cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14943575
title: Flow Cytometry Analysis of Tissue Factor Expression in Human Platelets

description: This record contains raw data related to the article "Flow Cytometry Analysis of Tissue Factor Expression in Human Platelets".

 

ABSTRACT

A subset of circulating human platelets stores Tissue Factor (TF) intracellularly, the key activator of the blood coagulation cascade and thrombus formation. Upon platelet activation, TF is exposed on the cell membrane, where it binds to FVII, ultimately leading to thrombin generation. Considering that (1) levels of TF-positive platelets increase in various clinical settings, contributing to the patient's prothrombotic phenotype, and (2) different drugs can modulate platelet-associated TF expression, a standardized method for assessing TF-positive platelets is valuable, as its evaluation has been controversial in the past. Here, we outline a protocol for measuring the percentage of TF-positive platelets using flow cytometry in whole blood and platelet-rich plasma (PRP)/washed platelets. This protocol aims to provide detailed instructions for quantifying the percentage of TF-positive platelets by assessing the protein (1) intracellularly in resting conditions, and (2) on the cell surface, in both resting and activated conditions. The first section provides essential information for correctly performing blood withdrawal to ensure that pre-analytical procedures do not affect the results. Next, the protocol focuses on sample preparation and labeling procedures for flow cytometry analysis. Detailed steps for cell stimulation, labeling, fixation, and permeabilization—where necessary—are outlined. Finally, instructions for flow cytometry settings to correctly identify the platelet population and analyze TF-positive events are described. Lastly, the method includes the procedure for preparing PRP if TF-positive platelets are to be measured in isolated platelets. Since only a subset of platelets contains TF, it is important to ensure that these platelets are not lost during the centrifugation steps required to obtain PRP.
DOI: 10.5281/zenodo.14936755
title: Dataset related to the article "N-Acetylcysteine, N-Acetylcysteine Amide, and Thioredoxin  Mimetic Peptides Regenerate Mercaptoalbumin and Exhibit Antioxidant Activity"

description: This record contains row data related to the article "N-Acetylcysteine, N-Acetylcysteine Amide, and Thioredoxin  Mimetic Peptides Regenerate Mercaptoalbumin and Exhibit Antioxidant Activity"

Abstract:[M1] [ES2]  Albumin (HSA) is the most abundant circulating protein and plays a pivotal role in maintaining the redox state of the plasma. Three HSA proteoforms have been identified based on the redox state of cysteine 34. These include the reduced proteoform (HSA-SH), non-mercaptoalbumin-1, containing a disulfide with small thiols such as cysteine (HSA-Cys), and non-mercaptoalbumin-2, the higher oxidized proteoform. Several clinical studies have shown a relationship between an individual’s serum HSA redox status and the severity of diseases such as heart failure, diabetes mellitus, and liver disease. Furthermore, when HSA undergoes oxidation, it can worsen certain health conditions and contribute to their advancement. This study aimed to evaluate the ability of the redox compounds AD4/NACA and the thioredoxin mimetic (TXM) peptides TXM-CB3, TXM-CB13, and TXM-CB30 to regenerate HSA-SH and to improve its redox activity. The HSA proteoforms were quantified by LC-MS, and the antioxidant activity was determined using dichlorofluorescin. Each of the compounds exhibited a significant increase in HSA-SH and a reduction in HSA-Cys levels. The increase in HSA-SH was associated with a recovery of its antioxidant activity. Herein, we reveal a new mechanistic facet contributing to the antioxidant activity of AD4/NACA and TXM peptides. These antioxidant properties propose an additional therapeutic approach for addressing oxidative stress-related conditions.








 [M1]Abbreviations:

Abbreviations need to be defined the first time they appear in the abstract, keywords section, headings, main text and figures/tables. Please double check through the whole paper and define them where needed.

Genes & Proteins:

Please check if all the genes’ symbols and species’ names are written in italics typeface. Proteins and enzymes should NOT be in italics. Please double check through the whole paper and keep them consistent and in the correct format.







 [ES2]I have checked and revised all











 [M1]Abbreviations:

Abbreviations need to be defined the first time they appear in the abstract, keywords section, headings, main text and figures/tables. Please double check through the whole paper and define them where needed.

Genes & Proteins:

Please check if all the genes’ symbols and species’ names are written in italics typeface. Proteins and enzymes should NOT be in italics. Please double check through the whole paper and keep them consistent and in the correct format.







 [ES2]I have checked and revised all
DOI: 10.5281/zenodo.14936756
title: Dataset related to the article "N-Acetylcysteine, N-Acetylcysteine Amide, and Thioredoxin  Mimetic Peptides Regenerate Mercaptoalbumin and Exhibit Antioxidant Activity"

description: This record contains row data related to the article "N-Acetylcysteine, N-Acetylcysteine Amide, and Thioredoxin  Mimetic Peptides Regenerate Mercaptoalbumin and Exhibit Antioxidant Activity"

Abstract:[M1] [ES2]  Albumin (HSA) is the most abundant circulating protein and plays a pivotal role in maintaining the redox state of the plasma. Three HSA proteoforms have been identified based on the redox state of cysteine 34. These include the reduced proteoform (HSA-SH), non-mercaptoalbumin-1, containing a disulfide with small thiols such as cysteine (HSA-Cys), and non-mercaptoalbumin-2, the higher oxidized proteoform. Several clinical studies have shown a relationship between an individual’s serum HSA redox status and the severity of diseases such as heart failure, diabetes mellitus, and liver disease. Furthermore, when HSA undergoes oxidation, it can worsen certain health conditions and contribute to their advancement. This study aimed to evaluate the ability of the redox compounds AD4/NACA and the thioredoxin mimetic (TXM) peptides TXM-CB3, TXM-CB13, and TXM-CB30 to regenerate HSA-SH and to improve its redox activity. The HSA proteoforms were quantified by LC-MS, and the antioxidant activity was determined using dichlorofluorescin. Each of the compounds exhibited a significant increase in HSA-SH and a reduction in HSA-Cys levels. The increase in HSA-SH was associated with a recovery of its antioxidant activity. Herein, we reveal a new mechanistic facet contributing to the antioxidant activity of AD4/NACA and TXM peptides. These antioxidant properties propose an additional therapeutic approach for addressing oxidative stress-related conditions.








 [M1]Abbreviations:

Abbreviations need to be defined the first time they appear in the abstract, keywords section, headings, main text and figures/tables. Please double check through the whole paper and define them where needed.

Genes & Proteins:

Please check if all the genes’ symbols and species’ names are written in italics typeface. Proteins and enzymes should NOT be in italics. Please double check through the whole paper and keep them consistent and in the correct format.







 [ES2]I have checked and revised all











 [M1]Abbreviations:

Abbreviations need to be defined the first time they appear in the abstract, keywords section, headings, main text and figures/tables. Please double check through the whole paper and define them where needed.

Genes & Proteins:

Please check if all the genes’ symbols and species’ names are written in italics typeface. Proteins and enzymes should NOT be in italics. Please double check through the whole paper and keep them consistent and in the correct format.







 [ES2]I have checked and revised all
DOI: 10.15468/dl.kgvczb
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Lithocarpus megastachyus (Hickel & A.Camus) A.Camus"
 ]
}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006028-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.64bmvj
title: Occurrence Download

description: A dataset containing 181 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Israel, Jordan, Lebanon, Syrian Arab Republic, Türkiye, Iraq, Iran (Islamic Republic of), Greece, Bulgaria, Ukraine)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Aegilops speltoides subsp. ligustica (Savign.) Zhuk."
 ]
}

 The dataset includes 181 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006027-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26188/25264408
title: Field bounding boxes for primary specimen labels on herbarium specimen sheets

description: This dataset contains the bounding boxes for text fields on primary specimen labels (also known as 'institutional labels') on herbarium specimen sheets. The annotations are in YOLO format. It contains the following classes:0. genus<br>1. species<br>2. year<br>3. month<br>4. day<br>5. family<br>6. collector<br>7. authority<br>8. locality<br>9. geolocation<br>10. collector_number<br>11. infrasp_taxon<br>These classes were annotated on 3,642 images of institutional labels from 10 herbaria. 2,603 images are from the University of Melbourne's herbarium (MELU) and the remainder are from the nine herbaria represented in the benchmark dataset described by Dillen (10.3897/BDJ.7.e31817). The images are in subdirectories by the code of the respective herbarium. The institution corresponding to each code is:MELU: The University of Melbourne<br>BR: Meise Botanic Garden<br>K: Royal Botanic Gardens, Kew<br>BM: Natural History Museum, London<br>B: Botanic Garden and Botanical Museum, Berlin<br>E: Royal Botanic Garden Edinburgh<br>P: National Museum of Natural History, Paris<br>TU: Natural History Museum, University of Tartu<br>L: Naturalis Biodiversity Center<br>H: Finnish Museum of Natural History LUOMUS, University of Helsinki<br>These were broken down into 2,887 training images and 755 validation images and these are listed in train.txt and valid.txt respectively.For more information, see https://github.com/rbturnbull/hespi
DOI: 10.5281/zenodo.6372393
title: A benchmark dataset of herbarium specimen images with label data: Summary

description: This landing page contains a CSV file compiling all data associated with herbarium specimens that are part of this dataset, as they could be found on GBIF, JACQ or FinBIF. A CSV file with and without Darwin Core extension data is available, as some CSV readers have trouble with the JSON format that is used for those extensions. In addition, DOI's of the individual specimens uploaded to Zenodo and direct links to the different files (JPEG, TIFF, JSON, PNG) are also included. Index of these added variables: - persistentID: Persistent Identifier of the collection specimen. Data uploaded as part of this dataset will not be kept in sync with changes at the collection's repository. Hence, this URI will always point to the most up to date information known about the herbarium specimen. - jpegURL, tiffURL, jsonURL: URL's pointing straight to the respective image and data files themselves, to facilitate (selective) batch downloads. - pngSegAllURL and pngSegSelURL: Segmented overlays of the herbarium specimens indicating the location of different labels and reference material on the sheet ("All") and their content ("Sel"). More information can be found in the paper (in prep) associated with this data publication and the individual depositions themselves. - DOI: The DOI of the deposition of images and data of these specimens on Zenodo. DOI's point to the most up-to-date version of these depositions at the time of the publication of this CSV file. As a rule, this CSV file will be updated should any changes happen to any of the depositions. - jpegURL2, tiffURL2: A few herbarium sheets had labels on the back and consisted therefore of two scans. As a rule, the label scans are in this category.
DOI: 10.26188/25264408.v1
title: Field bounding boxes for institutional labels on herbarium specimen sheets

description: This dataset contains the bounding boxes for text fields on institutional labels on herbarium specimen sheets. The annotations are in YOLO format. It contains the following classes:0. genus<br>1. species<br>2. year<br>3. month<br>4. day<br>5. family<br>6. collector<br>7. authority<br>8. locality<br>9. geolocation<br>10. collector_number<br>11. infrasp_taxon<br>These classes were annotated on 3,642 images of institutional labels from 10 herbaria. 2,603 images are from the University of Melbourne's herbarium (MELU) and the remainder are from the nine herbaria represented in the benchmark dataset described by Dillen (10.3897/BDJ.7.e31817). The images are in subdirectories by the code of the respective herbarium. The institution corresponding to each code is:MELU: The University of Melbourne<br>BR: Meise Botanic Garden<br>K: Royal Botanic Gardens, Kew<br>BM: Natural History Museum, London<br>B: Botanic Garden and Botanical Museum, Berlin<br>E: Royal Botanic Garden Edinburgh<br>P: National Museum of Natural History, Paris<br>TU: Natural History Museum, University of Tartu<br>L: Naturalis Biodiversity Center<br>H: Finnish Museum of Natural History LUOMUS, University of Helsinki<br>These were broken down into 2,887 training images and 755 validation images and these are listed in train.txt and valid.txt respectively.For more information, see https://github.com/rbturnbull/hespi
DOI: 10.15468/dl.y7uewq
title: Occurrence Download

description: A dataset containing 1233616 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((6.07744 53.45149,5.98287 53.32824,6.24908 53.24448,6.5468 53.29685,6.45924 53.43062,6.48726 53.52026,6.07744 53.45149))",
 "HasCoordinate is true",
 "Year 2015-2025"
 ]
}

 The dataset includes 1233616 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006016-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14973730
title: MURAKKAB ARALASH TURDAGI UCHINCHI TARTIBLI BIR TENGLAMA UCHUN CHEGARAVIY MASALANING YECHIMNI MAVJUDLIGI TEOREMASI

description: Mazkur maqolada chegaralanmagan sohada uchinchi tartibli tenglama uchun chegaraviy masala qaralgan bo‘lib yechimining mavjudligi  Fredgolmning ikkinchi tur integral tenglamalari nazariyasidan foydalangan holda isbotlangan.
DOI: 10.5281/zenodo.14973731
title: MURAKKAB ARALASH TURDAGI UCHINCHI TARTIBLI BIR TENGLAMA UCHUN CHEGARAVIY MASALANING YECHIMNI MAVJUDLIGI TEOREMASI

description: Mazkur maqolada chegaralanmagan sohada uchinchi tartibli tenglama uchun chegaraviy masala qaralgan bo‘lib yechimining mavjudligi  Fredgolmning ikkinchi tur integral tenglamalari nazariyasidan foydalangan holda isbotlangan.
DOI: 10.15468/dl.tvn3jb
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Euphorbia transtagana Boiss."
 ]
}

 The dataset includes 15 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006029-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/10929625
title: Daily Public Opinion on Israel-Palestine War
DOI: 10.5281/zenodo.14973757
title: arXiv:2503.00363

description: data for




arXiv:2503.00363
DOI: 10.5281/zenodo.14973758
title: arXiv:2503.00363

description: data for




arXiv:2503.00363
DOI: 10.5281/zenodo.17106944
title: Opportunistic diver-assisted eDNA sampling unpicks fine-scale ecological and conservation signals in tropical reef fishes

description: Description of the data and file structure

This project contains raw reads data and ngs file for demultiplexing from eDNA samples collected from coral reefs in the Seychelles archipelago employing a versatile low-tech passive environmental DNA collector, the ‘metaprobe’, in association with the recreational activity of SCUBA divers. 

Raw reads files and ngsfilter files with sample barcodes are from a library prepared using the Elas02 12S barcode and sequenced with an iSeq Illumina sequencing platform. 

Files and variables

File: Lib01_S1_L001_R1_001.fastq.gz

Description: Forward FastQ file from the library sequenced with an Illumina iSeq 2x150 bp run

File: Lib01_S1_L001_R2_001.fastq.gz

Description: Reverse FastQ file from the library sequenced with an Illumina iSeq 2x150 bp run

File: ngsSeychelles.txt

Description: Primers and unique dual-tag combinations (forward and reverse) associated with each of the samples. The columns of the file correspond to: name of the project, samples, dual oligo-tags, forward primer and reverse primer.
Variables



name of the project

name of the samples

dual oligo-tags

forward primer

reverse primer


File: MOTUTable_Seychelles.csv

Description: Raw MOTU table where each row represents an OTU with its corresponding taxonomic assignment. Columns represent sampling sites, and the cell values indicate the number of sequence reads per OTU at each site.

File: Seychelles_taxo_abund_dataset.csv

Description: Final filtered dataset where only taxonomic assignments to species and/or genus level above 90% identity are kept. Each row represents an OTU with its corresponding taxonomic assignment, while columns represent sampling sites, and the cell values indicate the number of sequence reads per OTU at each site.
DOI: 10.5281/zenodo.17106945
title: Opportunistic diver-assisted eDNA sampling unpicks fine-scale ecological and conservation signals in tropical reef fishes

description: Description of the data and file structure

This project contains raw reads data and ngs file for demultiplexing from eDNA samples collected from coral reefs in the Seychelles archipelago employing a versatile low-tech passive environmental DNA collector, the ‘metaprobe’, in association with the recreational activity of SCUBA divers. 

Raw reads files and ngsfilter files with sample barcodes are from a library prepared using the Elas02 12S barcode and sequenced with an iSeq Illumina sequencing platform. 

Files and variables

File: Lib01_S1_L001_R1_001.fastq.gz

Description: Forward FastQ file from the library sequenced with an Illumina iSeq 2x150 bp run

File: Lib01_S1_L001_R2_001.fastq.gz

Description: Reverse FastQ file from the library sequenced with an Illumina iSeq 2x150 bp run

File: ngsSeychelles.txt

Description: Primers and unique dual-tag combinations (forward and reverse) associated with each of the samples. The columns of the file correspond to: name of the project, samples, dual oligo-tags, forward primer and reverse primer.
Variables



name of the project

name of the samples

dual oligo-tags

forward primer

reverse primer


File: MOTUTable_Seychelles.csv

Description: Raw MOTU table where each row represents an OTU with its corresponding taxonomic assignment. Columns represent sampling sites, and the cell values indicate the number of sequence reads per OTU at each site.

File: Seychelles_taxo_abund_dataset.csv

Description: Final filtered dataset where only taxonomic assignments to species and/or genus level above 90% identity are kept. Each row represents an OTU with its corresponding taxonomic assignment, while columns represent sampling sites, and the cell values indicate the number of sequence reads per OTU at each site.
DOI: 10.15468/dl.r647pw
title: Occurrence Download

description: A dataset containing 857 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is South Africa",
 "OccurrenceStatus is Present",
 "TaxonKey is Campuloclinium macrocephalum (Less.) DC."
 ]
}

 The dataset includes 857 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010743-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g324ft
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Salsola oppositifolia (Pall.) Pall.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018127-250402121839773/datasets/export for details.
DOI: 10.5281/zenodo.15199585
title: Amazon fishes
DOI: 10.5281/zenodo.15199586
title: Amazon fishes
DOI: 10.15156/bio/sh0216177.10fu
title: SH0216177.10FU

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: 10.15156/bio/sh0216178.10fu
title: SH0216178.10FU

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.