cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5697571
title: Brain Embeddings

description: Data-driven brain embeddings
DOI: 10.6084/m9.figshare.5697571.v2
title: Brain Embeddings

description: Data-driven brain embeddings
DOI: 10.6084/m9.figshare.5697571.v1
title: Brain Embeddings

description: Data-driven brain embeddings
DOI: 10.6084/m9.figshare.5697535
title: <i>SLC9B1</i> methylation predicts fetal intolerance of labor

description: Fetal intolerance of labor is a common indication for delivery by Caesarean section. Diagnosis is based on the presence of category III fetal heart rate tracing, which is an abnormal heart tracing associated with increased likelihood of fetal hypoxia and metabolic acidemia. This study analyzed data from 177 unique women who, during their prenatal visits (7-15 weeks and/or 24–32 weeks) to Atlanta area prenatal care clinics, consented to provide blood samples for DNA methylation (HumanMethylation450 BeadChip) and gene expression (Human HT-12 v4 Expression BeadChip) analyses. We focused on 57 women aged 18–36 (mean 25.4), who had DNA methylation data available from their second prenatal visit. DNA methylation patterns at CpG sites across the genome were interrogated for associations with fetal intolerance of labor. Four CpG sites (<i>P</i> value &lt;8.9 × 10<sup>−9</sup>, FDR &lt;0.05) in gene <i>SLC9B1</i>, a Na<sup>+</sup>/H<sup>+</sup> exchanger, were associated with fetal intolerance of labor. DNA methylation and gene expression were negatively associated when examined longitudinally during pregnancy using a linear mixed-effects model. Positive predictive values of methylation of these four sites ranged from 0.80 to 0.89, while negative predictive values ranged from 0.91 to 0.92. The four CpG sites were also associated with fetal intolerance of labor in an independent cohort (the Johns Hopkins Prospective PPD cohort). Therefore, fetal intolerance of labor could be accurately predicted from maternal blood samples obtained between 24–32 weeks gestation. Fetal intolerance of labor may be accurately predicted from maternal blood samples obtained between 24–32 weeks gestation by assessing DNA methylation patterns of <i>SLC9B1.</i> The identification of pregnant women at elevated risk for fetal intolerance of labor may allow for the development of targeted treatments or management plans.
DOI: 10.6084/m9.figshare.5697505.v2
title: Data sets for "Nouns slow down speech across structurally and culturally diverse languages"

description: This item contains data tables for the study "Nouns slow down speech across structurally and culturally diverse languages" published in the Proceedings of the National Academy of Sciences (PNAS) by Frank Seifart, Jan Strunk, Swintha Danielsen, Iren Hartmann, Brigitte Pakendorf, Søren Wichmann, Alena Witzlack-Makarevich, Nivja H. de Jong, and Balthasar Bickel.<br>
DOI: 10.6084/m9.figshare.5697505
title: Data sets and analysis scripts for "Nouns slow down speech across structurally and culturally diverse languages"

description: This item contains data tables and analysis scripts for the study "Nouns slow down speech across structurally and culturally diverse languages" published in the Proceedings of the National Academy of Sciences (PNAS) by Frank Seifart, Jan Strunk, Swintha Danielsen, Iren Hartmann, Brigitte Pakendorf, Søren Wichmann, Alena Witzlack-Makarevich, Nivja H. de Jong, and Balthasar Bickel.https://doi.org/10.1073/pnas.1800708115<br>
DOI: 10.6084/m9.figshare.5697469
title: Supplementary Material for: Effects of Early-Life Adversity on Hippocampal Structures and Associated HPA Axis Functions

description: Early-life adversity (ELA) is one of the major risk factors for serious mental and physical health risks later in life. ELA has been associated with dysfunctional neurodevelopment, especially in brain structures such as the hippocampus, and with dysfunction of the stress system, including the hypothalamic-pituitary-adrenal (HPA) axis. Children who have experienced ELA are also more likely to suffer from mental health disorders such as depression later in life. The exact interplay of aberrant neurodevelopment and HPA axis dysfunction as risks for psychopathology is not yet clear. We investigated volume differences in the bilateral hippocampus and in stress-sensitive hippocampal subfields, behavior problems, and diurnal cortisol activity in 24 children who had experienced documented ELA (including out-of-home placement) in a circumscribed duration of adversity only in their first 3 years of life in comparison to data on 25 control children raised by their biological parents. Hippocampal volumes and stress-sensitive hippocampal subfields (Cornu ammonis [CA]1, CA3, and the granule-cell layer of the dentate gyrus [GCL-DG]) were significantly smaller in children who had experienced ELA, taking psychiatric diagnoses and dimensional psychopathological symptoms into account. ELA moderated the relationship between left hippocampal volume and cortisol: in the control group, hippocampal volumes were not related to diurnal cortisol, while in ELA children, a positive linear relationship between left hippocampal volume and diurnal cortisol was present. Our findings show that ELA is associated with altered development of the hippocampus, and an altered relationship between hippocampal volume and HPA axis activity in youth in care, even after they have lived in stable and caring foster family environments for years. Altered hippocampal development after ELA could thus be associated with a risk phenotype for the development of psychiatric disorders later in life.
DOI: 10.6084/m9.figshare.5697454
title: Late Pleistocene and Holocene lithic variability in Southeastern Ethiopia: implications for the understanding of the Middle and Late Stone Age of the Horn of Africa - Supplementary Material

description: The Late Pleistocene is a key period to understand the shift from the Middle (MSA) to the Late Stone Age (LSA) in Africa. More generally, it is also a crucial time for elucidation of changes in the technological behaviours of human populations in Africa after the main Out of Africa event of modern humans ca. 60-50 thousand years ago. However, the archaeological record for this period is relatively poor, particularly for the Horn of Africa. Here we present a detailed analysis of the lithic assemblages from Goda Buticha (GB), a cave in southeastern Ethiopia, which has yielded a long stratigraphic sequence including Late Pleistocene and Holocene levels. This study (1) contributes to a better knowledge of the late MSA in the Horn of Africa; (2) documents a late Holocene LSA level (GB – Complex I); (3) highlights the presence of MSA characteristics associated with LSA features in the Holocene (GB – Layer IIc). This adds to the emerging record of great lithic technological variability during the Late Pleistocene and Holocene in this region. <br> <br> Le Pléistocène récent est une période clé pour comprendre le changement du Middle (MSA) vers le Late Stone Age (LSA) en Afrique. Plus généralement, c’est une période-clé pour comprendre les changements dans les comportements techniques des populations humaines en Afrique, après l'épisode principal Out of Africa des Hommes modernes, ca 60-50 ka. Cependant, les données archéologiques pour cette période sont relativement rares, particulièrement pour la Corne de l'Afrique. Nous présentons ici une analyse détaillée des assemblages lithiques de la grotte de Goda Buticha (GB), située près de Dire-Dawa, en Ethiopie, et qui a livré une longue séquence stratigraphique incluant des niveaux datés du Pléistocène récent et de l'Holocène. Cette étude (1) contribue à une meilleure connaissance du MSA récent de la Corne de l'Afrique ; (2) décrit un niveau LSA de l'Holocène récent (GB – complexe I) ; (3) souligne la présence de caractéristiques MSA associées à des traits LSA très tard dans l'Holocène (GB – couche IIc). Ces nouvelles données attestent de la grande variabilité technique au Pléistocène récent et à l'Holocène dans cette région. <br>
DOI: 10.6084/m9.figshare.5697454.v1
title: Late Pleistocene and Holocene lithic variability in Southeastern Ethiopia: implications for the understanding of the Middle and Late Stone Age of the Horn of Africa - Supplementary Material

description: The Late Pleistocene is a key period to understand the shift from the Middle (MSA) to the Late Stone Age (LSA) in Africa. More generally, it is also a crucial time for elucidation of changes in the technological behaviours of human populations in Africa after the main Out of Africa event of modern humans ca. 60-50 thousand years ago. However, the archaeological record for this period is relatively poor, particularly for the Horn of Africa. Here we present a detailed analysis of the lithic assemblages from Goda Buticha (GB), a cave in southeastern Ethiopia, which has yielded a long stratigraphic sequence including Late Pleistocene and Holocene levels. This study (1) contributes to a better knowledge of the late MSA in the Horn of Africa; (2) documents a late Holocene LSA level (GB – Complex I); (3) highlights the presence of MSA characteristics associated with LSA features in the Holocene (GB – Layer IIc). This adds to the emerging record of great lithic technological variability during the Late Pleistocene and Holocene in this region. <br> <br> Le Pléistocène récent est une période clé pour comprendre le changement du Middle (MSA) vers le Late Stone Age (LSA) en Afrique. Plus généralement, c’est une période-clé pour comprendre les changements dans les comportements techniques des populations humaines en Afrique, après l'épisode principal Out of Africa des Hommes modernes, ca 60-50 ka. Cependant, les données archéologiques pour cette période sont relativement rares, particulièrement pour la Corne de l'Afrique. Nous présentons ici une analyse détaillée des assemblages lithiques de la grotte de Goda Buticha (GB), située près de Dire-Dawa, en Ethiopie, et qui a livré une longue séquence stratigraphique incluant des niveaux datés du Pléistocène récent et de l'Holocène. Cette étude (1) contribue à une meilleure connaissance du MSA récent de la Corne de l'Afrique ; (2) décrit un niveau LSA de l'Holocène récent (GB – complexe I) ; (3) souligne la présence de caractéristiques MSA associées à des traits LSA très tard dans l'Holocène (GB – couche IIc). Ces nouvelles données attestent de la grande variabilité technique au Pléistocène récent et à l'Holocène dans cette région. <br>
DOI: 10.6084/m9.figshare.5697445
title: Supplementary Material for: Functional Impact of Novel Androgen Receptor Mutations on the Clinical Manifestation of Androgen Insensitivity Syndrome

description: Androgens are responsible for the development and maintenance of male sex characteristics. Dysfunctions in androgen action due to mutations in the androgen receptor gene (<i>AR</i>) can lead to androgen insensitivity syndrome (AIS) that can be classified as mild (MAIS), partial (PAIS), or complete (CAIS). We have analyzed functional effects of p.Ser760Thr, p.Leu831Phe, p.Ile899Phe, p.Leu769Val, and p.Pro905Arg mutations and the combination p.Gln799Glu + p.Cys807Phe that were identified in patients with PAIS or CAIS. The p.Leu769Val and p.Pro905Arg mutations showed complete disruption of AR action under physiological hormone concentrations; however, they differed in high DHT concentrations especially in the N/C terminal interaction assay. Mutations p.Ser760Thr, p.Leu831Phe, p.Ile899Phe presented transactivation activities higher than 20% of the wild type in physiological hormone concentrations and increased with higher DHT concentrations. However, each one showed a different profile in the N/C interaction assay. When p.Gln799Glu and p.Cys807Phe were analyzed in combination, transactivation activities &lt;10% in physiologic hormone conditions indicated an association with a CAIS phenotype. We conclude that the functional analysis elucidated the role of mutant ARs, giving clues for the molecular mechanisms associated with different clinical AIS manifestations. Differences in hormone-dependent profiles may provide a basis for the response to treatment in each particular case.
DOI: 10.6084/m9.figshare.5697436
title: Supporting data

description: This folder contains three text files:<br><br> pipetting_counts.tab: Egg counts for 72 pipetting trials. 72 pipetting trials (trial) were performed and for each trial eggs were counted under a stereomicroscope (count).<br>medium_softness.tab: Egg counts of the medium hardness experiment. Egg counts (cnt) for each population (pop) assayed on four media differing in their agar concentrations (food, A07: 0.7% agar; A1: 1% agar; A2: 2% agar; A3: 3% agar).<br> manual_counts_pipeline_validation.tab: Manual egg counts of hard-medium plates for pipeline validation. Table giving the manual egg counts (cnts) for each population (pop), replicate (rep) and transfer (transfer) analyzed through the automated pipeline. <br>
DOI: 10.6084/m9.figshare.5697445.v1
title: Supplementary Material for: Functional Impact of Novel Androgen Receptor Mutations on the Clinical Manifestation of Androgen Insensitivity Syndrome

description: Androgens are responsible for the development and maintenance of male sex characteristics. Dysfunctions in androgen action due to mutations in the androgen receptor gene (<i>AR</i>) can lead to androgen insensitivity syndrome (AIS) that can be classified as mild (MAIS), partial (PAIS), or complete (CAIS). We have analyzed functional effects of p.Ser760Thr, p.Leu831Phe, p.Ile899Phe, p.Leu769Val, and p.Pro905Arg mutations and the combination p.Gln799Glu + p.Cys807Phe that were identified in patients with PAIS or CAIS. The p.Leu769Val and p.Pro905Arg mutations showed complete disruption of AR action under physiological hormone concentrations; however, they differed in high DHT concentrations especially in the N/C terminal interaction assay. Mutations p.Ser760Thr, p.Leu831Phe, p.Ile899Phe presented transactivation activities higher than 20% of the wild type in physiological hormone concentrations and increased with higher DHT concentrations. However, each one showed a different profile in the N/C interaction assay. When p.Gln799Glu and p.Cys807Phe were analyzed in combination, transactivation activities &lt;10% in physiologic hormone conditions indicated an association with a CAIS phenotype. We conclude that the functional analysis elucidated the role of mutant ARs, giving clues for the molecular mechanisms associated with different clinical AIS manifestations. Differences in hormone-dependent profiles may provide a basis for the response to treatment in each particular case.
DOI: 10.6084/m9.figshare.5697400
title: Raw output of the Java plug-in for particle detection

description: The folder contains 50 excel files (one per picture) produced by the Java plug-in for particle detection. In each file, the particles are indicated by row. For each particle are provided the name of the picture analyzed (Label), the area of the particle (Area, in px<sup>2</sup>), the coordinates on the picture (X & Y, in px), the perimeter of the particle (Perim., in px), its major and minor dimensions (Major & Minor, in px), the angle between both dimensions (Angle, in degrees) and the number of the picture (Slice, here equals 1). The folder content can be simply processed using the custom R function produce_counts_from_tables.R.
DOI: 10.6084/m9.figshare.5697283
title: CpdA is involved in amino acid metabolism in <i>Shewanella oneidensis</i> MR-1

description: Cyclic 3′,5′-adenosine monophosphate (cAMP) phosphodiesterase (CPD) is an enzyme that catalyzes the hydrolysis of cAMP, a signaling molecule affecting diverse cellular and metabolic processes in bacteria. Some CPDs are also known to function in cAMP-independent manners, while their physiological roles remain largely unknown. Here, we investigated physiological roles of CPD in <i>Shewanella oneidensis</i> MR-1, a model environmental bacterium, and report that CPD is involved in amino-acid metabolism. We found that a CPD-deficient mutant of MR-1 (Δ<i>cpdA</i>) showed decreased expression of genes for the synthesis of methionine, <i>S</i>-adenosylmethionine, and histidine and required these three compounds to grow in minimal media. Interestingly, deletion of adenylate cyclases in Δ<i>cpdA</i> did not restore the ability to grow in minimal media, indicating that the amino acid requirements were not due to the accumulation of cAMP. These results suggest that CPD is involved in the regulation of amino acid metabolism in MR-1 in a cAMP-independent manner. cAMP and cGMP levels and growth rates of cells aerobically grown in lactate minimal medium are shown in panels A, B, and C, respectively.
DOI: 10.6084/m9.figshare.5697283.v1
title: CpdA is involved in amino acid metabolism in <i>Shewanella oneidensis</i> MR-1

description: Cyclic 3′,5′-adenosine monophosphate (cAMP) phosphodiesterase (CPD) is an enzyme that catalyzes the hydrolysis of cAMP, a signaling molecule affecting diverse cellular and metabolic processes in bacteria. Some CPDs are also known to function in cAMP-independent manners, while their physiological roles remain largely unknown. Here, we investigated physiological roles of CPD in <i>Shewanella oneidensis</i> MR-1, a model environmental bacterium, and report that CPD is involved in amino-acid metabolism. We found that a CPD-deficient mutant of MR-1 (Δ<i>cpdA</i>) showed decreased expression of genes for the synthesis of methionine, <i>S</i>-adenosylmethionine, and histidine and required these three compounds to grow in minimal media. Interestingly, deletion of adenylate cyclases in Δ<i>cpdA</i> did not restore the ability to grow in minimal media, indicating that the amino acid requirements were not due to the accumulation of cAMP. These results suggest that CPD is involved in the regulation of amino acid metabolism in MR-1 in a cAMP-independent manner. cAMP and cGMP levels and growth rates of cells aerobically grown in lactate minimal medium are shown in panels A, B, and C, respectively.
DOI: 10.6084/m9.figshare.5697262
title: Additional file 2 of Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data

description: Analysis report. A.html file that details all the analysis included herein, including additional figures referred to in the manuscript as well as some further analyses. (HTML 8315 kb)
DOI: 10.6084/m9.figshare.5697262.v1
title: Additional file 2 of Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data

description: Analysis report. A.html file that details all the analysis included herein, including additional figures referred to in the manuscript as well as some further analyses. (HTML 8315 kb)
DOI: 10.6084/m9.figshare.5697259
title: Additional file 1 of Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data

description: Code for analysis. A gzipped tarball containing all code used for analysis, as well as the.html report referred to above. A package to run aneuploidy assessment in R is also included, alongside a script to download the data we have used. The latest version of these files may be found on https://github.com/MarioniLab/Aneuploidy2017 . (GZ 6405 kb)
DOI: 10.6084/m9.figshare.5697259.v1
title: Additional file 1 of Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data

description: Code for analysis. A gzipped tarball containing all code used for analysis, as well as the.html report referred to above. A package to run aneuploidy assessment in R is also included, alongside a script to download the data we have used. The latest version of these files may be found on https://github.com/MarioniLab/Aneuploidy2017 . (GZ 6405 kb)
DOI: 10.6084/m9.figshare.5697232
title: Additional file 5: Table S1. of Phylogenetics of subtribe Orchidinae s.l. (Orchidaceae; Orchidoideae) based on seven markers (plastid matK, psaB, rbcL, trnL-F, trnH-psba, and nuclear nrITS, Xdh): implications for generic delimitation

description: Voucher information and GenBank accession numbers for the sequences analysed in this study, *indicates newly produced sequences for this paper. The dash (â ) indicates the missing sequences. (XLSX 46Â kb)
DOI: 10.6084/m9.figshare.5697232.v1
title: Additional file 5: Table S1. of Phylogenetics of subtribe Orchidinae s.l. (Orchidaceae; Orchidoideae) based on seven markers (plastid matK, psaB, rbcL, trnL-F, trnH-psba, and nuclear nrITS, Xdh): implications for generic delimitation

description: Voucher information and GenBank accession numbers for the sequences analysed in this study, *indicates newly produced sequences for this paper. The dash (â ) indicates the missing sequences. (XLSX 46Â kb)
DOI: 10.6084/m9.figshare.5697187
title: Additional file 7: of MitoCore: a curated constraint-based model for simulating human central metabolism

description: Flux distributions from the MitoCore model when simulating maximum ATP production with varying proton leak through the reaction representing UCP2. (XLSX 245Â kb)
DOI: 10.6084/m9.figshare.5697187.v1
title: Additional file 7: of MitoCore: a curated constraint-based model for simulating human central metabolism

description: Flux distributions from the MitoCore model when simulating maximum ATP production with varying proton leak through the reaction representing UCP2. (XLSX 245Â kb)
DOI: 10.6084/m9.figshare.5697184
title: Additional file 6: of MitoCore: a curated constraint-based model for simulating human central metabolism

description: Flux distributions from MitoCore and Recon 2.2 models when simulating fumarase deficiency and maximum ATP production. (XLSX 444Â kb)
DOI: 10.6084/m9.figshare.5697184.v1
title: Additional file 6: of MitoCore: a curated constraint-based model for simulating human central metabolism

description: Flux distributions from MitoCore and Recon 2.2 models when simulating fumarase deficiency and maximum ATP production. (XLSX 444Â kb)
DOI: 10.6084/m9.figshare.5697181
title: Additional file 5: of MitoCore: a curated constraint-based model for simulating human central metabolism

description: Flux distributions from the MitoCore and Recon 2.2 models for maximum ATP production with different metabolic fuels. (XLSX 445Â kb)
DOI: 10.6084/m9.figshare.5697181.v1
title: Additional file 5: of MitoCore: a curated constraint-based model for simulating human central metabolism

description: Flux distributions from the MitoCore and Recon 2.2 models for maximum ATP production with different metabolic fuels. (XLSX 445Â kb)
DOI: 10.6084/m9.figshare.5697178
title: Additional file 4: of MitoCore: a curated constraint-based model for simulating human central metabolism

description: MitoCore model encoded in the SBML format. (XML 776Â kb)
DOI: 10.6084/m9.figshare.5697178.v1
title: Additional file 4: of MitoCore: a curated constraint-based model for simulating human central metabolism

description: MitoCore model encoded in the SBML format. (XML 776Â kb)
DOI: 10.6084/m9.figshare.5697175
title: Additional file 3: of MitoCore: a curated constraint-based model for simulating human central metabolism

description: 105 new or altered reactions in the MitoCore model that differ from those in the Virtual Metabolic Human database (and used by the Recon 2.2 model). (XLSX 82Â kb)
DOI: 10.6084/m9.figshare.5697172
title: Additional file 2: of MitoCore: a curated constraint-based model for simulating human central metabolism

description: Experimental measurements of the relative contributions of Î pH and Î Î¨ to the proton motive force. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.5697175.v1
title: Additional file 3: of MitoCore: a curated constraint-based model for simulating human central metabolism

description: 105 new or altered reactions in the MitoCore model that differ from those in the Virtual Metabolic Human database (and used by the Recon 2.2 model). (XLSX 82Â kb)
DOI: 10.6084/m9.figshare.5697172.v1
title: Additional file 2: of MitoCore: a curated constraint-based model for simulating human central metabolism

description: Experimental measurements of the relative contributions of Î pH and Î Î¨ to the proton motive force. (XLSX 11Â kb)