cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.tzn7pd
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "MULTIPOLYGON (((148.326832 -34.361257, 148.326832 -34.363502, 148.32234 -34.363502, 148.32234 -34.37024, 148.335815 -34.37024, 148.335815 -34.374731, 148.331323 -34.374731, 148.331323 -34.376977, 148.335815 -34.376977, 148.335815 -34.379223, 148.338061 -34.379223, 148.338061 -34.38596, 148.347044 -34.38596, 148.347044 -34.390452, 148.351535 -34.390452, 148.351535 -34.38596, 148.353781 -34.38596, 148.353781 -34.383715, 148.351535 -34.383715, 148.351535 -34.379223, 148.344798 -34.379223, 148.344798 -34.383715, 148.342552 -34.383715, 148.342552 -34.376977, 148.344798 -34.376977, 148.344798 -34.37024, 148.347044 -34.37024, 148.347044 -34.376977, 148.351535 -34.376977, 148.351535 -34.37024, 148.360519 -34.37024, 148.360519 -34.367994, 148.353781 -34.367994, 148.353781 -34.363502, 148.351535 -34.363502, 148.351535 -34.365748, 148.347044 -34.365748, 148.347044 -34.363502, 148.342552 -34.363502, 148.342552 -34.367994, 148.338061 -34.367994, 148.338061 -34.363502, 148.331323 -34.363502, 148.331323 -34.361257, 148.326832 -34.361257)), ((148.338061 -34.38596, 148.335815 -34.38596, 148.335815 -34.390452, 148.338061 -34.390452, 148.338061 -34.38596)), ((148.351535 -34.379223, 148.360519 -34.379223, 148.360519 -34.374731, 148.358273 -34.374731, 148.358273 -34.376977, 148.351535 -34.376977, 148.351535 -34.379223)))"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071066-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.26637606.v1
title: Additional file 3 of Longitudinal metagenomic study reveals the dynamics of fecal antibiotic resistome in pigs throughout the lifetime

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.26637618
title: Additional file 7 of Longitudinal metagenomic study reveals the dynamics of fecal antibiotic resistome in pigs throughout the lifetime

description: Supplementary Material 7
DOI: 10.6084/m9.figshare.26639608
title: Additional file 9 of Oncogenic activation revealed by FGFR2 genetic alterations in intrahepatic cholangiocarcinomas

description: Additional file 9: 65 FGFR2 in-frame deletions cases searched in total 91,129 cases.
DOI: 10.6084/m9.figshare.26637609.v1
title: Additional file 4 of Longitudinal metagenomic study reveals the dynamics of fecal antibiotic resistome in pigs throughout the lifetime

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.26639497
title: Additional file 6 of MBD4 loss results in global reactivation of promoters and retroelements with low methylated CpG density

description: Additional file 6: Supplementary Table 5. Listing of the most significantly deregulated genes (|fc|&gt;2 and P &lt; 0.01) in absence of MBD4. The following information are indicated for each deregulated gene: Ensemble gene id, raw read counts (KOrep1, KOrep2, WTrep1, WTrep2), normalized read counts (KOrep1, KOrep2, WTrep1, WTrep2), fold change (log2-ratio KO/WT), p-value, p-value adjusted for multi-testing, gene name, gene description.
DOI: 10.5281/zenodo.10999820
title: Molecular simulation-based 3D structural construction of olfactory receptor with agonist binding

description: The structure of representative LSD No. 3, the structure of representative LSD No. 6, the structure of representative LSD No. 7, the initial structure of OR9Q2, SMILES of decoys used for docking, the python script of LSD analysis, the parameter file of colabfold, the output file of CHARMM-GUI, the parameter file of virtual screening test and the parameter file of production MD are deposited in this dataset.
DOI: 10.5281/zenodo.13328860
title: Molecular simulation-based 3D structural construction of olfactory receptor with agonist binding

description: The structure of representative LSD No. 3, the structure of representative LSD No. 6, the structure of representative LSD No. 7, the initial structure of OR9Q2, SMILES of decoys used for docking, the python script of LSD analysis, the parameter file of colabfold, the output file of CHARMM-GUI, the parameter file of virtual screening test and the parameter file of production MD are deposited in this dataset.
DOI: 10.6084/m9.figshare.24547047
title: Additional file 2 of Skeletal muscle regeneration failure in ischemic-damaged limbs is associated with pro-inflammatory macrophages and premature differentiation of satellite cells

description: Additional file 2: Table S1. List of PCR primers used in this study.
DOI: 10.6084/m9.figshare.26724041.v1
title: Additional file 2 of The mRNA surveillance factor Pelo restricts rice virus propagation in insect vectors and host plants

description: Additional file 2: Table S1. The primers used in this study.
DOI: 10.3886/e113705
title: Replication data for: The Neighborhood Impacts of Local Infrastructure Investment: Evidence from Urban Mexico

description: This paper reports on the results of a large infrastructure investment experiment in which $68 million in spending was randomly allocated across a set of low-income urban neighborhoods in Mexico. We show that the program resulted in substantial improvements in access to infrastructure and increases in private investment in housing. While a pre-committed index of social capital did not improve, we find an apparent decrease in the incidence of personal assault and teen misbehavior in neighborhoods where investments were made. The program increased the aggregate real estate value in program neighborhoods by two dollars for every dollar invested.
DOI: 10.3886/e113705v1-156029
title: Replication data for: The Neighborhood Impacts of Local Infrastructure Investment: Evidence from Urban Mexico

description: This paper reports on the results of a large infrastructure investment experiment in which $68 million in spending was randomly allocated across a set of low-income urban neighborhoods in Mexico. We show that the program resulted in substantial improvements in access to infrastructure and increases in private investment in housing. While a pre-committed index of social capital did not improve, we find an apparent decrease in the incidence of personal assault and teen misbehavior in neighborhoods where investments were made. The program increased the aggregate real estate value in program neighborhoods by two dollars for every dollar invested.
DOI: 10.6084/m9.figshare.26638314
title: Additional file 4 of Skeletal muscle regeneration failure in ischemic-damaged limbs is associated with pro-inflammatory macrophages and premature differentiation of satellite cells

description: Additional file 4: Table S3. The top 20 marker genes for each sub-cluster of macrophages shown in Additional file 1: Figs S3A and B. Related to Fig. 3 and Additional file 1: Fig S3.
DOI: 10.6084/m9.figshare.26639500
title: Additional file 7 of MBD4 loss results in global reactivation of promoters and retroelements with low methylated CpG density

description: Additional file 7: Supplementary Table 6. Listing of the most significantly differentially methylated regions (DMR, P &lt; 0.01) between MEFs WT and KO for Mbd4. The following information are indicated for each DMR: genomic annotation, methylation rate (KO, WT, WT/KO) and variation (KO, WT), coverage depth and variation (KO, WT), number of CpG, number of uncovered CpG (KO, WT).
DOI: 10.6084/m9.figshare.26639509.v1
title: Additional file 9 of MBD4 loss results in global reactivation of promoters and retroelements with low methylated CpG density

description: Additional file 9: Supplementary Table 9. Genome-wide transcriptome analyses of repetitive elements. This table list each mouse repeat family with the following informations: Repeat-Masker family name, raw read counts (KOrep1, KOrep2, WTrep1, WTrep2), normalized read counts (KOrep1, KOrep2, WTrep1, WTrep2), base mean, log2-ratio (KO/WT), p-value, p-value adjusted for multi-testing.
DOI: 10.6084/m9.figshare.26724059.v1
title: Additional file 6 of Complete series method (CSM): a convenient method to reduce daily heterogeneity when evaluating the regeneration time (RT) of insecticide-treated nets (ITNs)

description: Supplementary Material 6. Dataset S2. WHO longitudinal method second round.
DOI: 10.6084/m9.figshare.26638431.v1
title: Additional file 2 of Sex-differences in proteasome-dependent K48-polyubiquitin signaling in the amygdala are developmentally regulated in rats

description: Additional file 2. Proteomics data.
DOI: 10.6084/m9.figshare.26638467
title: Additional file 6 of Exploration of biomarkers for systemic lupus erythematosus by machine-learning analysis

description: Additional file 6: Table S6. 214 overlapping genes from WGCNA and DEGs.
DOI: 10.6084/m9.figshare.26638467.v1
title: Additional file 6 of Exploration of biomarkers for systemic lupus erythematosus by machine-learning analysis

description: Additional file 6: Table S6. 214 overlapping genes from WGCNA and DEGs.
DOI: 10.6084/m9.figshare.26638587.v1
title: Additional file 3 of Photoactivated chromophore-corneal cross-linking accelerates corneal healing in fungal keratitis: an updated meta-analysis

description: Additional file 3: Supplementary material 3. Data extraction.
DOI: 10.5519/qd.gofpq32y
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (2056 records)
DOI: 10.15468/dl.z3w2zp
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.767008 -34.379223, 148.767008 -34.38596, 148.7715 -34.38596, 148.7715 -34.383715, 148.773746 -34.383715, 148.773746 -34.379223, 148.767008 -34.379223))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071067-240626123714530/datasets/export for details.
DOI: 10.6084/m9.figshare.26638602
title: Additional file 3 of Anti-tumor activity of all-trans retinoic acid in gastric-cancer: gene-networks and molecular mechanisms

description: Additional file 3: Table S4. RNA-sequencing data. The table contains the processed RNA-seq data obtained with our panel of gastric cancer cell-lines exposed to vehicle and ATRA.
DOI: 10.6084/m9.figshare.26638605
title: Additional file 4 of Anti-tumor activity of all-trans retinoic acid in gastric-cancer: gene-networks and molecular mechanisms

description: Additional file 4: Table S5. Effects of ATRA on the expression of the RNAs derived from endogenous retroviruses. The table contains the levels of endogenous retroviral RNAs determined by RNA-seq data obtained from the indicated cell lines exposed to vehicle and ATRA.
DOI: 10.6084/m9.figshare.26639689
title: Additional file 4 of Genetic diversity, linkage disequilibrium, and population structure of tetraploid wheat landraces originating from Europe and Asia

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.26240582
title: Supplementary datasets for Interactions with cetaceans fueled the evolution of fish endothermy

description: Endothermy has independently evolved in several vertebrate lineages but remains rare among fishes. Using an integrated approach combining phylogenomic and ecomorphological data, including body size, swimming mode, depth range, and diet for 1,051 ray-finned fishes, coupled with a newly developed time-dependent evolutionary model and comparative genomic analyses of 205 marine vertebrates, we propose that ecological interactions with modern cetaceans coincided with the evolution of endothermy in ray-finned fishes during the Eocene–Miocene. This result is further supported by evidence of temporal and geographical overlap between cetaceans and endothermic fish lineages in the fossil record, as well as correlations between cetacean fossil and extant diversification patterns and the origin or endothermy in fishes. Phylogenetic comparative analyses also identified significant correlations between the origins of endothermy and large body sizes as well as specialized swimming modes while challenging hypotheses focusing on specialized diets and depth range expansion. Comparative genomic analyses identified 51 orthologous genes under positive selection related to metabolism, muscle function, and neural responses, showing convergence across major lineages of endothermic marine vertebrates, including key genes like carnmt1 and dcaf6. Our findings advance the understanding of how ecological interactions and genomic factors shape the evolution of innovative adaptations in the oceans.
DOI: 10.6084/m9.figshare.26724110.v1
title: Additional file 3 of An RNA-seq study in Friedreich ataxia patients identified hsa-miR-148a-3p as a putative prognostic biomarker of the disease

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.26240582.v9
title: Supplementary datasets for Ecological interactions and genomic innovations fueled evolution of fish endothermy

description: Endothermy has independently evolved in several vertebrate lineages but remains rare among fishes. Using an integrated approach combining phylogenomic and ecomorphological data, including body size, swimming mode, depth range, and diet for 1,051 ray-finned fishes, coupled with a newly developed time-dependent evolutionary model and comparative genomic analyses of 205 marine vertebrates, we propose that ecological interactions with modern cetaceans coincided with the evolution of endothermy in ray-finned fishes during the Eocene–Miocene. This result is further supported by evidence of temporal and geographical overlap between cetaceans and endothermic fish lineages in the fossil record, as well as correlations between cetacean fossil and extant diversification patterns and the origin or endothermy in fishes. Phylogenetic comparative analyses also identified significant correlations between the origins of endothermy and large body sizes as well as specialized swimming modes while challenging hypotheses focusing on specialized diets and depth range expansion. Comparative genomic analyses identified 51 orthologous genes under positive selection related to metabolism, muscle function, and neural responses, showing convergence across major lineages of endothermic marine vertebrates, including key genes like carnmt1 and dcaf6. Our findings advance the understanding of how ecological interactions and genomic factors shape the evolution of innovative adaptations in the oceans.
DOI: 10.6084/m9.figshare.26724116.v1
title: Additional file 5 of An RNA-seq study in Friedreich ataxia patients identified hsa-miR-148a-3p as a putative prognostic biomarker of the disease

description: Supplementary Material 5
DOI: 10.15156/bio/sh0196700.10fu
title: SH0196700.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0196701.10fu
title: SH0196701.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0196702.10fu
title: SH0196702.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0196703.10fu
title: SH0196703.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0196704.10fu
title: SH0196704.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0196705.10fu
title: SH0196705.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0196706.10fu
title: SH0196706.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0196707.10fu
title: SH0196707.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.