cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.jg8fbd
title: Occurrence Download

description: A dataset containing 69 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cupha myronides (Felder, 1867)"
 ]
}

 The dataset includes 69 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011686-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7sxhhk
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "DatasetKey is iNaturalist Research-grade Observations",
 "GadmGid is CAN.11_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Sturnella magna (Linnaeus, 1758)",
 "Year 1990-2024"
 ]
}

 The dataset includes 55 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011687-241107131044228/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.27683759
title: Additional file 3 of TRIM28 regulates the coagulation cascade inhibited by p72 of African swine fever virus

description: Additional file 3. GO terms and corresponding proteins of p72-interacting partners.
DOI: 10.6084/m9.figshare.27683759.v1
title: Additional file 3 of TRIM28 regulates the coagulation cascade inhibited by p72 of African swine fever virus

description: Additional file 3. GO terms and corresponding proteins of p72-interacting partners.
DOI: 10.6084/m9.figshare.27683765
title: Additional file 5 of TRIM28 regulates the coagulation cascade inhibited by p72 of African swine fever virus

description: Additional file 5. Protein accession numbers and descriptions of p72-interacting partners.
DOI: 10.6084/m9.figshare.27683762.v1
title: Additional file 4 of TRIM28 regulates the coagulation cascade inhibited by p72 of African swine fever virus

description: Additional file 4. KEGG pathways and corresponding proteins associated with p72-interacting partners.
DOI: 10.6084/m9.figshare.27683765.v1
title: Additional file 5 of TRIM28 regulates the coagulation cascade inhibited by p72 of African swine fever virus

description: Additional file 5. Protein accession numbers and descriptions of p72-interacting partners.
DOI: 10.6084/m9.figshare.27683762
title: Additional file 4 of TRIM28 regulates the coagulation cascade inhibited by p72 of African swine fever virus

description: Additional file 4. KEGG pathways and corresponding proteins associated with p72-interacting partners.
DOI: 10.5281/zenodo.14123358
title: Mussel attachment geometric models

description: The provided data includes the geometric model files (in STL format) of fouling mussel (Limnoperna fortunei) attachment. The geometric model of an individual adult mussel was generated in Blender. Considering the size of an individual adult mussel (about 20 mm), a 20 cm × 20 cm plane was selected to place a certain density of mussels. The density of the attachment model was set from 500 ind/m2 to 20,000 ind/m2. The location and orientation of each individual mussel was randomly placed on the plane, and three replicates were provided. Besides, the mussel attachment considered the mussel size distributions based on the sampling data from South China and North China.
DOI: 10.5281/zenodo.14123357
title: Mussel attachment geometric models

description: The provided data includes the geometric model files (in STL format) of fouling mussel (Limnoperna fortunei) attachment. The geometric model of an individual adult mussel was generated in Blender. Considering the size of an individual adult mussel (about 20 mm), a 20 cm × 20 cm plane was selected to place a certain density of mussels. The density of the attachment model was set from 500 ind/m2 to 20,000 ind/m2. The location and orientation of each individual mussel was randomly placed on the plane, and three replicates were provided. Besides, the mussel attachment considered the mussel size distributions based on the sampling data from South China and North China.
DOI: 10.5281/zenodo.14125516
title: Firemaker_words
DOI: 10.5281/zenodo.14125517
title: Firemaker_words
DOI: 10.15468/dl.4wfqjd
title: Occurrence Download

description: A dataset containing 350 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Agropyron cristatum (L.) Gaertn.",
 "Year 1970-2024"
 ]
}

 The dataset includes 350 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011688-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14125776
title: IAM_words
DOI: 10.5281/zenodo.14125777
title: IAM_words
DOI: 10.5281/zenodo.7840235
title: Supplementary files: LoxCode in vivo barcoding resolves epiblast clonal fate to fetal organs

description: Supplementary files (raw and processed data files, C++ code) related to the manuscript: LoxCode in vivo barcoding resolves epiblast clonal fate to fetal organs (Tom S. Weber, Christine Biben, Denise C. Miles, Stefan Glaser, Sara Tomei, Stephen Zhang, Patrick P. L. Tam, Samir Taoudi, Shalin H. Naik)
DOI: 10.5281/zenodo.14089542
title: Supplementary files: LoxCode in vivo barcoding resolves epiblast clonal fate to fetal organs

description: Supplementary files (raw and processed data files, C++ code) related to the manuscript: LoxCode in vivo barcoding resolves epiblast clonal fate to fetal organs (Tom S. Weber, Christine Biben, Denise C. Miles, Stefan Glaser, Sara Tomei, Michael Lin, Andrew Kueh, Martin Pal, Stephen Zhang, Patrick P. L. Tam, Samir Taoudi, Shalin H. Naik)
DOI: 10.5281/zenodo.7840234
title: Supplementary files: LoxCode in vivo barcoding resolves epiblast clonal fate to fetal organs

description: Supplementary files (raw and processed data files, C++ code) related to the manuscript: LoxCode in vivo barcoding resolves epiblast clonal fate to fetal organs (Tom S. Weber, Christine Biben, Denise C. Miles, Stefan Glaser, Sara Tomei, Michael Lin, Andrew Kueh, Martin Pal, Stephen Zhang, Patrick P. L. Tam, Samir Taoudi, Shalin H. Naik)
DOI: 10.15468/dl.qrx6dp
title: Occurrence Download

description: A dataset containing 31045 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cotula coronopifolia L."
 ]
}

 The dataset includes 31045 records from 428 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011689-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rge8zm
title: Occurrence Download

description: A dataset containing 1634 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gymnocoronis spilanthoides DC."
 ]
}

 The dataset includes 1634 records from 120 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011690-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q3rhgq
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Symphyllocarpus exilis Maxim."
 ]
}

 The dataset includes 50 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011691-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vdypd7
title: Occurrence Download

description: A dataset containing 1518 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "DatasetKey is one of (EOD – eBird Observation Dataset, iNaturalist Research-grade Observations)",
 "GadmGid is CAN.11_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Ammodramus savannarum (J.F.Gmelin, 1789)",
 "Year 1990-2024"
 ]
}

 The dataset includes 1518 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011693-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3pv63e
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pantoporia mysia (Felder, 1860)"
 ]
}

 The dataset includes 50 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011692-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t52db4
title: Occurrence Download

description: A dataset containing 1219 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Downingia elegans (Douglas ex Lindl.) Torr."
 ]
}

 The dataset includes 1219 records from 116 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011694-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s7ynwb
title: Occurrence Download

description: A dataset containing 238 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Papilio tydeus Felder & Felder, 1860"
 ]
}

 The dataset includes 238 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011695-241107131044228/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.26395129
title: Liver-targeted delivery based on prodrug: passive and active approaches

description: The liver, a central organ in human metabolism, is often the primary target for drugs. However, conditions such as viral hepatitis, cirrhosis, non-alcoholic fatty liver disease (NAFLD), and hepatocellular carcinoma (HCC) present substantial health challenges worldwide. Existing treatments, which suffer from the non-specific distribution of drugs, frequently fail to achieve desired efficacy and safety, risking unnecessary liver harm and systemic side effects. The aim of this review is to synthesise the latest progress in the design of liver-targeted prodrugs, with a focus on passive and active targeting strategies, providing new insights into the development of liver-targeted therapeutic approaches. This study conducted an extensive literature search through databases like Google Scholar, PubMed, Web of Science, and China National Knowledge Infrastructure (CNKI), systematically collecting and selecting recent research on liver-targeted prodrugs. The focus was on targeting mechanisms, including the Enhanced Permeability and Retention (EPR) effect, the unique microenvironment of liver cancer, and active targeting through specific transporters and receptors. Active targeting strategies achieve precise drug delivery by binding specific ligands to liver surface receptors. Passive targeting takes advantage of the EPR effect and tumour characteristics to enrich drugs in liver tumours. The review details successful cases of using small molecule ligands, peptides, antibodies and nanoparticles as drug carriers. Liver-targeted prodrug strategies show great potential in enhancing the efficacy of drug treatment and reducing side effects for liver diseases. Future research should balance the advantages and limitations of both targeting strategies, focusing on optimising drug design and targeting efficiency, especially for clinical application. In-depth research on liver-specific receptors and the development of innovative targeting molecules are crucial for advancing the field of liver-targeted prodrugs.
DOI: 10.6084/m9.figshare.26395129.v2
title: Liver-targeted delivery based on prodrug: passive and active approaches

description: The liver, a central organ in human metabolism, is often the primary target for drugs. However, conditions such as viral hepatitis, cirrhosis, non-alcoholic fatty liver disease (NAFLD), and hepatocellular carcinoma (HCC) present substantial health challenges worldwide. Existing treatments, which suffer from the non-specific distribution of drugs, frequently fail to achieve desired efficacy and safety, risking unnecessary liver harm and systemic side effects. The aim of this review is to synthesise the latest progress in the design of liver-targeted prodrugs, with a focus on passive and active targeting strategies, providing new insights into the development of liver-targeted therapeutic approaches. This study conducted an extensive literature search through databases like Google Scholar, PubMed, Web of Science, and China National Knowledge Infrastructure (CNKI), systematically collecting and selecting recent research on liver-targeted prodrugs. The focus was on targeting mechanisms, including the Enhanced Permeability and Retention (EPR) effect, the unique microenvironment of liver cancer, and active targeting through specific transporters and receptors. Active targeting strategies achieve precise drug delivery by binding specific ligands to liver surface receptors. Passive targeting takes advantage of the EPR effect and tumour characteristics to enrich drugs in liver tumours. The review details successful cases of using small molecule ligands, peptides, antibodies and nanoparticles as drug carriers. Liver-targeted prodrug strategies show great potential in enhancing the efficacy of drug treatment and reducing side effects for liver diseases. Future research should balance the advantages and limitations of both targeting strategies, focusing on optimising drug design and targeting efficiency, especially for clinical application. In-depth research on liver-specific receptors and the development of innovative targeting molecules are crucial for advancing the field of liver-targeted prodrugs.
DOI: 10.6084/m9.figshare.26395129.v1
title: Liver-Targeted Delivery Based on Prodrug: Passive and Active Approaches

description: Background: The liver, a central organ in human metabolism, is often the primary target for drugs. However, conditions such as viral hepatitis, cirrhosis, non-alcoholic fatty liver disease (NAFLD), and hepatocellular carcinoma (HCC) present substantial health challenges worldwide. Existing treatments, which suffer from the non-specific distribution of drugs, frequently fail to achieve desired efficacy and safety, risking unnecessary liver harm and systemic side effects. Purpose: The aim of this review is to synthesize the latest progress in the design of liver-targeted prodrugs, with a focus on passive and active targeting strategies, providing new insights into the development of liver-targeted therapeutic approaches. Methods: This study conducted an extensive literature search through databases like Google Scholar, PubMed, Web of Science, and China National Knowledge Infrastructure (CNKI), systematically collecting and selecting recent research on liver-targeted prodrugs. The focus was on targeting mechanisms, including the Enhanced Permeability and Retention (EPR) effect, the unique microenvironment of liver cancer, and active targeting through specific transporters and receptors. Results: Active targeting strategies achieve precise drug delivery by binding specific ligands to liver surface receptors. Passive targeting takes advantage of the EPR effect and tumor characteristics to enrich drugs in liver tumors. The review details successful cases of using small molecule ligands, peptides, antibodies and nanoparticles as drug carriers. Conclusion: Liver-targeted prodrug strategies show great potential in enhancing the efficacy of drug treatment and reducing side effects for liver diseases. Future research should balance the advantages and limitations of both targeting strategies, focusing on optimizing drug design and targeting efficiency, especially for clinical application. In-depth research on liver-specific receptors and the development of innovative targeting molecules are crucial for advancing the field of liver-targeted prodrugs.
DOI: 10.5281/zenodo.14126044
title: CVL words
DOI: 10.5281/zenodo.14126045
title: CVL words
DOI: 10.5281/zenodo.14062665
title: SpaMask: Dual Masking Graph Autoencoder with Contrastive Learning for Spatial Transcriptomics

description: Understanding the spatial locations of cell within tissues is crucial for unraveling the organization of cellular diversity. Recent advancements in spatial resolved transcriptomics (SRT) have enabled the analysis of gene expression while preserving the spatial context within tissues. Spatial domain characterization is a critical first step in SRT data analysis, providing the foundation for subsequent analyses and insights into biological implications. Graph neural networks (GNNs) have emerged as a common tool for addressing this challenge due to the structural nature of SRT data. However, current graph-based deep learning approaches often overlook the instability caused by the high sparsity of SRT data. Masking mechanisms, as an effective self-supervised learning strategy, can enhance the robustness of these models. To this end, we propose SpaMask, dual masking graph autoencoder with contrastive learning for SRT analysis. Unlike previous GNNs, SpaMask masks a portion of spot nodes and spot-to-spot edges to enhance its performance and robustness. SpaMask combines Masked Graph Autoencoders (MGAE) and Masked Graph Contrastive Learning (MGCL) modules, with MGAE using node masking to leverage spatial neighbors for improved clustering accuracy, while MGCL applies edge masking to create a contrastive loss framework that tightens embeddings of adjacent nodes based on spatial proximity and feature similarity. We conducted a comprehensive evaluation of SpaMask on eight datasets from five different platforms. Compared to existing methods, SpaMask achieves superior clustering accuracy and effective batch correction.
DOI: 10.5281/zenodo.14062664
title: SpaMask: Dual Masking Graph Autoencoder with Contrastive Learning for Spatial Transcriptomics

description: Understanding the spatial locations of cell within tissues is crucial for unraveling the organization of cellular diversity. Recent advancements in spatial resolved transcriptomics (SRT) have enabled the analysis of gene expression while preserving the spatial context within tissues. Spatial domain characterization is a critical first step in SRT data analysis, providing the foundation for subsequent analyses and insights into biological implications. Graph neural networks (GNNs) have emerged as a common tool for addressing this challenge due to the structural nature of SRT data. However, current graph-based deep learning approaches often overlook the instability caused by the high sparsity of SRT data. Masking mechanisms, as an effective self-supervised learning strategy, can enhance the robustness of these models. To this end, we propose SpaMask, dual masking graph autoencoder with contrastive learning for SRT analysis. Unlike previous GNNs, SpaMask masks a portion of spot nodes and spot-to-spot edges to enhance its performance and robustness. SpaMask combines Masked Graph Autoencoders (MGAE) and Masked Graph Contrastive Learning (MGCL) modules, with MGAE using node masking to leverage spatial neighbors for improved clustering accuracy, while MGCL applies edge masking to create a contrastive loss framework that tightens embeddings of adjacent nodes based on spatial proximity and feature similarity. We conducted a comprehensive evaluation of SpaMask on eight datasets from five different platforms. Compared to existing methods, SpaMask achieves superior clustering accuracy and effective batch correction.
DOI: 10.15468/dl.fh3wsp
title: Occurrence Download

description: A dataset containing 3475 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lobelia chinensis Lour."
 ]
}

 The dataset includes 3475 records from 151 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011696-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.57ekph
title: Occurrence Download

description: A dataset containing 655 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "TaxonKey is Setaria viridis (L.) P.Beauv.",
 "Year 1990-2024"
 ]
}

 The dataset includes 655 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011697-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25345/c59883029
title: MassIVE MSV000096395 - Mitochondrial tumor suppressor 1A attenuates myocardial infarction injury by maintaining the coupling between mitochondria and endoplasmic reticulum
title: Proteomics data to identify Mtus1A-interacting proteins.
DOI: 10.15468/dl.utnfhk
title: Occurrence Download

description: A dataset containing 38913 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lobelia dortmanna L."
 ]
}

 The dataset includes 38913 records from 342 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011698-241107131044228/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.25976434
title: Supplementary Data for "<b>Mapper: fast and accurate sequence alignment via gapped x-mers</b>"

description: Evaluation Results:Suboptimal alignment rates:The folder "alignment_accuracy/" and "alignment_accuracy_ANI" contains the following:Alignment results for the same read compared across different aligners. Files ending with <code>withtag.txt</code> represent all alignment results, while files ending with <code>withtagclean.txt</code> exclude middle soft clips reported by BWA and Minimap2.A summary of suboptimal alignment rates.Potential causes of suboptimal alignments.Code to visualize the results (Figures 4, 5, S1, and S3) is available at https://github.com/caozhichongchong/Mapper_eva (Alignment_accuracy.ipynb and Alignment_accuracy_ANI.ipynb)Alignment inconsistency rate:The folder "alignment_consistency/" contains a summary of alignment inconsistency rates and suboptimal alignment rates.Code to visualize the results (Figures 6 and S4) is available at https://github.com/caozhichongchong/Mapper_eva (Alignment_consistency.ipynb)Speed:The folder "speed_evaluation" contains runtime and memory usage data for all aligners during library indexing and read alignment.Code to visualize the results (Figures 7, S5. and S6) can be found at https://github.com/caozhichongchong/Mapper_eva (Alignment_accuracy.ipynb)Alignment example for Figure S2: The folder "alignment_example" contains the code and SAM files supporting the alignment results for an example read shown in Figure S2.<br>