cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5788293.v1
title: Additional file 2: Table S1. of Epidermal Wnt signalling regulates transcriptome heterogeneity and proliferative fate in neighbouring cells

description: Related to Fig. 1e. List of marker genes for each keratinocyte cell state (states A–E). Table S2. Related to Fig. 3f. Differentially dispersed genes for states A–E. Table S3. Related to Fig. 4a. Genes dynamically expressed (and statistically significant) along the NCA Wnt-induced cell state transition. Cluster represents the four clusters of gene expression shown in Fig. 4a. Table S4. Related to Fig. 4b-d. List of TFs identified as regulating the NCA Wnt-induced cell state transition. (XLSX 71 kb)
DOI: 10.6084/m9.figshare.5788290
title: Additional file 4: Table S3. of Sex differences in the late first trimester human placenta transcriptome

description: Sex different genes in late first trimester placenta. DESeq2 results for FDRâ
DOI: 10.6084/m9.figshare.5788290.v1
title: Additional file 4: Table S3. of Sex differences in the late first trimester human placenta transcriptome

description: Sex different genes in late first trimester placenta. DESeq2 results for FDRâ
DOI: 10.6084/m9.figshare.5788254
title: Additional file 2: Table S1. of Sex differences in the late first trimester human placenta transcriptome

description: Expressed genes in late first trimester human placenta, sorted by FPKM. Ensembl IDs, gene symbols, biotypes, FPKM values, baseMean values, gene descriptions, and statistics from DESeq2 are given. (XLS 25631Â kb)
DOI: 10.6084/m9.figshare.5788254.v1
title: Additional file 2: Table S1. of Sex differences in the late first trimester human placenta transcriptome

description: Expressed genes in late first trimester human placenta, sorted by FPKM. Ensembl IDs, gene symbols, biotypes, FPKM values, baseMean values, gene descriptions, and statistics from DESeq2 are given. (XLS 25631Â kb)
DOI: 10.6084/m9.figshare.5788248
title: Additional file 5: of Multi-omics differentially classify disease state and treatment outcome in pediatric Crohnâ s disease

description: Ranking of variable importance in significant treatment response models. (XLSX 151 kb)
DOI: 10.6084/m9.figshare.5788248.v1
title: Additional file 5: of Multi-omics differentially classify disease state and treatment outcome in pediatric Crohnâ s disease

description: Ranking of variable importance in significant treatment response models. (XLSX 151 kb)
DOI: 10.6084/m9.figshare.5788233
title: Additional file 4: of Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease

description: Ranking of variable importance in significant disease state models. (XLSX 226 kb)
DOI: 10.6084/m9.figshare.5788233.v1
title: Additional file 4: of Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease

description: Ranking of variable importance in significant disease state models. (XLSX 226 kb)
DOI: 10.6084/m9.figshare.5788224
title: Additional file 10: of Sex differences in the late first trimester human placenta transcriptome

description: Table S6 and Table S7. Sexually dimorphic genes in human placenta at weeks 11 and 13. Spreadsheet of significantly different genes for gestational age subanalysis (female vs male, FDRâ
DOI: 10.6084/m9.figshare.5788224.v1
title: Additional file 10: of Sex differences in the late first trimester human placenta transcriptome

description: Table S6 and Table S7. Sexually dimorphic genes in human placenta at weeks 11 and 13. Spreadsheet of significantly different genes for gestational age subanalysis (female vs male, FDRâ
DOI: 10.6084/m9.figshare.5788215
title: Additional file 3: of Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease

description: Random forest model summaries. (XLSX 65 kb)
DOI: 10.6084/m9.figshare.5788215.v1
title: Additional file 3: of Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease

description: Random forest model summaries. (XLSX 65 kb)
DOI: 10.6084/m9.figshare.5788212
title: Additional file 3: of Expression characterization of the herbicide tolerance gene Aryloxyalkanoate Dioxygenase (aad-1) controlled by seven combinations of regulatory elements

description: Herbicide tolerance by visual injury scoring data. (CSV 18Â kb)
DOI: 10.6084/m9.figshare.5788212.v1
title: Additional file 3: of Expression characterization of the herbicide tolerance gene Aryloxyalkanoate Dioxygenase (aad-1) controlled by seven combinations of regulatory elements

description: Herbicide tolerance by visual injury scoring data. (CSV 18Â kb)
DOI: 10.6084/m9.figshare.5788191
title: Additional file 2: of Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease

description: Sample sequencing coverage and metadata. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.5788191.v1
title: Additional file 2: of Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease

description: Sample sequencing coverage and metadata. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.5788182
title: Additional file 2: of Expression characterization of the herbicide tolerance gene Aryloxyalkanoate Dioxygenase (aad-1) controlled by seven combinations of regulatory elements

description: Protein accumulation by ELISA data. (CSV 29Â kb)
DOI: 10.6084/m9.figshare.5788182.v1
title: Additional file 2: of Expression characterization of the herbicide tolerance gene Aryloxyalkanoate Dioxygenase (aad-1) controlled by seven combinations of regulatory elements

description: Protein accumulation by ELISA data. (CSV 29Â kb)
DOI: 10.6084/m9.figshare.5788161
title: Additional file 1: of Expression characterization of the herbicide tolerance gene Aryloxyalkanoate Dioxygenase (aad-1) controlled by seven combinations of regulatory elements

description: Transcript abundance by RT-qPCR data. (CSV 90Â kb)
DOI: 10.6084/m9.figshare.5788161.v1
title: Additional file 1: of Expression characterization of the herbicide tolerance gene Aryloxyalkanoate Dioxygenase (aad-1) controlled by seven combinations of regulatory elements

description: Transcript abundance by RT-qPCR data. (CSV 90Â kb)
DOI: 10.6084/m9.figshare.5788152
title: Additional file 1: of The association of the N-terminal pro-brain-type natriuretic peptide response to exercise with disease severity in therapy-naive pulmonary arterial hypertension: a cohort study

description: Correlation plots of NT-proBNP at rest and at peak exercise and the Î NT-proBNP with the 6MWT distance, mean PAP and the VO2/kg. (ZIP 540 kb)
DOI: 10.6084/m9.figshare.5788152.v1
title: Additional file 1: of The association of the N-terminal pro-brain-type natriuretic peptide response to exercise with disease severity in therapy-naive pulmonary arterial hypertension: a cohort study

description: Correlation plots of NT-proBNP at rest and at peak exercise and the Î NT-proBNP with the 6MWT distance, mean PAP and the VO2/kg. (ZIP 540 kb)
DOI: 10.6084/m9.figshare.5788128
title: Supporting Data for Fig. 5 of "In vitro and in vivo phasor analysis of stoichiometry and pharmacokinetics using short lifetime near-infrared dyes and time-gated imaging"

description: This data is part of the manuscript "<i>In vitro </i>and<i> in vivo</i> phasor analysis of stoichiometry and pharmacokinetics using short lifetime near-infrared dyes and time-gated imaging" by Sez-Jade Chen, Nattawut Sinsuebphon, Alena Rudkouskaya, Margarida Barroso, Xavier Intes and Xavier Michalet<br>
DOI: 10.6084/m9.figshare.5788128.v2
title: Supporting Data for Fig. 5 of "In vitro and in vivo phasor analysis of stoichiometry and pharmacokinetics using short lifetime near-infrared dyes and time-gated imaging"

description: This data is part of the manuscript "<i>In vitro </i>and<i> in vivo</i> phasor analysis of stoichiometry and pharmacokinetics using short lifetime near-infrared dyes and time-gated imaging" by Sez-Jade Chen, Nattawut Sinsuebphon, Alena Rudkouskaya, Margarida Barroso, Xavier Intes and Xavier Michalet<br>
DOI: 10.6084/m9.figshare.5788128.v1
title: Supporting Data for Fig. 5 of "In vitro and in vivo phasor analysis of stoichiometry and pharmacokinetics using near-infrared dyes"

description: This data is part of the manuscript "In vitro and in vivo phasor analysis of stoichiometry and pharmacokinetics using near-infrared dyes" by Sez-Jade Chen, Nattawut Sinsuebphon, Alena Rudkouskaya, Margarida Barroso, Xavier Intes and Xavier Michalet<br>
DOI: 10.6084/m9.figshare.5787927
title: Timelapse 6 - raw confocal files

description: See accompanying word documents<br><br>
DOI: 10.6084/m9.figshare.5787927.v1
title: Timelapse 6 - raw confocal files

description: See accompanying word documents<br><br>
DOI: 10.6084/m9.figshare.5787927.v2
title: Timelapse 6 - raw confocal files

description: See accompanying word documents<br><br>
DOI: 10.6084/m9.figshare.5787927.v3
title: Timelapse 6 - raw confocal files

description: See accompanying word documents<br><br>
DOI: 10.6084/m9.figshare.5787927.v4
title: Timelapse 6 - raw confocal files

description: See accompanying word documents<br><br>
DOI: 10.6084/m9.figshare.5787927.v5
title: Timelapse 6 - raw confocal files

description: See accompanying word documents<br><br>
DOI: 10.6084/m9.figshare.5787927.v8
title: Timelapse 6 - raw confocal files

description: See accompanying word documents<br><br>
DOI: 10.6084/m9.figshare.5787927.v7
title: Timelapse 6 - raw confocal files

description: See accompanying word documents<br><br>
DOI: 10.24376/rd.sgul.5787888
title: Data supporting: 'A tyrosinse-to-asparagine mutation in TRAPPC6A leads to build-up of the protein and results in a novel syndrome with intellectual disability, speech delay and dysmorphic features'.

description: TRAPPC6A is associated with a novel phenotype and joins a growing list of proteins belonging to the TRAPP complex implicated in clinical syndromes with neurodevelopmental features.<br>
DOI: 10.6084/m9.figshare.5787873
title: Timelapse 5b - Maximum intensity projections - bleach corrected

description: See accompanying word documents<br><br>
DOI: 10.6084/m9.figshare.5787873.v1
title: Timelapse 5b - Maximum intensity projections - bleach corrected

description: See accompanying word documents<br><br>
DOI: 10.6084/m9.figshare.5787846
title: GWAS data for "Natural variation in stochastic photoreceptor specification and color preference in Drosophila"

description: Complete data for genome-wide association study (GWAS) using the SsON (Rh4) phenotype data and inferred full genome sequences of the progeny of each DGRP line crossed with the ss deficiency line.<br>From https://elifesciences.org/articles/29593
DOI: 10.6084/m9.figshare.5787846.v2
title: GWAS data for "Natural variation in stochastic photoreceptor specification and color preference in Drosophila"

description: Complete data for genome-wide association study (GWAS) using the SsON (Rh4) phenotype data and inferred full genome sequences of the progeny of each DGRP line crossed with the ss deficiency line.<br>From https://elifesciences.org/articles/29593
DOI: 10.6084/m9.figshare.5787846.v1
title: GWAS data for "Natural variation in stochastic photoreceptor specification and color preference in Drosophila"

description: Complete data for genome-wide association study (GWAS) using the SsON (Rh4) phenotype data and inferred full genome sequences of the progeny of each DGRP line crossed with the ss deficiency line.<br>From https://elifesciences.org/articles/29593
DOI: 10.6084/m9.figshare.5787774
title: Modeling the impact of interaction on pedestrian group motion

description: Mobile social robots aimed at interacting with and assisting humans in pedestrian areas need to understand the dynamics of pedestrian social interaction. In this work, we investigate the effect of interaction on pedestrian group motion by defining three motion models to represent (1) interpersonal-distance, (2) relative orientation and (3) absolute difference of velocities; and model them using a dataset of 12000+ pedestrian trajectories recorded in uncontrolled settings. Our contributions include: (i) Demonstrating that interaction has a prominent effect on the empirical distributions of the proposed joint motion attributes, where increasing levels of interaction lead to more regular behavior (ii) Developing analytic motion models of such distributions and reflect the effect of interaction on model parameters (iii) Detecting the social groups in a crowd with almost perfect accuracy utilizing the proposed models, despite the constant flow direction in the environment which causes unrelated pedestrians to move in a correlated way, and thus makes group recognition more difficult (iv) Estimating the level of intensity with considerable rates utilizing the proposed models
DOI: 10.6084/m9.figshare.5787774.v1
title: Modeling the impact of interaction on pedestrian group motion

description: Mobile social robots aimed at interacting with and assisting humans in pedestrian areas need to understand the dynamics of pedestrian social interaction. In this work, we investigate the effect of interaction on pedestrian group motion by defining three motion models to represent (1) interpersonal-distance, (2) relative orientation and (3) absolute difference of velocities; and model them using a dataset of 12000+ pedestrian trajectories recorded in uncontrolled settings. Our contributions include: (i) Demonstrating that interaction has a prominent effect on the empirical distributions of the proposed joint motion attributes, where increasing levels of interaction lead to more regular behavior (ii) Developing analytic motion models of such distributions and reflect the effect of interaction on model parameters (iii) Detecting the social groups in a crowd with almost perfect accuracy utilizing the proposed models, despite the constant flow direction in the environment which causes unrelated pedestrians to move in a correlated way, and thus makes group recognition more difficult (iv) Estimating the level of intensity with considerable rates utilizing the proposed models
DOI: 10.6084/m9.figshare.5787726
title: Data and stimuli for "Developmental differences in approaches to nonsymbolic comparison tasks", QJEP (2018)

description: Full data sets, stimuli, and variable description key for all three studies included in the paper: "Developmental differences in approaches to non symbolic comparison tasks" published in QJEP (2018).
DOI: 10.6084/m9.figshare.5787726.v1
title: Data and stimuli for "Developmental differences in approaches to nonsymbolic comparison tasks", QJEP (2018)

description: Full data sets, stimuli, and variable description key for all three studies included in the paper: "Developmental differences in approaches to non symbolic comparison tasks" published in QJEP (2018).
DOI: 10.6084/m9.figshare.5787723.v2
title: DNA barcoding for species identification in deep-sea clams (Mollusca: Bivalvia: Vesicomyidae)

description: Deep-sea clams (Bivalvia: Vesicomyidae) have been found in reduced environments over the world oceans, but taxonomy of this group remains confusing at species and supraspecific levels due to their high-morphological similarity and plasticity. In the present study, we collected mitochondrial COI sequences to evaluate the utility of DNA barcoding on identifying vesicomyid species. COI dataset identified 56 well-supported putative species/operational taxonomic units (OTUs), approximately covering half of the extant vesicomyid species. One species (OTU2) was first detected, and may represent a new species. Average distances between species ranged from 1.65 to 29.64%, generally higher than average intraspecific distances (0–1.41%) when excluding <i>Pliocardia</i> sp.10 cf. <i>venusta</i> (average intraspecific distance 1.91%). Local barcoding gap existed in 33 of the 35 species when comparing distances of maximum interspecific and minimum interspecific distances with two exceptions (<i>Abyssogena southwardae</i> and <i>Calyptogena rectimargo-starobogatovi</i>). The barcode index number (BIN) system determined 41 of the 56 species/OTUs, each with a unique BIN, indicating their validity. Three species were found to have two BINs, together with their high level of intraspecific variation, implying cryptic diversity within them. Although fewer 16 S sequences were collected, similar results were obtained. Nineteen putative species were determined and no overlap observed between intra- and inter-specific variation. Implications of DNA barcoding for the Vesicomyidae taxonomy were then discussed. Findings of this study will provide important evidence for taxonomic revision in this problematic clam group, and accelerate the discovery of new vesicomyid species in the future.
DOI: 10.6084/m9.figshare.5787717
title: A rosette by any other name: species diversity in the Bangiales (Rhodophyta) along the South African coast

description: The Bangiales is an order of Rhodophyta, widely distributed around the globe and best known for its economic value in the nori industry. The morphological simplicity of the group offers limited distinguishing characters for species identification. We therefore delimited species of the Bangiales along the South African coast based on two unlinked loci, the mitochondrial <i>cox</i>1 gene and the plastid <i>rbc</i>L gene, supplemented with additional sequence data from a third gene, the nuclear nSSU. Application of DNA-based species delimitation methods including the Automatic Barcode Gap Discovery (ABGD), General Mixed Yule Coalescent (GYMC) and Poisson Tree Processes (PTP), resulted in the recognition of 10 <i>Porphyra</i> and three <i>Pyropia</i> species in South Africa, only three of which had been previously described. Additional species of Bangiales previously recorded along the South African coast were added to our final species list despite not being found in the present study, resulting in an estimate of 14–16 Bangiales species occurring along this shoreline. Most of this extensive genetic diversity has been misidentified as the commonly rosette-forming species <i>P. capensis</i>. The name <i>P. capensis</i> currently refers to a species complex and cannot be attached to any one species with certainty. All species in this complex, confirmed using genetic data, are endemic to South Africa. Our results compare well with other Southern Hemisphere countries, such as Chile and New Zealand, where high genetic diversity, species richness and endemicity have also been found.
DOI: 10.6084/m9.figshare.5787717.v1
title: A rosette by any other name: species diversity in the Bangiales (Rhodophyta) along the South African coast

description: The Bangiales is an order of Rhodophyta, widely distributed around the globe and best known for its economic value in the nori industry. The morphological simplicity of the group offers limited distinguishing characters for species identification. We therefore delimited species of the Bangiales along the South African coast based on two unlinked loci, the mitochondrial <i>cox</i>1 gene and the plastid <i>rbc</i>L gene, supplemented with additional sequence data from a third gene, the nuclear nSSU. Application of DNA-based species delimitation methods including the Automatic Barcode Gap Discovery (ABGD), General Mixed Yule Coalescent (GYMC) and Poisson Tree Processes (PTP), resulted in the recognition of 10 <i>Porphyra</i> and three <i>Pyropia</i> species in South Africa, only three of which had been previously described. Additional species of Bangiales previously recorded along the South African coast were added to our final species list despite not being found in the present study, resulting in an estimate of 14–16 Bangiales species occurring along this shoreline. Most of this extensive genetic diversity has been misidentified as the commonly rosette-forming species <i>P. capensis</i>. The name <i>P. capensis</i> currently refers to a species complex and cannot be attached to any one species with certainty. All species in this complex, confirmed using genetic data, are endemic to South Africa. Our results compare well with other Southern Hemisphere countries, such as Chile and New Zealand, where high genetic diversity, species richness and endemicity have also been found.
DOI: 10.6084/m9.figshare.5787702
title: The contribution of algae to freshwater dissolved organic matter: implications for UV spectroscopic analysis

description: Dissolved organic matter (DOM) is an important constituent of freshwater that participates in a number of key ecological and biogeochemical processes but can be problematic during water treatment. Thus, the demand for rapid and reliable monitoring is growing, and spectroscopic methods are potentially useful. A model with 3 components—2 that absorb in the ultraviolet (UV) range and are present at variable concentrations and a third that does not absorb light and is present at a low constant concentration—was previously found to yield reliable predictions of dissolved organic carbon concentration [DOC]. The model underestimated [DOC] in shallow eutrophic lakes in the Yangtze Basin, China, however, raising the possibility that DOM derived from algae might be poorly estimated, an idea supported by new data reported here for eutrophic British lakes. We estimated the extinction coefficients in the UV range of algae-derived DOM from published data on algal cultures and from new data from outdoor mesocosm experiments in which high concentrations of DOC were generated under conditions comparable to those in eutrophic freshwaters. The results demonstrate the weak UV absorbance of DOM from algae compared to DOM from terrestrial sources. A modified model, in which the third component represents algae-derived DOM present at variable concentrations, allowed contributions of such DOM to be estimated by combining the spectroscopic data with [DOC] measured by laboratory combustion. Estimated concentrations of algae-derived DOC in 77 surface freshwater samples ranged from 0 to 8.6 mg L<sup>−1</sup>, and the fraction of algae-derived DOM ranged from 0% to 100%.
DOI: 10.6084/m9.figshare.5787702.v1
title: The contribution of algae to freshwater dissolved organic matter: implications for UV spectroscopic analysis

description: Dissolved organic matter (DOM) is an important constituent of freshwater that participates in a number of key ecological and biogeochemical processes but can be problematic during water treatment. Thus, the demand for rapid and reliable monitoring is growing, and spectroscopic methods are potentially useful. A model with 3 components—2 that absorb in the ultraviolet (UV) range and are present at variable concentrations and a third that does not absorb light and is present at a low constant concentration—was previously found to yield reliable predictions of dissolved organic carbon concentration [DOC]. The model underestimated [DOC] in shallow eutrophic lakes in the Yangtze Basin, China, however, raising the possibility that DOM derived from algae might be poorly estimated, an idea supported by new data reported here for eutrophic British lakes. We estimated the extinction coefficients in the UV range of algae-derived DOM from published data on algal cultures and from new data from outdoor mesocosm experiments in which high concentrations of DOC were generated under conditions comparable to those in eutrophic freshwaters. The results demonstrate the weak UV absorbance of DOM from algae compared to DOM from terrestrial sources. A modified model, in which the third component represents algae-derived DOM present at variable concentrations, allowed contributions of such DOM to be estimated by combining the spectroscopic data with [DOC] measured by laboratory combustion. Estimated concentrations of algae-derived DOC in 77 surface freshwater samples ranged from 0 to 8.6 mg L<sup>−1</sup>, and the fraction of algae-derived DOM ranged from 0% to 100%.
DOI: 10.6084/m9.figshare.5787693
title: COMRADES Crowdsourced Informativeness Dataset (CCSID)

description: Crowdsourced annotations for informativeness of messages in crisis response. Developed for training an automatic classifier, as part of the EC COMRADES project.