cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29487953.v3
title: Identifying a type of toxic effectors exported by <i>Streptococcus suis</i> to enhance competitive fitness

description: <i>Streptococcus suis</i> poses a significant threat to both pig farming and public health, causing severe disease such as septicemia, meningitis and streptococcal toxic shock-like syndrome. Type VII secretion system (T7SS) delivers toxic effectors to play a crucial role in interbacterial competition and is vital for the zoonotic pathogen <i>S. suis</i> to colonize host tonsils effectively. Here we identified a type of hypothetical T7SS effectors in <i>S. suis</i>, seeming to be the fragmented toxins cut off N-terminal YeeF domain, redesignated as MSE-ExTs. MSE (marker for searching effectors) is a conserved sequence at the N-termini of modular effectors showing a diverse range of toxicities targeting NAD<sup>+</sup>. EssC is a core component of T7SS apparatus, while genetic rearrangements frequently occur within T7SS loci in <i>S</i><i>.</i><i> suis</i>, leading to the duplication and truncation of EssC. Most MSE-ExTs (MSE fusing exported toxins) are located downstream of a truncated EssC and lack cognate WXG100-like proteins, but still exported to mediate interbacterial antagonism for gaining a competitive advantage over the bacterial isolates from tonsil microbiota. Neither deletion of truncated<i> essC2</i> nor <i>essC3</i> could not diminish the MSE-ExT1 delivery, while the full-length EssC1 encoded in T7SS core locus was required for the lethality of MSE-ExT1 to sensitive bacterial cells. MapC2, an upstream small helical protein, shares a nearly identical C-terminal 50 aa sequence with EIC-CR (C-terminal conserved region of effector-paired immunity protein). This conserved fragment harbours a “YxxxD” targeting signal and interact with the D1 ATPase domain of the non-neighboring EssC, thereby activating the secretion of MSE-ExTs. These findings suggest that MapC2 and EIC-CR mediate the recruitment of effector-immunity pairs to T7SS apparatus under the absence of a full-length cognate EssC and WXG100-like proteins. This alternative strategy facilitates effectors’ delivery, even for fragmented substrates resulting from genetic rearrangements, highlighting its importance in ensuring the functionality of T7SS.
DOI: 10.6084/m9.figshare.29487953.v2
title: Identifying a type of toxic effectors exported by <i>Streptococcus suis</i> to enhance competitive fitness

description: <i>Streptococcus suis</i> poses a significant threat to both pig farming and public health, causing severe disease such as septicemia, meningitis and streptococcal toxic shock-like syndrome. Type VII secretion system (T7SS) delivers toxic effectors to play a crucial role in interbacterial competition and is vital for the zoonotic pathogen <i>S. suis</i> to colonize host tonsils effectively. Here we identified a type of hypothetical T7SS effectors in <i>S. suis</i>, seeming to be the fragmented toxins cut off N-terminal YeeF domain, redesignated as MSE-ExTs. MSE (marker for searching effectors) is a conserved sequence at the N-termini of modular effectors showing a diverse range of toxicities targeting NAD<sup>+</sup>. EssC is a core component of T7SS apparatus, while genetic rearrangements frequently occur within T7SS loci in <i>S</i><i>.</i><i> suis</i>, leading to the duplication and truncation of EssC. Most MSE-ExTs (MSE fusing exported toxins) are located downstream of a truncated EssC and lack cognate WXG100-like proteins, but still exported to mediate interbacterial antagonism for gaining a competitive advantage over the bacterial isolates from tonsil microbiota. Neither deletion of truncated<i> essC2</i> nor <i>essC3</i> could not diminish the MSE-ExT1 delivery, while the full-length EssC1 encoded in T7SS core locus was required for the lethality of MSE-ExT1 to sensitive bacterial cells. MapC2, an upstream small helical protein, shares a nearly identical C-terminal 50 aa sequence with EIC-CR (C-terminal conserved region of effector-paired immunity protein). This conserved fragment harbours a “YxxxD” targeting signal and interact with the D1 ATPase domain of the non-neighboring EssC, thereby activating the secretion of MSE-ExTs. These findings suggest that MapC2 and EIC-CR mediate the recruitment of effector-immunity pairs to T7SS apparatus under the absence of a full-length cognate EssC and WXG100-like proteins. This alternative strategy facilitates effectors’ delivery, even for fragmented substrates resulting from genetic rearrangements, highlighting its importance in ensuring the functionality of T7SS.
DOI: 10.15468/dl.2t93cp
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Aimophila ruficeps)",
 "Country is one of (Åland Islands, Albania, Andorra, Austria, Belarus, Belgium, Bosnia and Herzegovina, Bulgaria, Croatia, Czechia, Denmark, Estonia, Faroe Islands, Finland, France, Germany, Gibraltar, Greece, Guernsey, Holy See, Hungary, Iceland, Ireland, Isle of Man, Italy, Jersey, Latvia, Liechtenstein, Lithuania, Luxembourg, Malta, Moldova, Republic of, Monaco, Montenegro, Netherlands, North Macedonia, Norway, Poland, Portugal, Romania, Russian Federation, San Marino, Serbia, Slovakia, Slovenia, Spain, Svalbard and Jan Mayen, Sweden, Switzerland, Ukraine, United Kingdom of Great Britain and Northern Ireland)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008728-250802193616735/datasets/export for details.
DOI: 10.15468/dl.4qc6xy
title: Occurrence Download

description: A dataset containing 4149 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lampornis sybillae)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 4149 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008729-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21227/j6es-yz39
title: "Aesthetics Attack Adversarial Examples Dataset"

description: "We analyzed successful attack samples across 26 image aesthetics assessment models and curated the Aesthetics Attack Adversarial Examples (3AE) dataset, containing 60K images."
DOI: 10.15468/dl.rd8yh9
title: Occurrence Download

description: A dataset containing 104 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Variabilichromis moorii)",
 "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 104 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008730-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16730809
title: sevir

description: This repository contains the dataset from the paper titled "Precipitation Nowcasting Based on Convolutional LSTM with Spatio-Temporal Information Transformation Using Multi-Meteorological Factors."

The SEVIR (Storm Event Imagery) dataset is a publicly available, open dataset released and maintained by the MIT Lincoln Laboratory (https://registry.opendata.aws/sevir/, with a total size of approximately 480 GB). We did not create or modify any data; our research directly utilizes the original dataset.  We strongly recommend downloading from the official repository.
DOI: 10.15468/dl.5hqxrs
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gossypium hirsutum",
 "Country is Cook Islands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008731-250802193616735/datasets/export for details.
DOI: 10.15468/dl.3vzkdc
title: Occurrence Download

description: A dataset containing 17503 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lampornis viridipallens)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 17503 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008732-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6073/pasta/e56e5bd937c274be8c1669a5d10522a3
title: WPE02 Shrub stem data to quantify woody encroachment in Konza watersheds from 2020, 2022, and 2023

description: Woody plant encroachment (WPE) is one of the most widespread and acute threats affecting grasslands worldwide. Nature-based solutions to reversing WPE in mesic
 grasslands have proven largely ineffective, with decades of frequent prescribed fire failing to reverse WPE in some instances. One solution is to conduct more extreme fires compared to traditional prescribed fire. However, most tests of this idea have occurred at small scales, a mismatch with the need for landscape-scale land management. We considered two catchments, each with long-term destocking of grazers to increase fuel loads, one which accidentally burned under dry windy conditions that produced an extreme fire, while one burned under prescribed fire conditions. The extreme fire caused a sharp decline in woody cover without corresponding negative externalities such as decreases in grass cover or biodiversity. However, after three years, the woody community completely recoverd with a 23% increase in woody cover from the first to third year post-fire. The prescribed fire catchment saw minor decreases in woody plant dominance that rebounded quickly to pre-fire values. Our results suggest that reversing encroachment will likely require a long-term approach, along with applying a combination of pressures that reduce woody abundance and promote fuel loads to intensify fire.
DOI: 10.15468/dl.2bduda
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:ABU8169"
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008733-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ekp329
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Peucaea aestivalis)",
 "Country is one of (Afghanistan, Armenia, Azerbaijan, Bahrain, Bangladesh, Bhutan, Brunei Darussalam, Cambodia, China, Cyprus, Georgia, Hong Kong, India, Indonesia, Iran (Islamic Republic of), Iraq, Israel, Japan, Jordan, Kazakhstan, Korea (Democratic People’s Republic of), Korea, Republic of, Kuwait, Kyrgyzstan, Lao People’s Democratic Republic, Lebanon, Macao, Malaysia, Maldives, Mongolia, Myanmar, Nepal, Oman, Pakistan, Palestine, State of, Philippines, Qatar, Saudi Arabia, Singapore, Sri Lanka, Syrian Arab Republic, Tajikistan, Thailand, Timor-Leste, Türkiye, Turkmenistan, United Arab Emirates, Uzbekistan, Viet Nam, Yemen)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008735-250802193616735/datasets/export for details.
DOI: 10.15468/dl.ayj356
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Peucaea aestivalis)",
 "Country is one of (Anguilla, Antigua and Barbuda, Argentina, Aruba, Bahamas, Barbados, Belize, Bolivia (Plurinational State of), Bonaire, Sint Eustatius and Saba, Bouvet Island, Brazil, Cayman Islands, Chile, Colombia, Costa Rica, Cuba, Curaçao, Dominica, Dominican Republic, Ecuador, El Salvador, Falkland Islands (Malvinas), French Guiana, Grenada, Guadeloupe, Guatemala, Guyana, Haiti, Honduras, Jamaica, Martinique, Mexico, Montserrat, Nicaragua, Panama, Paraguay, Peru, Puerto Rico, Saint Barthélemy, Saint Kitts and Nevis, Saint Lucia, Saint Martin (French part), Saint Vincent and the Grenadines, Sint Maarten (Dutch part), South Georgia and the South Sandwich Islands, Suriname, Trinidad and Tobago, Turks and Caicos Islands, Uruguay, Venezuela (Bolivarian Republic of), Virgin Islands (British), Virgin Islands (U.S.))"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008736-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4xvuy9
title: Occurrence Download

description: A dataset containing 89 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Heteranthera reniformis",
 "Country is Italy",
 "HasCoordinate is true"
 ]
}

 The dataset includes 89 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008737-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5vbmut
title: Occurrence Download

description: A dataset containing 718 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((68.34807 6.83278,79.72879 6.83278,79.72879 24.73095,68.34807 24.73095,68.34807 6.83278))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Muridae"
 ]
}

 The dataset includes 718 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008738-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16735704
title: Final results
DOI: 10.5281/zenodo.16735705
title: Final results
DOI: 10.15468/dl.8rsnwk
title: Occurrence Download

description: A dataset containing 56 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lamprolia klinesmithi)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 56 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008739-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pv8nt7
title: Occurrence Download

description: A dataset containing 556 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eleutherococcus sieboldianus",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 556 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008740-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16735798
title: Operationalizing sustainable transparency in software ecosystems portals
DOI: 10.15468/dl.7s7ts7
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gossypium hirsutum",
 "Country is Congo, Democratic Republic of the",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008741-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15592471
title: AMP Project Data

description: # AMP Dataset Documentation

This repository contains several datasets used for conducting ProteoGPT, AMPSorter, AMPGenix and BioToxiPept and datasets conducted with prediction results. Below is a description of each dataset included in this repository.

## Datasets

### 1. `uniprot-compressed_true_download_true_format_fasta_includeIsoform_tr-2022.10.13-02.51.31.70.fasta`- **Description**: 609,216 non-redundant canonical and isoform protein sequences.

### 2. `protein_seqs_1000.json`- **Description**: Contains the training data for ProteoGPT.

### 3. `amp_unique_16062.json`- **Description**: Contains the training data for AMPGenix.

### 4. `AMPSorter&BioToxiPept dataset.xlsx`- **Description**: Contains the fine-tuning data, including:  - **AMP_data split**: Data used for training,  validating and  evaluating AMPSorter.  - **AMP_test Set**: Data used for test AMPSorter.  - **AMP_benchmarking Set**: A set of peptides used for benchmarking the AMP models.  - **AMP_external Validation Dataset**: A separate dataset for external model validation for AMPSorter.  - **Toxin_data split**: Data used for training,  validating and  evaluating BioToxiPept.  - **Toxin_test set**: A set of peptides used for testing the toxin models.

### 5. `NRSPDs`- **Description**: A large dataset that includes:  - **410,192,277 non-redundant short peptides**.  - **A candidate pool of 82,694,928 peptides**.  - **Logits** with results predicted by  AMPsorter and BioToxiPept.

### 6. `GNRSPDs`- **Description**: Contains:  - **7,798 generated sequences**.  - **A candidate pool of 4,736 peptides**.  - **Logits**with results predicted by  AMPsorter and BioToxiPept.

### 7. `196 tested peptides.xlsx`- **Description**: A set of  196 selected and experimentally tested peptides, with experimentally measured values.

### 8. `20 pilot tested peptides.xlsx`- **Description**: 20 selected  peptides with prediction results and experimentally values measured in pilot test.

### 9. `Sequences generated by different models.xlsx`- **Description**: Sequences generated by different models with prediction results.
DOI: 10.5281/zenodo.16633186
title: AMP Project Data

description: # AMP Dataset Documentation

This repository contains several datasets used for conducting ProteoGPT, AMPSorter, AMPGenix and BioToxiPept and datasets conducted with prediction results. Below is a description of each dataset included in this repository.

## Datasets

### 1. `uniprot-compressed_true_download_true_format_fasta_includeIsoform_tr-2022.10.13-02.51.31.70.fasta`- **Description**: 609,216 non-redundant canonical and isoform protein sequences.

### 2. `protein_seqs_1000.json`- **Description**: Contains the training data for ProteoGPT.

### 3. `amp_unique_16062.json`- **Description**: Contains the training data for AMPGenix.

### 4. `AMPSorter&BioToxiPept dataset.xlsx`- **Description**: Contains the fine-tuning data, including:  - **AMP_data split**: Data used for training,  validating and  evaluating AMPSorter.  - **AMP_test Set**: Data used for test AMPSorter.  - **AMP_benchmarking Set**: A set of peptides used for benchmarking the AMP models.  - **AMP_external Validation Dataset**: A separate dataset for external model validation for AMPSorter.  - **Toxin_data split**: Data used for training,  validating and  evaluating BioToxiPept.  - **Toxin_test set**: A set of peptides used for testing the toxin models.

### 5. `NRSPDs`- **Description**: A large dataset that includes:  - **410,192,277 non-redundant short peptides**.  - **A candidate pool of 82,694,928 peptides**.  - **Logits** with results predicted by  AMPsorter and BioToxiPept.

### 6. `GNRSPDs`- **Description**: Contains:  - **7,798 generated sequences**.  - **A candidate pool of 4,736 peptides**.  - **Logits**with results predicted by  AMPsorter and BioToxiPept.

### 7. `196 tested peptides.xlsx`- **Description**: A set of  196 selected and experimentally tested peptides, with experimentally measured values.

### 8. `20 pilot tested peptides.xlsx`- **Description**: 20 selected  peptides with prediction results and experimentally values measured in pilot test.

### 9. `Sequences generated by different models.xlsx`- **Description**: Sequences generated by different models with prediction results.
DOI: 10.5281/zenodo.15520932
title: USENIX'25 Artifact Datasets: Towards Internet-Based State Learning of TLS State Machines

description: Artifacts for our USENIX Security '25 paper 'Towards Internet-Based State Learning of TLS State Machines'. The artifact includes:- the tools we used to learn and analyze state machines of TLS implementations- the state machines we collected and discuss in our paper- additional statistics and information on our analysis methodologyPlease see the artifact_appendix.pdf for details on how to reproduce our experiments form the USENIX Security artifact evaluation.
DOI: 10.5281/zenodo.16735883
title: USENIX'25 Artifact Datasets: Towards Internet-Based State Learning of TLS State Machines

description: Artifacts for our USENIX Security '25 paper 'Towards Internet-Based State Learning of TLS State Machines'. The artifact includes:- the tools we used to learn and analyze state machines of TLS implementations- the state machines we collected and discuss in our paper- additional statistics and information on our analysis methodologyPlease see the artifact_appendix.pdf for details on how to reproduce our experiments form the USENIX Security artifact evaluation.
DOI: 10.15468/dl.2s8fe5
title: Occurrence Download

description: A dataset containing 2502348 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lepidoptera",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015",
 "Year is less than or equal to 2024",
 "Month is greater than or equal to May",
 "Month is less than or equal to August",
 {
 "or" : [
 "DatasetKey is Swedish Butterfly Monitoring Scheme (SeBMS)",
 "DatasetKey is Artportalen"
 ]
 },
 "BasisOfRecord is Human Observation",
 "Country is Sweden",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 2502348 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008722-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.53f2pm
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Psilorhynchus arunachalensis)",
 "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 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008742-250802193616735/datasets/export for details.