cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8280677.v1
title: DESFLU_data_20190614.csv

description: Design fluency performance, including counts of correct responses and errors, for two groups of Parkinson's disease subjects separated by side of initial symptom onset and matched controls.<br>subnum Subject numbergrp Group: 1)Control, 2)PDR, 3)PDLage Agesex Sexedu EducationMMSE MMSE raw scoreHMD Hamilton Depression scoreGPB Grooved Pegboard z-score, right handfill_nov Filled Dots - novel designsfill_all Filled Dots - all designsem_nov Empty Dots - novel designsem_all Empty Dots - all designssw_nov Switching Dots - novel designssw_all Switching Dots - all designsfill_totrep Filled Dots - tot repetition errorsfill_totsle Filled Dots - tot setloss errorsfill_sle3 Filled Dots - setloss 3 linesfill_sle5 Filled Dots - setloss 5 linesem_totrep Empty Dots - tot repetition errorsem_totsle Empty Dots - tot setloss errorsem_sle3 Empty Dots - setloss 3 linesem_sle5 Empty Dots- setloss 5 linesem_slex Empty Dots - setloss othersw_totrep Switching Dots - tot repetition errorssw_tsle Switching Dots - tot setloss errorssw_3sle Switching Dots - setloss 3 linessw_5sle Switching Dots- setloss 5 linessw_slex Switching Dots - setloss other
DOI: 10.6084/m9.figshare.8280674.v1
title: Supplementary_Table S2-Details of four genetic maps, including raw segregation data.xlsx

description: 180K SoyaSNP array genotype data for construction of genetic maps in WH, HI, WI, and II populations -- Details of four genetic maps, including raw segregation data
DOI: 10.6084/m9.figshare.8280755.v3
title: prostate psychopathology Benign images

description: this is prostate histopathology dataset, which includes benign, g3 and g4<br><br><br>
DOI: 10.6084/m9.figshare.8280284
title: Additional file 4: of On-treatment biomarkers can improve prediction of response to neoadjuvant chemotherapy in breast cancer

description: Table S1. Gene lists of pairwise analysis of pre- and on-treatment sequential patient-matched samples from NEO and I-SPY datasets using Significance analysis of microarrays with FDR = 10%. Table S2. Gene lists distinguishing between responders and non-responders at different time points across the NEO and ISPY datasets using rank product analysis with p
DOI: 10.6084/m9.figshare.8280284.v1
title: Additional file 4: of On-treatment biomarkers can improve prediction of response to neoadjuvant chemotherapy in breast cancer

description: Table S1. Gene lists of pairwise analysis of pre- and on-treatment sequential patient-matched samples from NEO and I-SPY datasets using Significance analysis of microarrays with FDR = 10%. Table S2. Gene lists distinguishing between responders and non-responders at different time points across the NEO and ISPY datasets using rank product analysis with p
DOI: 10.6084/m9.figshare.8280248
title: MOESM4 of Differential genetic and functional background in inflammatory bowel disease phenotypes of a Greek population: a systems bioinformatics approach

description: Additional file 4. The table represents all the KEGG pathways per IBD phenotype and sub-phenotype by utilizing the results in Additional files 2 and 3. These have all been ranked using the protein centrality scores for the proteins contributing to each one of them as explained in the manuscript.
DOI: 10.6084/m9.figshare.8280239
title: MOESM2 of Differential genetic and functional background in inflammatory bowel disease phenotypes of a Greek population: a systems bioinformatics approach

description: Additional file 2. The ranked proteins associated with each IBD phenotype and sub-phenotype after centrality analysis, in their respective sheets.
DOI: 10.6084/m9.figshare.8280245
title: MOESM3 of Differential genetic and functional background in inflammatory bowel disease phenotypes of a Greek population: a systems bioinformatics approach

description: Additional file 3. Unique and shared KEGG pathways between different phenotype groupings after enrichment via STRING: CD vs UC, B1 vs B2 and E1 vs E3. The results are shown in the respective sheets. a) CD vs UC, b) B1 vs B2, c) E1 vs E2.
DOI: 10.6084/m9.figshare.8280248.v1
title: MOESM4 of Differential genetic and functional background in inflammatory bowel disease phenotypes of a Greek population: a systems bioinformatics approach

description: Additional file 4. The table represents all the KEGG pathways per IBD phenotype and sub-phenotype by utilizing the results in Additional files 2 and 3. These have all been ranked using the protein centrality scores for the proteins contributing to each one of them as explained in the manuscript.
DOI: 10.6084/m9.figshare.8280245.v1
title: MOESM3 of Differential genetic and functional background in inflammatory bowel disease phenotypes of a Greek population: a systems bioinformatics approach

description: Additional file 3. Unique and shared KEGG pathways between different phenotype groupings after enrichment via STRING: CD vs UC, B1 vs B2 and E1 vs E3. The results are shown in the respective sheets. a) CD vs UC, b) B1 vs B2, c) E1 vs E2.
DOI: 10.6084/m9.figshare.8280239.v1
title: MOESM2 of Differential genetic and functional background in inflammatory bowel disease phenotypes of a Greek population: a systems bioinformatics approach

description: Additional file 2. The ranked proteins associated with each IBD phenotype and sub-phenotype after centrality analysis, in their respective sheets.
DOI: 10.6084/m9.figshare.8280206
title: MOESM2 of Extracellular vesicles carry cellulases in the industrial fungus Trichoderma reesei

description: Additional file 2. List of vesicular proteins identified in T. reesei EVs in the presence of cellulose.
DOI: 10.6084/m9.figshare.8280206.v1
title: MOESM2 of Extracellular vesicles carry cellulases in the industrial fungus Trichoderma reesei

description: Additional file 2. List of vesicular proteins identified in T. reesei EVs in the presence of cellulose.
DOI: 10.6084/m9.figshare.8280155
title: Additional file 1: of â Regardless, you are not the first womanâ : an illustrative case study of contextual risk factors impacting sexual and reproductive health and rights in Nicaragua

description: Interview Guide. (ZIP 32 kb)
DOI: 10.6084/m9.figshare.8280155.v1
title: Additional file 1: of â Regardless, you are not the first womanâ : an illustrative case study of contextual risk factors impacting sexual and reproductive health and rights in Nicaragua

description: Interview Guide. (ZIP 32 kb)
DOI: 10.6084/m9.figshare.8280083
title: Additional file 1: of Cilastatin protects against tacrolimus-induced nephrotoxicity via anti-oxidative and anti-apoptotic properties

description: Table S1-S3.P value of normality test in experimental data. P value of normality test in basic parameters, TAC concentration, animal and cell experimental variables. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.8280083.v1
title: Additional file 1: of Cilastatin protects against tacrolimus-induced nephrotoxicity via anti-oxidative and anti-apoptotic properties

description: Table S1-S3.P value of normality test in experimental data. P value of normality test in basic parameters, TAC concentration, animal and cell experimental variables. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.8279978
title: Additional file 3: of Mapping gastrointestinal gene expression patterns in wild primates and humans via fecal RNA-seq

description: Table S3. Comparative expression of specific markers to gastrointestinal tract and immune responses from gorilla and human fecal RNA-seq (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8279972
title: Additional file 2: of Mapping gastrointestinal gene expression patterns in wild primates and humans via fecal RNA-seq

description: Table S2. Percentage proportions of classified and unclassified reads out of 10,000 randomly selected non-host RNA-seq reads (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8279978.v1
title: Additional file 3: of Mapping gastrointestinal gene expression patterns in wild primates and humans via fecal RNA-seq

description: Table S3. Comparative expression of specific markers to gastrointestinal tract and immune responses from gorilla and human fecal RNA-seq (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8279972.v1
title: Additional file 2: of Mapping gastrointestinal gene expression patterns in wild primates and humans via fecal RNA-seq

description: Table S2. Percentage proportions of classified and unclassified reads out of 10,000 randomly selected non-host RNA-seq reads (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8279963
title: Additional file 1: of Mapping gastrointestinal gene expression patterns in wild primates and humans via fecal RNA-seq

description: Table S1. Read statistics, percentage alignments and percentage proportions of non-host RNA-seq reads (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8279957
title: Additional file 6: of The effects of meteoric diagenesis on the geochemical composition and microstructure of Pliocene fossil Terebratalia coreanica and Laqueus rubellus brachiopod shells from northeastern Japan

description: Figure S2. Sampling spots, δ13C and δ18O values, minor element (Mn, Fe, and Sr) concentrations, mean CL intensities, altered fiber ratios, and altered fiber and puncta-filling cement ratios of the modern (Figure S2-1, SGLR) and fossil (Figures S2-2–6, MNLR1–MNLR5) L. rubellus shells. Composite CL images are presented for each shell. SEM and CL images of selected shell portions are also shown. (ZIP 25125 kb)
DOI: 10.6084/m9.figshare.8279957.v1
title: Additional file 6: of The effects of meteoric diagenesis on the geochemical composition and microstructure of Pliocene fossil Terebratalia coreanica and Laqueus rubellus brachiopod shells from northeastern Japan

description: Figure S2. Sampling spots, δ13C and δ18O values, minor element (Mn, Fe, and Sr) concentrations, mean CL intensities, altered fiber ratios, and altered fiber and puncta-filling cement ratios of the modern (Figure S2-1, SGLR) and fossil (Figures S2-2–6, MNLR1–MNLR5) L. rubellus shells. Composite CL images are presented for each shell. SEM and CL images of selected shell portions are also shown. (ZIP 25125 kb)
DOI: 10.6084/m9.figshare.8279963.v1
title: Additional file 1: of Mapping gastrointestinal gene expression patterns in wild primates and humans via fecal RNA-seq

description: Table S1. Read statistics, percentage alignments and percentage proportions of non-host RNA-seq reads (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8279945
title: Additional file 5: of The effects of meteoric diagenesis on the geochemical composition and microstructure of Pliocene fossil Terebratalia coreanica and Laqueus rubellus brachiopod shells from northeastern Japan

description: Figure S1. Sampling spots, δ13C and δ18O values, minor element (Mn, Fe, and Sr) concentrations, mean CL intensities, altered fiber ratios, and altered fiber and puncta-filling cement ratios of the modern (Figure S1-1, OTTCo) and fossil (Figures S1-2–6, MNTCo1–MNTCo5) T. coreanica shells. Composite CL images are presented for each shell. SEM and CL images of selected shell portions are also shown. Red and blue arrows indicate local minima in δ13C and δ18Ο, respectively. (ZIP 26310 kb)
DOI: 10.6084/m9.figshare.8279939
title: Additional file 4: of The effects of meteoric diagenesis on the geochemical composition and microstructure of Pliocene fossil Terebratalia coreanica and Laqueus rubellus brachiopod shells from northeastern Japan

description: Table S4. Minor element (Mn, Fe, and Sr) concentrations and MCLIs (mean CL intensities) of the fossil Terebratalia coreanica (MNTCo1â MNTCo5) and Laqueus rubellus (MNLR1â MNLR5) shells. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.8279945.v1
title: Additional file 5: of The effects of meteoric diagenesis on the geochemical composition and microstructure of Pliocene fossil Terebratalia coreanica and Laqueus rubellus brachiopod shells from northeastern Japan

description: Figure S1. Sampling spots, δ13C and δ18O values, minor element (Mn, Fe, and Sr) concentrations, mean CL intensities, altered fiber ratios, and altered fiber and puncta-filling cement ratios of the modern (Figure S1-1, OTTCo) and fossil (Figures S1-2–6, MNTCo1–MNTCo5) T. coreanica shells. Composite CL images are presented for each shell. SEM and CL images of selected shell portions are also shown. Red and blue arrows indicate local minima in δ13C and δ18Ο, respectively. (ZIP 26310 kb)
DOI: 10.6084/m9.figshare.8279939.v1
title: Additional file 4: of The effects of meteoric diagenesis on the geochemical composition and microstructure of Pliocene fossil Terebratalia coreanica and Laqueus rubellus brachiopod shells from northeastern Japan

description: Table S4. Minor element (Mn, Fe, and Sr) concentrations and MCLIs (mean CL intensities) of the fossil Terebratalia coreanica (MNTCo1â MNTCo5) and Laqueus rubellus (MNLR1â MNLR5) shells. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.8279930
title: Additional file 3: of The effects of meteoric diagenesis on the geochemical composition and microstructure of Pliocene fossil Terebratalia coreanica and Laqueus rubellus brachiopod shells from northeastern Japan

description: Table S3. Minor element (Mn, Fe, and Sr) concentrations of the modern Terebratalia coreanica (OTTCo) and Laqueus rubellus (SGLR) shells. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8279924
title: Additional file 2: of The effects of meteoric diagenesis on the geochemical composition and microstructure of Pliocene fossil Terebratalia coreanica and Laqueus rubellus brachiopod shells from northeastern Japan

description: Table S2. δ13C and δ18Ο value, AFRs (altered fiber ratios), and AF-PCRs (altered fiber and puncta-filling cement ratios) of the fossil Terebratalia coreanica (MNTCo1–MNTCo5) and Laqueus rubellus (MNLR1–MNLR5) shells. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.8279930.v1
title: Additional file 3: of The effects of meteoric diagenesis on the geochemical composition and microstructure of Pliocene fossil Terebratalia coreanica and Laqueus rubellus brachiopod shells from northeastern Japan

description: Table S3. Minor element (Mn, Fe, and Sr) concentrations of the modern Terebratalia coreanica (OTTCo) and Laqueus rubellus (SGLR) shells. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8279915
title: Additional file 1: of The effects of meteoric diagenesis on the geochemical composition and microstructure of Pliocene fossil Terebratalia coreanica and Laqueus rubellus brachiopod shells from northeastern Japan

description: Table S1. δ13C and δ18Ο values of the modern Terebratalia coreanica (OTTCo) and Laqueus rubellus (SGLR) shells. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8279924.v1
title: Additional file 2: of The effects of meteoric diagenesis on the geochemical composition and microstructure of Pliocene fossil Terebratalia coreanica and Laqueus rubellus brachiopod shells from northeastern Japan

description: Table S2. δ13C and δ18Ο value, AFRs (altered fiber ratios), and AF-PCRs (altered fiber and puncta-filling cement ratios) of the fossil Terebratalia coreanica (MNTCo1–MNTCo5) and Laqueus rubellus (MNLR1–MNLR5) shells. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.8279915.v1
title: Additional file 1: of The effects of meteoric diagenesis on the geochemical composition and microstructure of Pliocene fossil Terebratalia coreanica and Laqueus rubellus brachiopod shells from northeastern Japan

description: Table S1. δ13C and δ18Ο values of the modern Terebratalia coreanica (OTTCo) and Laqueus rubellus (SGLR) shells. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8279699
title: Dataset for: Derepression of Mmp gene transcription and an emphysema-like phenotype in Zbtb7c knockout mouse lungs

description: Dysregulated MMP expression is a major cause of the degradation of lung tissue that is integral to emphysema pathogenesis. Cigarette smoking (CS) increases MMP gene expression, a major contributor to emphysema development. We previously reported that Zbtb7c is a transcriptional repressor of several Mmp genes (Mmps-8, -10, -13, and -16). Here, we show that Zbtb7c knockout mice have mild emphysema-like phenotypes, including alveolar wall destruction, enlarged alveoli, and upregulated Mmp genes. Alveolar size and Mmp gene expression, in Zbtb7c-/- mouse lungs, were increased more severely upon exposure to CS, compared to those of Zbtb7c+/+ mouse lungs. These observations suggest that Zbtb7c degradation or absence may contribute to the pathogenesis of emphysema.
DOI: 10.6084/m9.figshare.8279699.v1
title: Dataset for: Derepression of Mmp gene transcription and an emphysema-like phenotype in Zbtb7c knockout mouse lungs

description: Dysregulated MMP expression is a major cause of the degradation of lung tissue that is integral to emphysema pathogenesis. Cigarette smoking (CS) increases MMP gene expression, a major contributor to emphysema development. We previously reported that Zbtb7c is a transcriptional repressor of several Mmp genes (Mmps-8, -10, -13, and -16). Here, we show that Zbtb7c knockout mice have mild emphysema-like phenotypes, including alveolar wall destruction, enlarged alveoli, and upregulated Mmp genes. Alveolar size and Mmp gene expression, in Zbtb7c-/- mouse lungs, were increased more severely upon exposure to CS, compared to those of Zbtb7c+/+ mouse lungs. These observations suggest that Zbtb7c degradation or absence may contribute to the pathogenesis of emphysema.
DOI: 10.6084/m9.figshare.8279618
title: Accurate inference of tree topologies from multiple sequence alignments using deep learning

description: Each directory contains Training, Validation and Test datasets in fasta format. Directory names contain the following information about the MSAs: <br>1) Gap (w/ indels) or nogap (w/o indels) MSAs2) Number of MSAs per topology generated for training (i.e. 50k MSA * 3 possible topologies = 150k MSAs in TRAIN.fasta file) Order of topologies: 50k x ((D,A),B,C); 50k x ((D,B),A,C); 50k x ((D,C),A,B);3) MSA length (500, 1000 or 10000)4) archive3 contains Keras models and its associated trained weights. They will generate identical CNN accuracies reported in Fig. 2 <br>List of all directories:<b>archive1_gap.tar.gz</b> gap50k_1000 gap50k_10000 gap50k_500<b>archive2_nogap.tar.gz</b> nogap150k_1000 nogap300k_1000 nogap50k_1000 nogap50k_10000 nogap50k_500<b>archive3_trained_keras.tar.gz</b><br>gap50k_1000<br>nogap150k_1000nogap300k_1000nogap50k_1000<br>
DOI: 10.6084/m9.figshare.8279618.v1
title: Archives

description: Each directory contains Training, Validation and Test datasets in fasta format. Directory names contain the following information about the MSAs: <br>1) Gap (w/ indels) or nogap (w/o indels) MSAs2) Number of MSAs per topology generated for training (i.e. 50k MSA * 3 possible topologies = 150k MSAs in TRAIN.fasta file) Order of topologies: 50k x ((D,A),B,C); 50k x ((D,B),A,C); 50k x ((D,C),A,B);3) MSA length (500, 1000 or 10000)<br>List of all directories:archive1_gap.tar.gz gap50k_1000 gap50k_10000 gap50k_500archive2_nogap.tar.gz nogap150k_1000 nogap300k_1000 nogap50k_1000 nogap50k_10000 nogap50k_500
DOI: 10.6084/m9.figshare.8279459
title: Metadata for Vaginal Microbiome OTU count data

description: Metadata for Vaginal Microbiome OTU count data
DOI: 10.6084/m9.figshare.8279459.v1
title: Metadata for Vaginal Microbiome OTU count data

description: Metadata for Vaginal Microbiome OTU count data
DOI: 10.6084/m9.figshare.8277626
title: Vaginal Microbiome OTU counts data

description: OTU count data for vaginal microbiome datasets
DOI: 10.6084/m9.figshare.8277623
title: Whole-genome sequencing metadata of Leptospira strains isolated from cattle in Uruguay

description: Metadata associated to 40 pathogenic Leptospira strains isolated from naturally infected cattle in Uruguay. These strains have been whole-genome sequenced.<br>
DOI: 10.6084/m9.figshare.8277623.v1
title: Whole-genome sequencing metadata of Leptospira strains isolated from cattle in Uruguay

description: Metadata associated to 40 pathogenic Leptospira strains isolated from naturally infected cattle in Uruguay. These strains have been whole-genome sequenced.<br>
DOI: 10.6084/m9.figshare.8277512
title: <i>Diaphorocetus poucheti</i> (Cetacea, Odontoceti, Physeteroidea) from Patagonia, Argentina: one of the earliest sperm whales

description: Sperm whales (Physeteroidea) are the basal-most surviving lineage of odontocetes, represented today by just three highly specialized, deep-diving suction feeders. By contrast, extinct sperm whales were relatively diverse, reflecting a major Miocene diversification into various suction feeding and macroraptorial forms. The beginnings of this diversification, however, remain poorly understood. The Atlantic coast of South America provides a crucial window into early physeteroid evolution and has yielded some of the oldest species known from cranial material, <i>Idiorophus patagonicus</i> and <i>Diaphorocetus poucheti</i> – both of which are in need of re-description and phylogenetic reappraisal. Here, we re-examine <i>Diaphorocetus</i> in detail and, in light of its complex taxonomic history, declare it a <i>nomen protectum</i>. Phylogenetically, the species forms part of a polytomy including ‘<i>Aulophyseter</i>’ <i>rionegresis</i> and the two crown lineages (Physeteridae and Kogiidae) and demonstrates that facial asymmetry and a clearly defined supracranial basin have characterized this lineage for at least 20 Ma. With a total body length of 3.5–4 m, <i>Diaphorocetus</i> is one of the smallest physeteroids yet known. Its cranial morphology hints at an intermediate raptorial/suction feeding strategy and it has a moderately developed spermaceti organ and junk.
DOI: 10.6084/m9.figshare.8277506
title: Vaccination with FAdV-8a induces protection against inclusion body hepatitis caused by homologous and heterologous strains

description: Fowl aviadenoviruses (FAdV) are important avian pathogens, responsible for several poultry diseases prevalent worldwide, including inclusion body hepatitis (IBH). FAdV intraspecies cross-protection has been clearly demonstrated, but there is little evidence that any interspecies cross-protection exists. The present study aimed to assess the inter- and intraspecies protection between three FAdV field isolates (FAdV-8a, FAdV-8b, FAdV-11) identified in association with severe IBH outbreaks. Inocula prepared using inactivated plaque-purified virus with adjuvant Montanide™ ISA 71VG, were injected intramuscularly into 3-week-old SPF chickens. At 6-weeks of age, the birds were challenged with 10<sup>6</sup> TCID<sub>50</sub> of homologous or heterologous virus intraperitoneally, and full <i>post mortem</i> examination performed at 4 days post-challenge. Various tissues were examined for gross and histological lesions and assessed for the presence of virus by PCR-HRM. All homologous-type vaccine/challenge groups exhibited protection against IBH lesions with no virus detected in the tissues. Unvaccinated groups challenged with virus showed evidence of FAdV-induced lesions; however, FAdV-8a demonstrated lower pathogenicity compared with FAdV-8b and FAdV-11. In the heterologous-type vaccine/challenge groups, FAdV-8a vaccine was shown to protect against challenge with both FAdV-8b and FAdV-11. FAdV-8a and 8b belong to species E and were therefore anticipated to cross-protect. However, FAdV-11 belongs to species D and therefore cross-protection by FAdV-8a was an uncharacteristic and unique finding of this study. Further research is required to disseminate the molecular basis for the interspecies cross-protection between FAdV-8a and FAdV-11. Nonetheless, the FAdV-8a isolate was shown to have substantial potential as a vaccine candidate in countries where FAdV-8a, 8b or 11 are prevalent.
DOI: 10.6084/m9.figshare.8277623.v3
title: Whole-genome sequencing metadata of Leptospira strains isolated from cattle in Uruguay

description: Metadata associated to 40 pathogenic Leptospira strains isolated from naturally infected cattle in Uruguay. These strains have been whole-genome sequenced.<br>