors (96%) developed complications. At 18-24 months, 7 (29%) had significant disabilities. <b><i>Conclusions:</i></b> Of the VLBW neonates with severe HRF rescued by HFOV and iNO, many survived without neurodevelopmental disability at early childhood, despite multiple short-term complications. Further research is necessary to understand the clinical course and risk factors of adverse outcomes and to improve the management care of these critically ill neonates.
DOI: 10.6084/m9.figshare.5203741
title: Supplementary Material for: The Impact of Low-Grade Germinal Matrix-Intraventricular Hemorrhage on Neurodevelopmental Outcome of Very Preterm Infants

description: <b><i>Background:</i></b> Very preterm infants often show germinal matrix-intraventricular hemorrhage (GMH-IVH) on cranial ultrasound (cUS). <b><i>Aim:</i></b> To determine the impact of low-grade GMH-IVH on early neurodevelopmental outcome in very preterm infants. <b><i>Methods:</i></b> A retrospective case-control study in very preterm infants with and without low-grade GMH-IVH on cUS. Additional magnetic resonance imaging (MRI) was available in all infants with a gestational age (GA) &lt;28 weeks and high-risk infants &gt;28 weeks. Infants were seen at 2 years' corrected age to assess neurodevelopment. <b><i>Results:</i></b> In total, 136 infants (GA 24-32 weeks) with low-grade GMH-IVH on cUS were matched with 255 controls. Outcome data was available for 342 (87%) infants. Adverse outcome (i.e., cerebral palsy [CP], neurodevelopmental delay) was present in 11 (9%) cases and 20 (9%) controls. No statistically significant differences in outcome were found between cases and controls. Additional MRI was performed in 165/391 infants (42%) and showed additional lesions in 73 (44%) infants that could explain subsequent development of CP in 2 out of 5 infants and epilepsy in 1 of 2 infants. <b><i>Conclusion:</i></b> Very preterm infants with low-grade GMH-IVH on cUS have a similar early neurodevelopmental outcome compared with controls. Additional MRI showed mostly subtle abnormalities that were missed with cUS, but these could not explain subsequent development of CP and developmental delay in all infants.
DOI: 10.6084/m9.figshare.5203723
title: Supplementary Material for: Prediction of Outcome in Neonates with Hypoxic-Ischemic Encephalopathy II: Role of Amplitude-Integrated Electroencephalography and Cerebral Oxygen Saturation Measured by Near-Infrared Spectroscopy

description: <b><i>Background:</i></b> Few data have been published on the combined use of amplitude-integrated electroencephalography (aEEG) and near-infrared spectroscopy (NIRS) for outcome prediction in neonates cooled for hypoxic-ischemic encephalopathy (HIE). <b><i>Objective:</i></b> Our aim<b> </b>was to evaluate the predictive values and the most powerful predictive combinations of single aEEG and NIRS parameters and the respective cut-off values with regard to short-term outcomes in HIE II. <b><i>Methods:</i></b> aEEG and NIRS were prospectively studied at the Medical University of Vienna in the first 102 h of life with regard to magnetic resonance imaging (MRI). Thirty-two neonates diagnosed with HIE II treated with hypothermia were investigated. The measurement period was divided into 6-h epochs. According to MRI, 2 outcome groups were defined and predictive values of aEEG parameters, regional cerebral oxygen saturation (rScO<sub>2</sub>), and the additional value of both methods combined were studied. Receiver operating curves (ROC) were obtained and area under the curve (AUC) values were calculated. ROC were then used to detect the optimal cut-off points, sensitivity, specificity, positive predictive values, and negative predictive values. <b><i>Results:</i></b> At all time epochs, combined parameter scores were more predictive than single parameter scores. The highest AUC were observed between 18 and 60 h of cooling for the aEEG summation score (0.72-0.84) and for (background pattern + seizures) × rScO<sub>2</sub> (0.79-0.85). At 42-60 h sensitivity was similar between those 2 scores (87.5-90.0%), but the addition of NIRS to aEEG led to an increase in specificity (from 52.4-59.1% to 72.7-90.5%). <b><i>Conclusions:</i></b> In HIE II, aEEG and NIRS are important predictors of short-term outcome. The combination of both methods improves prognostication. The highest predictive abilities were observed between 18 and 60 h of cooling.
DOI: 10.6084/m9.figshare.5203723.v1
title: Supplementary Material for: Prediction of Outcome in Neonates with Hypoxic-Ischemic Encephalopathy II: Role of Amplitude-Integrated Electroencephalography and Cerebral Oxygen Saturation Measured by Near-Infrared Spectroscopy

description: <b><i>Background:</i></b> Few data have been published on the combined use of amplitude-integrated electroencephalography (aEEG) and near-infrared spectroscopy (NIRS) for outcome prediction in neonates cooled for hypoxic-ischemic encephalopathy (HIE). <b><i>Objective:</i></b> Our aim<b> </b>was to evaluate the predictive values and the most powerful predictive combinations of single aEEG and NIRS parameters and the respective cut-off values with regard to short-term outcomes in HIE II. <b><i>Methods:</i></b> aEEG and NIRS were prospectively studied at the Medical University of Vienna in the first 102 h of life with regard to magnetic resonance imaging (MRI). Thirty-two neonates diagnosed with HIE II treated with hypothermia were investigated. The measurement period was divided into 6-h epochs. According to MRI, 2 outcome groups were defined and predictive values of aEEG parameters, regional cerebral oxygen saturation (rScO<sub>2</sub>), and the additional value of both methods combined were studied. Receiver operating curves (ROC) were obtained and area under the curve (AUC) values were calculated. ROC were then used to detect the optimal cut-off points, sensitivity, specificity, positive predictive values, and negative predictive values. <b><i>Results:</i></b> At all time epochs, combined parameter scores were more predictive than single parameter scores. The highest AUC were observed between 18 and 60 h of cooling for the aEEG summation score (0.72-0.84) and for (background pattern + seizures) × rScO<sub>2</sub> (0.79-0.85). At 42-60 h sensitivity was similar between those 2 scores (87.5-90.0%), but the addition of NIRS to aEEG led to an increase in specificity (from 52.4-59.1% to 72.7-90.5%). <b><i>Conclusions:</i></b> In HIE II, aEEG and NIRS are important predictors of short-term outcome. The combination of both methods improves prognostication. The highest predictive abilities were observed between 18 and 60 h of cooling.
DOI: 10.6084/m9.figshare.5203666
title: Activation of gene expression by histone deubiquitinase OTLD1

description: One of the main mechanisms of epigenetic control is post translational modification of histones, and one of the relatively less characterized, yet functionally important histone modifications is monoubiquitylation, which is reversed by histone deubiquitinases. In <i>Arabidopsis,</i> only two of such enzymes are known to date. One of them, OTLD1, deubiquitylates histone 2B and functions as a transcriptional repressor. But, could the same deubiquitinase act both as a repressor and an activator? Here, we addressed this question. Using gain-of-function and loss-of-function <i>Arabidopsis</i> alleles, we showed that OTLD1 can promote expression of a target gene. This transcriptional activation activity of OTLD1 involves occupation of the target chromatin by this enzyme, deubiquitination of monoubiquitylated H2B within the occupied regions, and formation of the euchromatic histone acetylation and methylation marks. Thus, OTLD1 can play a dual role in transcriptional repression and activation of its target genes. In these reactions, H2B ubiquitylation acts as both a repressive and an active mark whereas OTLD1 association with and deubiquitylation of the target chromatin may represent the key juncture between two opposing effects of this enzyme on gene expression.
DOI: 10.6084/m9.figshare.5203666.v1
title: Activation of gene expression by histone deubiquitinase OTLD1

description: One of the main mechanisms of epigenetic control is post translational modification of histones, and one of the relatively less characterized, yet functionally important histone modifications is monoubiquitylation, which is reversed by histone deubiquitinases. In <i>Arabidopsis,</i> only two of such enzymes are known to date. One of them, OTLD1, deubiquitylates histone 2B and functions as a transcriptional repressor. But, could the same deubiquitinase act both as a repressor and an activator? Here, we addressed this question. Using gain-of-function and loss-of-function <i>Arabidopsis</i> alleles, we showed that OTLD1 can promote expression of a target gene. This transcriptional activation activity of OTLD1 involves occupation of the target chromatin by this enzyme, deubiquitination of monoubiquitylated H2B within the occupied regions, and formation of the euchromatic histone acetylation and methylation marks. Thus, OTLD1 can play a dual role in transcriptional repression and activation of its target genes. In these reactions, H2B ubiquitylation acts as both a repressive and an active mark whereas OTLD1 association with and deubiquitylation of the target chromatin may represent the key juncture between two opposing effects of this enzyme on gene expression.
DOI: 10.6084/m9.figshare.5203633
title: Publication_dataset.dta

description: Dataset incorporating all data employed for the publication "Depression Screening with Patient-Targeted Feedback in Cardiology: The Cost-Effectiveness of DEPSCREEN-INFO" published in PLoS One.
DOI: 10.6084/m9.figshare.5203621
title: Cdx2 ChIP-seq and Microarray Data

description: This data set contains raw sequencing data for Cdx2 ChIP-seq in mouse TS cells as well as raw microarray data for Cdx2 overexpression in mouse ES cells.<br>The ChIP-seq data is generated by Illumina Genome Analyzer.<br><br>The microarray data is generated by Illumina MouseRef-8_v1_1 Array.
DOI: 10.6084/m9.figshare.5203633.v1
title: Publication_dataset.dta

description: Dataset incorporating all data employed for the publication "Depression Screening with Patient-Targeted Feedback in Cardiology: The Cost-Effectiveness of DEPSCREEN-INFO" published in PLoS One.
DOI: 10.6084/m9.figshare.5203618
title: Candida auris gene annotations

description: A Hybrid assembly of Illumina and nanopore reads was performed for C. auris using SPAdes version 3.9.0, with default k-mer lengths and 1D scaffolding. Annotation was achieved using Genemark, BLASTx against Swissprot and KEGG, and HMMER hmmscan against PFAM and TIGRFAM. We also ran tRNAscan and Rnammer to identify non-protein coding genes. Gene predictions were checked for a variety of issues including overlapping non-coding genes, overlaps coding genes, and containing in-frame stops. Genes were names according to BLAST and hmmer evidence in the following order of precedence: (1) Swissprot, (2) TIGRfam, and (3) KEGG, where BLAST hits must meet the 70% identity and 70% overlap criteria to be considered a good hit and for the name to be applied. Otherwise, genes are named hypothetical protein.<br>
DOI: 10.21954/ou.rd.5203606
title: Death and Dying Seminar: Addressing inequalities in end of life care in North East Essex (June 2017)

description: Seminar presentation by Dr Karen Chumbley (Clinical Director of St Helena Hospice, Colchester) about how the hospice has used data about inequalities and access to improve palliative and end of life care provision. This presentation was given on 20th June 2017 as part of the OU Death and Dying Seminar Series.
DOI: 10.6084/m9.figshare.5203621.v2
title: Cdx2 ChIP-seq and Microarray Data

description: This data set contains raw sequencing data for Cdx2 ChIP-seq in mouse TS cells as well as raw microarray data for Cdx2 overexpression in mouse ES cells.<br>The ChIP-seq data is generated by Illumina Genome Analyzer.<br><br>The microarray data is generated by Illumina MouseRef-8_v1_1 Array.
DOI: 10.6084/m9.figshare.5203483
title: Supplementary Material for: WNT/β-Catenin Pathway and Epigenetic Mechanisms Regulate the Pitt-Hopkins Syndrome and Schizophrenia Risk Gene TCF4

description: Genetic variation within the transcription factor <i>TCF4</i> locus can cause the intellectual disability and developmental disorder Pitt-Hopkins syndrome (PTHS), whereas single-nucleotide polymorphisms within noncoding regions are associated with schizophrenia. These genetic findings position TCF4 as a link between transcription and cognition; however, the neurobiology of TCF4 remains poorly understood. Here, we quantitated multiple distinct <i>TCF4</i> transcript levels in human induced pluripotent stem cell-derived neural progenitors and differentiated neurons, and PTHS patient fibroblasts. We identify two classes of pharmacological treatments that regulate <i>TCF4</i> expression: WNT pathway activation and inhibition of class I histone deacetylases. In PTHS fibroblasts, both of these perturbations upregulate a subset of <i>TCF4</i> transcripts. Finally, using chromatin immunoprecipitation sequencing in conjunction with genome-wide transcriptome analysis, we identified TCF4 target genes that may mediate the effect of TCF4 loss on neuroplasticity. Our studies identify new pharmacological assays, tools, and targets for the development of therapeutics for cognitive disorders.
DOI: 10.6084/m9.figshare.5203621.v1
title: Cdx2 ChIP-seq and Microarray Data

description: This data set contains raw sequencing data for Cdx2 ChIP-seq in mouse TS cells as well as raw microarray data for Cdx2 overexpression in mouse ES cells.<br>The ChIP-seq data is generated by Illumina Genome Analyzer.<br><br>The microarray data is generated by Illumina MouseRef-8_v1_1 Array.
DOI: 10.6084/m9.figshare.5203534.v1
title: Emotouch

description: Dataset, database and code concerning the manuscript: "Valence-space associations in touchscreen interactions: Valence match between emotional pictures and touch location leads to pictures' positive evaluation" (submission)