cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.31077382.v1
title: <b>Linking oxidative stress defense to biofilm architecture: Ohr mediates strain-dependent persistence in </b><b><i>Acinetobacter baumannii</i></b>

description: Biofilm formation is critical for the persistence of<i> Acinetobacter baumannii</i>, yet its directional correlation with antimicrobial resistance remains paradoxical. Here, we identify the organic hydroperoxide resistance protein (Ohr) as a master regulator that coordinates strain-specific biofilm strategies through dual mechanisms. Drug-sensitive and multidrug-resistant (MDR) strains employ distinct, temporally regulated biofilm developmental programs: susceptible strains excel at rapid biomass accumulation but undergo early collapse, while MDR strains delay biofilm initiation and optimize for the maintenance and reinforcement of mature biofilms. Transcriptomic profiling identified Ohr as a key determinant of this divergence, with its deletion resulting in severe biofilm defects. Metabolomics analyses further revealed that Ohr maintains biofilm integrity by modulating redox homeostasis and regulating extracellular polymeric substance (EPS) production through control of AdeAB and AdeFG efflux pumps. Moreover, we identified indole-3-lactic acid as a potent biofilm inhibitor. Our findings establish Ohr as a linchpin in <i>A. baumannii</i> biofilm development, elucidate the basis of temporal phenotypic divergence, and unveil promising therapeutic targets against biofilm-associated infections.
DOI: 10.6084/m9.figshare.31077382.v2
title: <b>Linking oxidative stress defense to biofilm architecture: Ohr mediates strain-dependent persistence in </b><b><i>Acinetobacter baumannii</i></b>

description: Biofilm formation is critical for the persistence of<i> Acinetobacter baumannii</i>, yet its directional correlation with antimicrobial resistance remains paradoxical. Here, we identify the organic hydroperoxide resistance protein (Ohr) as a master regulator that coordinates strain-specific biofilm strategies through dual mechanisms. Drug-sensitive and multidrug-resistant (MDR) strains employ distinct, temporally regulated biofilm developmental programs: susceptible strains excel at rapid biomass accumulation but undergo early collapse, while MDR strains delay biofilm initiation and optimize for the maintenance and reinforcement of mature biofilms. Transcriptomic profiling identified Ohr as a key determinant of this divergence, with its deletion resulting in severe biofilm defects. Metabolomics analyses further revealed that Ohr maintains biofilm integrity by modulating redox homeostasis and regulating extracellular polymeric substance (EPS) production through control of AdeAB and AdeFG efflux pumps. Moreover, we identified indole-3-lactic acid as a potent biofilm inhibitor. Our findings establish Ohr as a linchpin in <i>A. baumannii</i> biofilm development, elucidate the basis of temporal phenotypic divergence, and unveil promising therapeutic targets against biofilm-associated infections.
DOI: 10.15468/dl.chxyqr
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Homalium ceylanicum",
 "Year 1960-2010"
 ]
}

 The dataset includes 30 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013520-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dmeaza
title: Occurrence Download

description: A dataset containing 1621 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Cephalotaxus oliveri, Taiwania cryptomerioides)"
 ]
}

 The dataset includes 1621 records from 106 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013521-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc28g2qk
title: CCDC 2098908: Experimental Crystal Structure Determination

description: Related Article: Tales A. C. Goulart, Davi Fernando Back, Sidnei Moura E. Silva, Gilson Zeni|2022|J.Org.Chem.|87|3341|doi:10.1021/acs.joc.1c02978
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc28g2rl
title: CCDC 2098909: Experimental Crystal Structure Determination

description: Related Article: Tales A. C. Goulart, Davi Fernando Back, Sidnei Moura E. Silva, Gilson Zeni|2022|J.Org.Chem.|87|3341|doi:10.1021/acs.joc.1c02978
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc28g2sm
title: CCDC 2098910: Experimental Crystal Structure Determination

description: Related Article: Tales A. C. Goulart, Davi Fernando Back, Sidnei Moura E. Silva, Gilson Zeni|2022|J.Org.Chem.|87|3341|doi:10.1021/acs.joc.1c02978
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.34740/kaggle/dsv/14514735
title: World Weather Repository ( Daily Updating )
DOI: 10.15468/dl.ny5egw
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Eurya megatrichocarpa"
 ]
}

 The dataset includes 11 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013523-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hkemme
title: Occurrence Download

description: A dataset containing 59 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Populus alba",
 "Year 1970-2000"
 ]
}

 The dataset includes 59 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013525-260108223611665/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.30760130
title: Rethinking Urban Inefficient Land Identification and Optimization: A Case Study in Shenzhen, China

description: Identification and optimization of urban inefficient lands is an important policy of Chinese government to achieve high quality urban development. Currently, the mechanism for identifying inefficient lands is lack of scientific support, which affects the policy effectiveness. Previous studies focused on exploring optimization strategies for inefficient lands from the perspective of land use classification. Few studies directly considering the specific optimization sequence of those different parcels with the same land use function. To fill these gaps, this study develops a typology-based framework including five aspects (functional vitality, built environment, development suitability, spatial integration and economic intensity). We build an inefficient lands identification and optimization system using PCA, K-Means and Random Forest approaches. Taking Shenzhen as an example, a rapidly developing city in China, we validate our framework and methods. Three conspicuous aspects in this study were identified to facilitate decision-making: (1) The typology-based framework has high identification accuracy and it can reliably reflect the current state of urban inefficient lands in Shenzhen. (2) The encoded expression from the typology pedigree provides detailed information. It helps to develop customized optimization strategies for each parcel. (3) The typology pedigree combined with the random forest algorithm has broad application prospects in studying the specific optimization sequence. This case can serve as an effective benchmark for future urban redevelopment decisions, especially for other cities facing the challenges of rapid urbanization and optimization decisions.
DOI: 10.6084/m9.figshare.30760130.v2
title: Rethinking Urban Inefficient Land Identification and Optimization: A Case Study in Shenzhen, China

description: Identification and optimization of urban inefficient lands is an important policy of Chinese government to achieve high quality urban development. Currently, the mechanism for identifying inefficient lands is lack of scientific support, which affects the policy effectiveness. Previous studies focused on exploring optimization strategies for inefficient lands from the perspective of land use classification. Few studies directly considering the specific optimization sequence of those different parcels with the same land use function. To fill these gaps, this study develops a typology-based framework including five aspects (functional vitality, built environment, development suitability, spatial integration and economic intensity). We build an inefficient lands identification and optimization system using PCA, K-Means and Random Forest approaches. Taking Shenzhen as an example, a rapidly developing city in China, we validate our framework and methods. Three conspicuous aspects in this study were identified to facilitate decision-making: (1) The typology-based framework has high identification accuracy and it can reliably reflect the current state of urban inefficient lands in Shenzhen. (2) The encoded expression from the typology pedigree provides detailed information. It helps to develop customized optimization strategies for each parcel. (3) The typology pedigree combined with the random forest algorithm has broad application prospects in studying the specific optimization sequence. This case can serve as an effective benchmark for future urban redevelopment decisions, especially for other cities facing the challenges of rapid urbanization and optimization decisions.
DOI: 10.15468/dl.ux6qbq
title: Occurrence Download

description: A dataset containing 3775520 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Plantae, Undaria pinnatifida, Lindavia intermedia)",
 "Country is New Zealand",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 0",
 "DecimalLongitude is greater than or equal to -180",
 "DecimalLatitude is greater than or equal to -90",
 {
 "not" : {
 "or" : [
 "Issue is Zero coordinate",
 "Issue is Coordinate out of range",
 "Issue is Country coordinate mismatch"
 ]
 }
 }
 ]
}

 The dataset includes 3775520 records from 310 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013505-260108223611665/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.31073449.v1
title: RBT v1 atlas

description: Rabbit V1
DOI: 10.6084/m9.figshare.31073449
title: empty

description: Rabbit V1
DOI: 10.6084/m9.figshare.31073449.v3
title: empty

description: Rabbit V1
DOI: 10.6084/m9.figshare.31073449.v2
title: RBT v1 atlas

description: Rabbit V1
DOI: 10.15468/dl.akdgfr
title: Occurrence Download

description: A dataset containing 787 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Polygonum dissitiflorum"
 ]
}

 The dataset includes 787 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013526-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tw4sh3
title: Occurrence Download

description: A dataset containing 56 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Populus cathayana",
 "Year 1970-2000"
 ]
}

 The dataset includes 56 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013527-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yn7p6v
title: Occurrence Download

description: A dataset containing 914 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dipterocarpus grandiflorus"
 ]
}

 The dataset includes 914 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013528-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gr9467
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Eurya persicifolia"
 ]
}

 The dataset includes 18 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013529-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uwpfup
title: Occurrence Download

description: A dataset containing 1343 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Parachromis managuensis"
 ]
}

 The dataset includes 1343 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013530-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n5trxp
title: Occurrence Download

description: A dataset containing 231 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Cephalotaxus oliveri"
 ]
}

 The dataset includes 231 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013531-260108223611665/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.26370955
title: VEHoP: A Versatile, Easy-to-use, and Homology-based Phylogenomic pipeline accommodating diverse sequences

description: Supplementary data for "Reliable inference of phylogenomic relationship via assembly-based strategy accommodating raw reads and proteins", including: initial assembly results of the used datasets, the generated supermatrix, and original tree files.This attachment contains analysis results related to the Oyster dataset, with details of each file/folder as follows:<br>Data_size_1G folder: Corresponds to the analysis results of the Oyster dataset when subsampled to 1G. It includes assembly results, supermatrix files, and partition information files for this data volume.<br>Data_size_2G folder: Corresponds to the analysis results of the Oyster dataset when subsampled to 2G. It includes assembly results, supermatrix files, and partition information files for this data volume.<br>Data_size_4G folder: Corresponds to the analysis results of the Oyster dataset when subsampled to 4G. It includes assembly results, supermatrix files, and partition information files for this data volume.<br>Data_size_6G folder: Corresponds to the analysis results of the Oyster dataset when subsampled to 6G. It includes assembly results, supermatrix files, and partition information files for this data volume.<br>Data_size_8G folder: Corresponds to the analysis results of the Oyster dataset when subsampled to 8G. It includes assembly results, supermatrix files, and partition information files for this data volume.<br>Full-size folder: Corresponds to the analysis results of the complete Oyster dataset. It contains: high-quality genome protein files (and their matching matrices & partition files); full-volume next-generation sequencing data (plus the corresponding matrix & partition files); and RNA dataset files.<br>tree_files folder: Contains phylogenetic tree files constructed based on analysis results of the Oyster dataset (covering all data volumes).<br>Mollusca.six.fasta file: A FASTA-format protein alignment file used in this Oyster dataset analysis, containing 6 sequences of the Mollusca group (file size: 67,095 KB).
DOI: 10.6084/m9.figshare.26370955.v2
title: VEHoP: A Versatile, Easy-to-use, and Homology-based Phylogenomic pipeline accommodating diverse sequences

description: Phylogenomics has become a prominent method in systematics, conservation biology, and biomedicine, as it can leverage hundreds to thousands of genes derived from genomic or transcriptomic data to infer evolutionary relationships. However, obtaining high-quality genomes and transcriptomes requires samples preserved with high-quality DNA and RNA and demands considerable sequencing costs and lofty bioinformatic efforts (e.g., genome/transcriptome assembly and annotation). Notably, only fragmented DNA reads are accessible in some rare species due to the difficulty in sample collection and preservation, such as those inhabiting the deep sea. To address this issue, we here introduce the VEHoP (Versatile, Easy-to-use Homology-based Phylogenomic) pipeline, designed to infer protein-coding regions from DNA assemblies and generate alignments of orthologous sequences, concatenated matrices, and phylogenetic trees. This pipeline aims to 1) expand taxonomic sampling by accommodating a wide range of input files, including draft genomes, transcriptomes, and well-annotated genomes, and 2) simplify the process of conducting phylogenomic analyses and thus make it more accessible to researchers from diverse backgrounds. We first evaluated the performance of VEHoP using datasets of Ostreida, yielding robust phylogenetic trees with strong bootstrap support. We then applied VEHoP to reconstruct the phylogenetic relationship in the enigmatic deep-sea gastropod order Neomphalida, obtaining a robust phylogenetic backbone for this group. The VEHoP is freely available on GitHub (https://github.com/ylify/VEHoP), whose dependencies can be easily installed using Bioconda.
DOI: 10.6084/m9.figshare.26370955.v3
title: VEHoP: A Versatile, Easy-to-use, and Homology-based Phylogenomic pipeline accommodating diverse sequences

description: Supplementary data for "Reliable inference of phylogenomic relationship via assembly-based strategy accommodating raw reads and proteins", including: initial assembly results of the used datasets, the generated supermatrix, and original tree files.This attachment contains analysis results related to the Oyster dataset, with details of each file/folder as follows:<br>Data_size_1G folder: Corresponds to the analysis results of the Oyster dataset when subsampled to 1G. It includes assembly results, supermatrix files, and partition information files for this data volume.<br>Data_size_2G folder: Corresponds to the analysis results of the Oyster dataset when subsampled to 2G. It includes assembly results, supermatrix files, and partition information files for this data volume.<br>Data_size_4G folder: Corresponds to the analysis results of the Oyster dataset when subsampled to 4G. It includes assembly results, supermatrix files, and partition information files for this data volume.<br>Data_size_6G folder: Corresponds to the analysis results of the Oyster dataset when subsampled to 6G. It includes assembly results, supermatrix files, and partition information files for this data volume.<br>Data_size_8G folder: Corresponds to the analysis results of the Oyster dataset when subsampled to 8G. It includes assembly results, supermatrix files, and partition information files for this data volume.<br>Full-size folder: Corresponds to the analysis results of the complete Oyster dataset. It contains: high-quality genome protein files (and their matching matrices & partition files); full-volume next-generation sequencing data (plus the corresponding matrix & partition files); and RNA dataset files.<br>tree_files folder: Contains phylogenetic tree files constructed based on analysis results of the Oyster dataset (covering all data volumes).<br>Mollusca.six.fasta file: A FASTA-format protein alignment file used in this Oyster dataset analysis, containing 6 sequences of the Mollusca group (file size: 67,095 KB).
DOI: 10.15468/dl.bjmgpv
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Populus ciliata",
 "Year 1970-2000"
 ]
}

 The dataset includes 44 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013532-260108223611665/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.31076710
title: <b>The microalgae-bacteria symbiotic inoculation</b>

description: 干旱地区的土地退化，表现为沙质土壤结构崩解和功能衰退，限制了可持续发展。虽然微生物接种剂提供了恢复途径，但单株应用通常受限于环境适应性较差。设计上功能互补的微藻-细菌共生群落，利用其代谢协同和生态位互补的核心优势，展现出超越单一菌株的土壤修复潜力。它在促进生物土壤地壳形成、增强土壤稳定性和强化生态功能方面尤为有效。 然而，该联盟通过调控本土微生物网络的结构和稳定性来推动生态系统功能恢复的根本机制尚不清楚。在这里，我们构建了一个微藻-细菌共生群落，并通过微观实验结合风洞试验、高通量测序和分子生态网络分析来测试其效果。该联盟产生了协同效应，使植物地面生物量增加了110%，并增强了生物地壳的形成。因此，临界阈值风速从5.5米提升至11.9米s⁻¹，土壤多功能性较对照组提升了205%。胞外聚合物质（EPS）与土壤骨团稳定性呈强正相关（R² ≥ 0.66）。关键是，接种增强了确定性环境过滤（例如，将蓝藻的均匀选择提升至39.8%），并塑造了一个更简洁、更稳定的微生物共出现网络。 结构方程建模指出，网络稳定性而非复杂性是推动土壤多功能性及最终生态系统抗性的核心枢纽。我们的研究展示了理性设计的微生物联盟在生态恢复中的潜力，并为可预测微生物组工程的机制提供了新见解。
DOI: 10.6084/m9.figshare.31076710.v1
title: <b>The microalgae-bacteria symbiotic inoculation</b>

description: 干旱地区的土地退化，表现为沙质土壤结构崩解和功能衰退，限制了可持续发展。虽然微生物接种剂提供了恢复途径，但单株应用通常受限于环境适应性较差。设计上功能互补的微藻-细菌共生群落，利用其代谢协同和生态位互补的核心优势，展现出超越单一菌株的土壤修复潜力。它在促进生物土壤地壳形成、增强土壤稳定性和强化生态功能方面尤为有效。 然而，该联盟通过调控本土微生物网络的结构和稳定性来推动生态系统功能恢复的根本机制尚不清楚。在这里，我们构建了一个微藻-细菌共生群落，并通过微观实验结合风洞试验、高通量测序和分子生态网络分析来测试其效果。该联盟产生了协同效应，使植物地面生物量增加了110%，并增强了生物地壳的形成。因此，临界阈值风速从5.5米提升至11.9米s⁻¹，土壤多功能性较对照组提升了205%。胞外聚合物质（EPS）与土壤骨团稳定性呈强正相关（R² ≥ 0.66）。关键是，接种增强了确定性环境过滤（例如，将蓝藻的均匀选择提升至39.8%），并塑造了一个更简洁、更稳定的微生物共出现网络。 结构方程建模指出，网络稳定性而非复杂性是推动土壤多功能性及最终生态系统抗性的核心枢纽。我们的研究展示了理性设计的微生物联盟在生态恢复中的潜力，并为可预测微生物组工程的机制提供了新见解。
DOI: 10.15468/dl.w2geth
title: Occurrence Download

description: A dataset containing 691 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is 2025_doosanbobcat_bioblitz_naturing"
 ]
}

 The dataset includes 691 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013533-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2t9uv3
title: Occurrence Download

description: A dataset containing 259595 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Salmo salar",
 "Country is Canada",
 "HasCoordinate is true"
 ]
}

 The dataset includes 259595 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013514-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.