cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh0101865.10fu
title: SH0101865.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.13145/bacdive110162.20241212.9.2
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive110162.20251217.10
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive110163.20241212.9.2
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive110163.20251217.10
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0101866.10fu
title: SH0101866.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.13145/bacdive110164.20241212.9.2
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive110164.20251217.10
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive110165.20241212.9.2
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive110165.20251217.10
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive110166.20241212.9.2
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.17632/7vgtrzrgvs
title: Step by Step Note for Polychlorinated Alkanes Analysis Data Processing

description: Samples (including blank sample, standards (A and B) for calibration and real environmental samples) are run with GC/MS method in full scan mode. The information about sample preparation and GC/MS method are available in our published paper, Chu, S.G. and Letcher, R. J., Determination of Individual Carbon Chain Homologue Groups of Polychlorinated Alkanes in Lipid-Rich Samples by Gas Chromatography with High-Resolution Mass Spectrometry, J. Chromatog. A, 2025. In this section there are eleven raw data for practice purposes. Users may need to modify some parameters in master methods according to their methods and standards
DOI: 10.17632/7vgtrzrgvs.1
title: Step by Step Note for Polychlorinated Alkanes Analysis Data Processing

description: Samples (including blank sample, standards (A and B) for calibration and real environmental samples) are run with GC/MS method in full scan mode. The information about sample preparation and GC/MS method are available in our published paper, Chu, S.G. and Letcher, R. J., Determination of Individual Carbon Chain Homologue Groups of Polychlorinated Alkanes in Lipid-Rich Samples by Gas Chromatography with High-Resolution Mass Spectrometry, J. Chromatog. A, 2025. In this section there are eleven raw data for practice purposes. Users may need to modify some parameters in master methods according to their methods and standards
DOI: 10.17632/bj9hz63hz4.2
title: SLC44A1 deficiency impedes myelin development in the central nervous system

description: Metabolomic profiling reveals disrupted choline metabolism in SLC44A1-deficient oligodendrocytes

We hypothesized that the deficiency of SLC44A1, a key choline transporter in oligodendrocytes, disrupts intracellular choline metabolism, thereby impairing the synthesis of critical phospholipid precursors essential for myelin biogenesis.

To investigate this, we performed quantitative metabolomic profiling on primary rat oligodendrocytes following lentivirus-mediated knockdown of Slc44a1. Cells were cultured under differentiation conditions for 3 days post-infection. Metabolites were extracted using a pre-cooled acetonitrile-methanol-water solvent system, followed by analysis with liquid chromatography-tandem mass spectrometry (LC-MS/MS) on a UPLC system coupled to an AB Sciex QTrap 6500 plus mass spectrometer. The platform employed a Z-HILIC column for separation and multiple reaction monitoring (MRM) for targeted quantification of metabolites.

Our data identified 86 significantly altered metabolites in Slc44a1-knockdown oligodendrocytes compared to controls, with 72 metabolites being downregulated. Pathway enrichment analysis of these downregulated metabolites highlighted a significant disruption in the choline metabolism pathway. Most notably, citicoline (also known as CDP-choline)—the direct metabolic intermediate and rate-limiting precursor for phosphatidylcholine (PC) synthesis—exhibited the most pronounced reduction. This finding aligns with our concurrent observation of decreased PCYT1A expression, the enzyme that catalyzes the conversion of phosphocholine to citicoline in the Kennedy pathway.

These metabolomic results demonstrate that SLC44A1 deficiency severely compromises the choline metabolic flux in oligodendrocytes, specifically at the critical step of citicoline production. This disruption provides a mechanistic explanation for the observed deficits in phosphatidylcholine levels and subsequent myelin membrane expansion failures. The data underscore the essential role of SLC44A1 in sustaining the metabolic backbone required for myelination.

This metabolomics dataset offers a detailed view of the metabolic perturbations underlying oligodendrocyte dysfunction in SLC44A1 deficiency. It serves as a valuable resource for understanding the metabolic demands of myelination and for identifying potential intervention points for disorders of myelin development.
DOI: 10.15468/dl.p624my
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Idona minuenda (Ball, 1921)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 23 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018175-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ak3ffp
title: Occurrence Download

description: A dataset containing 244 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "CoordinateUncertaintyInMeters 0.0-10000.0",
 "StateProvince is one of (Southern California, Utah, Nevada, Arizona)",
 "TaxonKey is Tamarix ramosissima Ledeb.",
 "Year 1980-2024"
 ]
}

 The dataset includes 244 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018176-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k4qfkd
title: Occurrence Download

description: A dataset containing 19976 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "Geometry POLYGON((-80.519 39.721,-78.038 39.721,-78.038 42.269,-80.519 42.269,-80.519 39.721))",
 "TaxonKey is Aves",
 "Year 2023-2024"
 ]
}

 The dataset includes 19976 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018177-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nsm7gn
title: Occurrence Download

description: A dataset containing 210 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Romania",
 "Sex is one of (Female, Male)",
 "TaxonKey is Colletidae"
 ]
}

 The dataset includes 210 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018178-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5bjexh
title: Occurrence Download

description: A dataset containing 194 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "GadmGid is CHN.13_1",
 "TaxonKey is Cerambycidae"
 ]
}

 The dataset includes 194 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018180-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14534966
title: CATHe2 Dataset and models

description: The dataset named "data.zip" consists of all the relevant data to train the CATHe2 models, from the primary sequences of the training, validation and test sets as well as many csv and fasta files created by the github project code. The main chunk of this dataset is the embeddings of the training set, for every pLM tested (pLM = Protein Language Model = LLM specialized in proteins).The saved_models.zip contains the trained models used to make CATH annotation prediction with CATHe2 as well as a model trained with the embeddings of each pLM tested.
DOI: 10.5281/zenodo.14534967
title: CATHe2 Dataset and models

description: The dataset named "data.zip" consists of all the relevant data to train the CATHe2 models, from the primary sequences of the training, validation and test sets as well as many csv and fasta files created by the github project code. The main chunk of this dataset is the embeddings of the training set, for every pLM tested (pLM = Protein Language Model = LLM specialized in proteins).The saved_models.zip contains the models used to make CATH annotation prediction with CATHe2 as well as a model trained with the embeddings of each pLM tested.
DOI: 10.5281/zenodo.14568772
title: CATHe2 Dataset and models

description: The dataset named "data.zip" consists of all the relevant data to train the CATHe2 models, from the primary sequences of the training, validation and test sets as well as many csv and fasta files created by the github project code. The main chunk of this dataset is the embeddings of the training set, for every pLM tested (pLM = Protein Language Model = LLM specialized in proteins).The saved_models.zip contains the trained models used to make CATH annotation prediction with CATHe2 as well as a model trained with the embeddings of each pLM tested.
DOI: 10.5281/zenodo.14970431
title: CATHe2 Dataset and models

description: The dataset named "data.zip" consists of all the relevant data to train the CATHe2 models, from the primary sequences of the training, validation and test sets as well as many csv and fasta files created by the github project code. The main chunk of this dataset is the embeddings of the training set, for every pLM tested (pLM = Protein Language Model = LLM specialized in proteins).The saved_models.zip contains the trained models used to make CATH annotation prediction with CATHe2 as well as a model trained with the embeddings of each pLM tested.
DOI: 10.5281/zenodo.10669735
title: FM-Tools Data Set of Metadata about Verifiers and Validators (SV-COMP 2024)

description: SV-COMP 2024


FM-Tools Data Set of Metadata about Verifiers and Validators

This file describes the contents of an archive of the 13th Competition on Software Verification (SV-COMP 2024). https://sv-comp.sosy-lab.org/2024/

The competition was organized by Dirk Beyer, LMU Munich, Germany. More information is available in the following article: Dirk Beyer. State of the Art in Software Verification and Witness Validation: SV-COMP 2024. In Proceedings of the 30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems (TACAS 2024, Luxembourg, April 6 - 11), 2024. Springer.

Copyright (C) Dirk Beyer https://www.sosy-lab.org/people/beyer/

SPDX-License-Identifier: CC-BY-4.0 https://spdx.org/licenses/CC-BY-4.0.html

Contents

This archive contains a folder with all tool archives that were used in the competition. Each tool archive contains one folder with the executable files, a README file, and a LICENSE file.

Other Archives

Overview of archives from SV-COMP 2024 that are available at Zenodo:



https://doi.org/10.5281/zenodo.10669737 Verification Witnesses from SV-COMP 2024 Verification Tools. Witness store (containing the generated verification witnesses)

https://doi.org/10.5281/zenodo.10669735 Verifiers and Validators: FM-Tools Data Set for SV-COMP 2024. Metadata snapshot of the evaluated tools (DOIs, options, etc.)

https://doi.org/10.5281/zenodo.10669731 Results of the 13th Intl. Competition on Software Verification (SV-COMP 2024). Results (XML result files, log files, file mappings, HTML tables)

https://doi.org/10.5281/zenodo.10669723 SV-Benchmarks: Benchmark Set of SV-COMP 2024. Verification tasks, version svcomp24

https://doi.org/10.5281/zenodo.10671136 BenchExec, version 3.21. Benchmarking framework


All benchmarks were executed for SV-COMP 2024 https://sv-comp.sosy-lab.org/2024/ by Dirk Beyer, LMU Munich, based on the following components:



https://gitlab.com/sosy-lab/benchmarking/sv-benchmarks svcomp24

https://gitlab.com/sosy-lab/sv-comp/bench-defs svcomp24

https://github.com/sosy-lab/benchexec 3.21

https://gitlab.com/sosy-lab/benchmarking/fm-tools svcomp24

https://gitlab.com/sosy-lab/benchmarking/sv-witnesses svcomp24

https://gitlab.com/sosy-lab/software/coveriteam 1.1

https://gitlab.com/sosy-lab/benchmarking/competition-scripts svcomp24


Contact

Feel free to contact me in case of questions: https://www.sosy-lab.org/people/beyer/
DOI: 10.5281/zenodo.11186493
title: FM-Tools Release 2.0

description: Collection of Information about Formal-Methods Tools

Motivation

There are many tools available that implement formal-methods approaches. This repository collects meta data about the tools, such that it becomes easier to reuse, integrate, and cooperate with formal-methods tools.

A description of the structure of this repository can be found in an article.

A formatted listing of some of the data in this repository can be found on a generated web site.
DOI: 10.5281/zenodo.15012119
title: FM-Tools Release 2.1

description: Collection of Information about Formal-Methods Tools

Motivation

There are many tools available that implement formal-methods approaches. This repository collects meta data about the tools, such that it becomes easier to reuse, integrate, and cooperate with formal-methods tools.

A description of the structure of this repository can be found in an article.

A formatted listing of some of the data in this repository can be found on a generated web site.

A schema definition of the data files in this repository can be found on a generated web site.
DOI: 10.6084/m9.figshare.28630835
title: Thymidine exerts anti-doxorubicin-induced cardiomyopathy effect through the regulation of the PPAR signaling pathways and ferroptosis pathways

description: To evaluate the anti-cardiomyopathic activity of thymine (Thy) and to elucidate its mechanism of action. Transgenic zebra sh with enhanced green uorescent protein (EGFP)-labelled hearts (Tg (cmlc2: EGFP)) and wild-type AB zebrafish were used as experimental animals. A blank control group, a doxorubicin (DOX) model group, a dexrazoxane (DEX)-positive drug group and Thy drug treatment group were established. After treatment, indicators closely related to cardiac function, such as the pericardial area, heart rate, stroke volume, short-axis shortening (SAS) rate, and ejection fraction of the zebra sh in each group,were evaluated to determine the protective activity of Thy against DOX-induced cardiomyopathy. The pathways involved in the cardioprotective activity of Thy were analyzed via transcriptomics, and the regulatory effects of Thy on key genes were investigated using RT‒qPCR. The results indicated that Thy effectively relieved DOX-induced pericardial edema; reversed the effects of DOX on heart rate, stroke volume, SAS rate, ejection fraction, and blood velocity; and relieved DOX-induced myocardial ischemia, myocardial cell apoptosis and pathological structural changes in heart tissues. The transcriptome results indicated that the PPAR signaling and ferroptosis pathways were involved in the anti-DOX-induced cardiomyopathy effect of Thy. The RT‒qPCR results revealed that Thy regulated the mRNA expression levels of genes related to the PPAR signaling pathway and ferroptosis pathway (such as pparg, apoa1a, acsl5, pltp, and tfa). Thy may exert its anti-DOX-induced cardiomyopathy effect through the regulation of the PPAR signaling and ferroptosis pathways.
DOI: 10.6084/m9.figshare.28630835.v1
title: Thymidine exerts anti-doxorubicin-induced cardiomyopathy effect through the regulation of the PPAR signaling pathways and ferroptosis pathways

description: To evaluate the anti-cardiomyopathic activity of thymine (Thy) and to elucidate its mechanism of action. Transgenic zebra sh with enhanced green uorescent protein (EGFP)-labelled hearts (Tg (cmlc2: EGFP)) and wild-type AB zebrafish were used as experimental animals. A blank control group, a doxorubicin (DOX) model group, a dexrazoxane (DEX)-positive drug group and Thy drug treatment group were established. After treatment, indicators closely related to cardiac function, such as the pericardial area, heart rate, stroke volume, short-axis shortening (SAS) rate, and ejection fraction of the zebra sh in each group,were evaluated to determine the protective activity of Thy against DOX-induced cardiomyopathy. The pathways involved in the cardioprotective activity of Thy were analyzed via transcriptomics, and the regulatory effects of Thy on key genes were investigated using RT‒qPCR. The results indicated that Thy effectively relieved DOX-induced pericardial edema; reversed the effects of DOX on heart rate, stroke volume, SAS rate, ejection fraction, and blood velocity; and relieved DOX-induced myocardial ischemia, myocardial cell apoptosis and pathological structural changes in heart tissues. The transcriptome results indicated that the PPAR signaling and ferroptosis pathways were involved in the anti-DOX-induced cardiomyopathy effect of Thy. The RT‒qPCR results revealed that Thy regulated the mRNA expression levels of genes related to the PPAR signaling pathway and ferroptosis pathway (such as pparg, apoa1a, acsl5, pltp, and tfa). Thy may exert its anti-DOX-induced cardiomyopathy effect through the regulation of the PPAR signaling and ferroptosis pathways.
DOI: 10.15468/dl.hrg89f
title: Occurrence Download

description: A dataset containing 982 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Apteromyia claviventris (Strobl, 1909)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 982 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018181-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p8gfzu
title: Occurrence Download

description: A dataset containing 210 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Romania",
 "Sex is one of (Female, Male)",
 "TaxonKey is Colletidae"
 ]
}

 The dataset includes 210 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018182-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9wmfwb
title: Occurrence Download

description: A dataset containing 5108 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "Geometry POLYGON((-80.519 39.721,-78.038 39.721,-78.038 42.269,-80.519 42.269,-80.519 39.721))",
 "TaxonKey is Amphibia",
 "Year 2023-2024"
 ]
}

 The dataset includes 5108 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018183-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6naex5
title: Occurrence Download

description: A dataset containing 6465 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Occurrence evidence, Observation)",
 "OccurrenceStatus is Present",
 "TaxonKey is Cyclachaena xanthiifolia (Nutt.) Fresen."
 ]
}

 The dataset includes 6465 records from 94 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018184-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bcjrj4
title: Occurrence Download

description: A dataset containing 4782 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "Geometry POLYGON((-80.519 39.721,-78.038 39.721,-78.038 42.269,-80.519 42.269,-80.519 39.721))",
 "TaxonKey is Mammalia",
 "Year 2023-2024"
 ]
}

 The dataset includes 4782 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018186-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.