cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30026656
title: Additional file 1 of Exploring the potential bioactive compounds group and mechanism of Ci Bai Capsule in treating leukopenia: a combined approach of network pharmacology and transcriptome evidences

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.30026656.v1
title: Additional file 1 of Exploring the potential bioactive compounds group and mechanism of Ci Bai Capsule in treating leukopenia: a combined approach of network pharmacology and transcriptome evidences

description: Supplementary Material 1.
DOI: 10.15468/dl.ek76q7
title: Occurrence Download

description: A dataset containing 4240431 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "License is one of (CC0 1.0, CC-BY 4.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 4240431 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017766-250827131500795/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.30019228.v1
title: 低密度脂蛋白胆固醇相关遗传变量数据

description: 该文件包含三个工作表，每个工作表记录不同的信息。补充表1提供了与低密度脂蛋白胆固醇（LDL胆固醇）相关的遗传工具变量的信息，这些变量位于HMGCR，PCSK9，NPC1L1，APOB，CETP或LDLR基因的100kb窗口内，涵盖染色体，碱基对，效应等位基因，其他等位基因，效应等位基因频率，β值，标准误差，p值和多个SNP（如rs12916，rs11591147等）的F统计数据;
DOI: 10.6084/m9.figshare.30026676
title: Additional file 3 of U-FISH: a fluorescent spot detector for imaging-based spatial-omics analysis and AI-assisted FISH diagnosis

description: Additional file 3: U-FISH Dataset Metadata Table.
DOI: 10.6084/m9.figshare.30026676.v1
title: Additional file 3 of U-FISH: a fluorescent spot detector for imaging-based spatial-omics analysis and AI-assisted FISH diagnosis

description: Additional file 3: U-FISH Dataset Metadata Table.
DOI: 10.15468/dl.dq64g2
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Guizotia abyssinica",
 "Country is Japan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017779-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2464xq
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Rineloricaria jaraguensis)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 17 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017778-250827131500795/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.30026686
title: Additional file 1 of Virulence and diversity of Blumeria graminis f. sp. tritici populations in Henan Province, China

description: Additional file 1: Table S1. Isolates of B. graminis f. sp. tritici from Henan Province from 2011 to 2020. Table S2. Virulence frequency of B. graminis f. sp. tritici from Henan Province from 2011 to 2020. Table S3. Distribution of pathotypes of B. graminis f. sp. tritici in Henan Province, 2011~2020. Table S4. Isolates of B. graminis f. sp. tritici used for SSR marker analysis in 2020. Table S5. SSR primers used for PCR amplification.
DOI: 10.6084/m9.figshare.30026686.v1
title: Additional file 1 of Virulence and diversity of Blumeria graminis f. sp. tritici populations in Henan Province, China

description: Additional file 1: Table S1. Isolates of B. graminis f. sp. tritici from Henan Province from 2011 to 2020. Table S2. Virulence frequency of B. graminis f. sp. tritici from Henan Province from 2011 to 2020. Table S3. Distribution of pathotypes of B. graminis f. sp. tritici in Henan Province, 2011~2020. Table S4. Isolates of B. graminis f. sp. tritici used for SSR marker analysis in 2020. Table S5. SSR primers used for PCR amplification.
DOI: 10.6084/m9.figshare.30026707
title: Additional file 1 of Antimicrobial susceptibility of Legionella gormanii: species-specific ECOFFs, distinct MICs for rifampin versus Legionella pneumophila

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.30026707.v1
title: Additional file 1 of Antimicrobial susceptibility of Legionella gormanii: species-specific ECOFFs, distinct MICs for rifampin versus Legionella pneumophila

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.30026710.v1
title: Additional file 2 of Antimicrobial susceptibility of Legionella gormanii: species-specific ECOFFs, distinct MICs for rifampin versus Legionella pneumophila

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.30026710
title: Additional file 2 of Antimicrobial susceptibility of Legionella gormanii: species-specific ECOFFs, distinct MICs for rifampin versus Legionella pneumophila

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.30026724.v1
title: Additional file 2 of Integrated metabolomics and the microbiome reveal the compatibility mechanism of the Suxiao Jiuxin pill in the treatment of stable coronary artery disease

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.30026724
title: Additional file 2 of Integrated metabolomics and the microbiome reveal the compatibility mechanism of the Suxiao Jiuxin pill in the treatment of stable coronary artery disease

description: Supplementary Material 2.
DOI: 10.15468/dl.pk9hku
title: Occurrence Download

description: A dataset containing 1419 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ranunculus millefoliatus"
 ]
}

 The dataset includes 1419 records from 102 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017781-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6byrr6
title: Occurrence Download

description: A dataset containing 49268 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Material sample, Material citation, Specimen, Living Specimen, Occurrence evidence)",
 "MediaType is Image",
 "TaxonKey is Dermaptera"
 ]
}

 The dataset includes 49268 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017780-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16975469
title: Computational approaches for virus host prediction: A review of methods and applications

description: By providing a rigorous, comparative analysis, this review serves two critical functions. First, it acts as a practical guide for researchers selecting the optimal tool for their work. Second, it establishes a foundational resource and a new performance benchmark intended to drive the next wave of innovation in deciphering the complex web of virus-host interactions.


Our key contributions are:


1. **A standardized problem formulation:** We establish a structured framework for the virus-host prediction problem, providing a consistent foundation for understanding and comparing diverse computational strategies.


2. **A comprehensive survey of tools and biological features:** We critically evaluate 27 existing tools, analyzing their methodologies, strengths, and weaknesses. We then survey the full spectrum of biological features they employed, from CRISPR spacer matching and prophage detection to alignment-free $k$-mer frequency analysis.


3. **Rigorous benchmarking using carefully designed datasets:** Another key novelty is the development and application of two distinct evaluation benchmarks. **RefSeq-VHDB** provides a curated set of phage-host pairs for standardized assessment, while **MetaHiC-VHDB** consists of three independent metagenomic Hi-C test sets designed to assess tool performance in realistic ecological contexts. These benchmarks provide a practical guide for researchers and expose performance gaps that future methods must address.


## Instructions


This repository store the results reported in the paper. There are four main folder:


* Data: The raw data used in the experiments, including sequences and CSV files

* Benchmark: The scripts/commands to run the host prediction tools and their outputs. We also provide a NoteBook to generate the results reported in the paper.

* FeatureExploration: The intermidiate files for analyze biological features. We also provide a NoteBook to generate the results reported in the paper.

* Figures: The figures used in the paper.




### Reproduce results

To reproduce the results, you should install some basic packages for your Python Environment.```conda install ete3 pandas matplotlib numpy tqdm upsetplotORpip install ete3 pandas matplotlib numpy tqdm upsetplot

```




Detiled information can be found via the README in each folder.


### Contacts and bug reports

Please feel free to send bug reports or questions to us. You can post an issue or directly email me (jiayushang@cuhk.edu.hk).
DOI: 10.5281/zenodo.16975470
title: Computational approaches for virus host prediction: A review of methods and applications

description: By providing a rigorous, comparative analysis, this review serves two critical functions. First, it acts as a practical guide for researchers selecting the optimal tool for their work. Second, it establishes a foundational resource and a new performance benchmark intended to drive the next wave of innovation in deciphering the complex web of virus-host interactions.


Our key contributions are:


1. **A standardized problem formulation:** We establish a structured framework for the virus-host prediction problem, providing a consistent foundation for understanding and comparing diverse computational strategies.


2. **A comprehensive survey of tools and biological features:** We critically evaluate 27 existing tools, analyzing their methodologies, strengths, and weaknesses. We then survey the full spectrum of biological features they employed, from CRISPR spacer matching and prophage detection to alignment-free $k$-mer frequency analysis.


3. **Rigorous benchmarking using carefully designed datasets:** Another key novelty is the development and application of two distinct evaluation benchmarks. **RefSeq-VHDB** provides a curated set of phage-host pairs for standardized assessment, while **MetaHiC-VHDB** consists of three independent metagenomic Hi-C test sets designed to assess tool performance in realistic ecological contexts. These benchmarks provide a practical guide for researchers and expose performance gaps that future methods must address.


## Instructions


This repository store the results reported in the paper. There are four main folder:


* Data: The raw data used in the experiments, including sequences and CSV files

* Benchmark: The scripts/commands to run the host prediction tools and their outputs. We also provide a NoteBook to generate the results reported in the paper.

* FeatureExploration: The intermidiate files for analyze biological features. We also provide a NoteBook to generate the results reported in the paper.

* Figures: The figures used in the paper.




### Reproduce results

To reproduce the results, you should install some basic packages for your Python Environment.```conda install ete3 pandas matplotlib numpy tqdm upsetplotORpip install ete3 pandas matplotlib numpy tqdm upsetplot

```




Detiled information can be found via the README in each folder.


### Contacts and bug reports

Please feel free to send bug reports or questions to us. You can post an issue or directly email me (jiayushang@cuhk.edu.hk).
DOI: 10.6084/m9.figshare.30026760
title: Additional file 2 of A harbor seal (Phoca vitulina) shows extensive respiratory control in sound production

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.30026760.v1
title: Additional file 2 of A harbor seal (Phoca vitulina) shows extensive respiratory control in sound production

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.30026784
title: Additional file 2 of Ignimbrite flare-up in Late Cretaceous–Paleocene Japan empowered by hot mantle inflow

description: Additional file 2.
DOI: 10.6084/m9.figshare.30026784.v1
title: Additional file 2 of Ignimbrite flare-up in Late Cretaceous–Paleocene Japan empowered by hot mantle inflow

description: Additional file 2.
DOI: 10.6084/m9.figshare.30026790.v1
title: Additional file 4 of Ignimbrite flare-up in Late Cretaceous–Paleocene Japan empowered by hot mantle inflow

description: Additional file 4.
DOI: 10.6084/m9.figshare.30026790
title: Additional file 4 of Ignimbrite flare-up in Late Cretaceous–Paleocene Japan empowered by hot mantle inflow

description: Additional file 4.
DOI: 10.6084/m9.figshare.30026812
title: Additional file 9 of Transforming growth factor beta (TGF-β) induces type 1 interferon signalling in systemic sclerosis keratinocytes through the chloride intracellular channel 4 (CLIC4)

description: Supplementary Material 9.
DOI: 10.6084/m9.figshare.30026812.v1
title: Additional file 9 of Transforming growth factor beta (TGF-β) induces type 1 interferon signalling in systemic sclerosis keratinocytes through the chloride intracellular channel 4 (CLIC4)

description: Supplementary Material 9.
DOI: 10.6084/m9.figshare.30026817
title: Additional file 2 of Phylogenetically and metabolically diverse active carbon-fixing microbes reside in mangrove sediments

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.30026817.v1
title: Additional file 2 of Phylogenetically and metabolically diverse active carbon-fixing microbes reside in mangrove sediments

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.30026823
title: Additional file 2 of PKP1 promotes lung cancer by modulating energy metabolism through stabilization of PFKP

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.30026823.v1
title: Additional file 2 of PKP1 promotes lung cancer by modulating energy metabolism through stabilization of PFKP

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.30026826
title: Additional file 3 of PKP1 promotes lung cancer by modulating energy metabolism through stabilization of PFKP

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.30026826.v1
title: Additional file 3 of PKP1 promotes lung cancer by modulating energy metabolism through stabilization of PFKP

description: Supplementary Material 3
DOI: 10.15468/dl.mh8knz
title: Occurrence Download

description: A dataset containing 377 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ranunculus microphyllus"
 ]
}

 The dataset includes 377 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017782-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2tcxz8
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hieracium glaucum"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017783-250827131500795/datasets/export for details.
DOI: 10.6084/m9.figshare.30026893
title: Additional file 1 of Dissociable impacts of physical and psychological factors on side effects after COVID-19 vaccination in Japan: A within-subject repeated measures design

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.30026893.v1
title: Additional file 1 of Dissociable impacts of physical and psychological factors on side effects after COVID-19 vaccination in Japan: A within-subject repeated measures design

description: Supplementary Material 1.
DOI: 10.15468/dl.m7g8cv
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Guizotia abyssinica",
 "Country is Mexico",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017784-250827131500795/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.30026905
title: Additional file 1 of Comparison of the readability of ChatGPT and Bard in medical communication: a meta-analysis

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.30026905.v1
title: Additional file 1 of Comparison of the readability of ChatGPT and Bard in medical communication: a meta-analysis

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.30026908
title: Additional file 2 of Comparison of the readability of ChatGPT and Bard in medical communication: a meta-analysis

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.30026908.v1
title: Additional file 2 of Comparison of the readability of ChatGPT and Bard in medical communication: a meta-analysis

description: Supplementary Material 2
DOI: 10.15468/dl.gnjez6
title: Occurrence Download

description: A dataset containing 839 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Guizotia abyssinica",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 839 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017785-250827131500795/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.30026895
title: Additional file 1 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S1
DOI: 10.6084/m9.figshare.30026895.v1
title: Additional file 1 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S1
DOI: 10.6084/m9.figshare.30026898
title: Additional file 2 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S2
DOI: 10.6084/m9.figshare.30026898.v1
title: Additional file 2 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S2
DOI: 10.6084/m9.figshare.30026901
title: Additional file 3 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S3
DOI: 10.6084/m9.figshare.30026901.v1
title: Additional file 3 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S3
DOI: 10.6084/m9.figshare.30026904
title: Additional file 4 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S4
DOI: 10.6084/m9.figshare.30026904.v1
title: Additional file 4 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S4
DOI: 10.6084/m9.figshare.30026907
title: Additional file 5 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S5
DOI: 10.6084/m9.figshare.30026907.v1
title: Additional file 5 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S5
DOI: 10.6084/m9.figshare.30026910
title: Additional file 6 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S6
DOI: 10.6084/m9.figshare.30026910.v1
title: Additional file 6 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S6
DOI: 10.6084/m9.figshare.30026916
title: Additional file 7 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S7
DOI: 10.6084/m9.figshare.30026916.v1
title: Additional file 7 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S7
DOI: 10.6084/m9.figshare.30026919
title: Additional file 8 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S8
DOI: 10.6084/m9.figshare.30026919.v1
title: Additional file 8 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S8
DOI: 10.6084/m9.figshare.30026922
title: Additional file 9 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S9
DOI: 10.6084/m9.figshare.30026922.v1
title: Additional file 9 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S9
DOI: 10.6084/m9.figshare.30026925
title: Additional file 10 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S10
DOI: 10.6084/m9.figshare.30026925.v1
title: Additional file 10 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S10
DOI: 10.6084/m9.figshare.30026928
title: Additional file 11 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S11
DOI: 10.6084/m9.figshare.30026928.v1
title: Additional file 11 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S11
DOI: 10.6084/m9.figshare.30026931
title: Additional file 12 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S12
DOI: 10.6084/m9.figshare.30026931.v1
title: Additional file 12 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S12
DOI: 10.6084/m9.figshare.30026934
title: Additional file 13 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S13
DOI: 10.6084/m9.figshare.30026934.v1
title: Additional file 13 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S13
DOI: 10.6084/m9.figshare.30026937
title: Additional file 14 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S14
DOI: 10.6084/m9.figshare.30026937.v1
title: Additional file 14 of Circadian disruption and ROS-NLRP3 signaling mediate sleep deprivation-enhanced silica nanoparticle toxicity in lacrimal glands

description: Table S14