cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24525821
title: <i>In vitro</i> and <i>in silico</i> analysis proving DPP4 inhibition and diabetes-associated gene network modulation by a polyherbal formulation: <i>Nisakathakadi Kashaya</i>

description: Dipeptidyl-peptidase IV (DPP4) inhibitors are an important class of anti-diabetic drugs recognised for their systemic biological actions. Polyherbal preparations like <i>Ayurveda</i> formulations are considered to be ideal sources for discovering novel DPP4 inhibitors owing to their rich phytochemical composition. The current study reports the DPP4 inhibitory potential of a clinically established Ayurvedic anti-diabetic formulation <i>Nisakathakadi Kashaya</i> (NK) using <i>in vitro</i> assay and substantiates it by identifying potential bioactives responsible for DPP4 inhibition using computational biology tools. NK showed a dose-dependent DPP4 inhibition with an IC<sub>50</sub> of 2.06 μg GAE/mL, and the molecular docking and simulation studies showed three compounds, namely Terchebin, Locaracemoside B and 1,2,4,6 Tetra o Galloyl Beta D Glucose having stable interactions with DPP4 similar to the standard drug Vildagliptin. Further, for the reason that polyherbal formulations exert a network pharmacology mode of action, <i>in silico</i> analysis was carried out to identify the other putative phytochemical-protein networks modulated by NK. The complex pharmacological network of the formulation was explored further using a subnetwork of diabetes proteins and their relationship with diabetes-associated comorbidities. A number of key targets like TNFα, TGFβ1, SOD1, SOD2, AKT1, DPP4 and GLP1R were identified in the protein-protein interaction network that is vital to diabetic progression and complications. A combination of <i>in vitro</i> and <i>in silico</i> methods allowed us to prove the DPP4 inhibition potential of NK as well as provided insights into the possible pharmacological networking through which NK potentially exerts its systemic effect in diabetes management. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24525821.v1
title: <i>In vitro</i> and <i>in silico</i> analysis proving DPP4 inhibition and diabetes-associated gene network modulation by a polyherbal formulation: <i>Nisakathakadi Kashaya</i>

description: Dipeptidyl-peptidase IV (DPP4) inhibitors are an important class of anti-diabetic drugs recognised for their systemic biological actions. Polyherbal preparations like <i>Ayurveda</i> formulations are considered to be ideal sources for discovering novel DPP4 inhibitors owing to their rich phytochemical composition. The current study reports the DPP4 inhibitory potential of a clinically established Ayurvedic anti-diabetic formulation <i>Nisakathakadi Kashaya</i> (NK) using <i>in vitro</i> assay and substantiates it by identifying potential bioactives responsible for DPP4 inhibition using computational biology tools. NK showed a dose-dependent DPP4 inhibition with an IC<sub>50</sub> of 2.06 μg GAE/mL, and the molecular docking and simulation studies showed three compounds, namely Terchebin, Locaracemoside B and 1,2,4,6 Tetra o Galloyl Beta D Glucose having stable interactions with DPP4 similar to the standard drug Vildagliptin. Further, for the reason that polyherbal formulations exert a network pharmacology mode of action, <i>in silico</i> analysis was carried out to identify the other putative phytochemical-protein networks modulated by NK. The complex pharmacological network of the formulation was explored further using a subnetwork of diabetes proteins and their relationship with diabetes-associated comorbidities. A number of key targets like TNFα, TGFβ1, SOD1, SOD2, AKT1, DPP4 and GLP1R were identified in the protein-protein interaction network that is vital to diabetic progression and complications. A combination of <i>in vitro</i> and <i>in silico</i> methods allowed us to prove the DPP4 inhibition potential of NK as well as provided insights into the possible pharmacological networking through which NK potentially exerts its systemic effect in diabetes management. Communicated by Ramaswamy H. Sarma
DOI: 10.15468/dl.3347sf
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Magnolia chiguila F.Arroyo, Á.J.Pérez & A.Vázquez"
 ]
}

 The dataset includes 17 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016234-241126133413365/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.24534209.v1
title: Network pharmacology combined with molecular docking and experimental verification to elucidate functional mechanism of Fufang Zhenzhu Tiaozhi against type 2 diabetes mellitus

description: Fufang Zhenzhu Tiaozhi (FTZ) capsules have been prescribed for treating glucose and lipid metabolism disorders such as type 2 diabetes mellitus (T2DM). However, the underlying mechanism remains unknown. In this study, network pharmacology and experimental verification were combined to investigate the mechanisms of FTZ in treating T2DM. A total of 176 active ingredients and 1169 corresponding targets were screened using biological databases. 598 potential targets of T2DM were retrieved from GeneCards, PharmGKB, OMIM, Drugbank, and TTD. The Venn diagram was employed to identify the 194 intersection targets, which were employed to construct the “Herb-Compound-Target” interacting networks. These common targets were also used to prepare a protein-protein interaction (PPI) network to uncover potential targets. The four core targets were docked to their corresponding targets for binding analysis. Additionally, the top-ranked poses of ingredients and the positive compounds from each protein were evaluated for stability using molecular dynamics. Our results suggest that core active ingredients such as kaempferol, luteolin, and baicalein have high binding affinity and stability with AKT1, PTGS2 (also known as COX-2), DPP4, and PAPRG. GO and KEGG analyses indicated that the treatment T2DM by FTZ might be related to different pathway like AMPK and EGFR pathways. The experimental validation results proved that kaempferol, luteolin, and baicalein could significantly inhibit the activity of DPP4 and COX-2, kaempferol and luteolin were also able to activate AKT and AMPK signaling pathway. This study further validated previous findings and enhanced our understanding of the potential effects of FTZ on T2DM. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24534209
title: Network pharmacology combined with molecular docking and experimental verification to elucidate functional mechanism of Fufang Zhenzhu Tiaozhi against type 2 diabetes mellitus

description: Fufang Zhenzhu Tiaozhi (FTZ) capsules have been prescribed for treating glucose and lipid metabolism disorders such as type 2 diabetes mellitus (T2DM). However, the underlying mechanism remains unknown. In this study, network pharmacology and experimental verification were combined to investigate the mechanisms of FTZ in treating T2DM. A total of 176 active ingredients and 1169 corresponding targets were screened using biological databases. 598 potential targets of T2DM were retrieved from GeneCards, PharmGKB, OMIM, Drugbank, and TTD. The Venn diagram was employed to identify the 194 intersection targets, which were employed to construct the “Herb-Compound-Target” interacting networks. These common targets were also used to prepare a protein-protein interaction (PPI) network to uncover potential targets. The four core targets were docked to their corresponding targets for binding analysis. Additionally, the top-ranked poses of ingredients and the positive compounds from each protein were evaluated for stability using molecular dynamics. Our results suggest that core active ingredients such as kaempferol, luteolin, and baicalein have high binding affinity and stability with AKT1, PTGS2 (also known as COX-2), DPP4, and PAPRG. GO and KEGG analyses indicated that the treatment T2DM by FTZ might be related to different pathway like AMPK and EGFR pathways. The experimental validation results proved that kaempferol, luteolin, and baicalein could significantly inhibit the activity of DPP4 and COX-2, kaempferol and luteolin were also able to activate AKT and AMPK signaling pathway. This study further validated previous findings and enhanced our understanding of the potential effects of FTZ on T2DM. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.27958065
title: PRISMA Checklist

description: This document contains the PRISMA checklist used in the systematic review titled "Leadership Agility in a VUCA World: A Systematic Review, Conceptual Insights, and Research Directions." The checklist outlines the key steps and criteria followed in the review process to ensure transparency and adherence to the PRISMA guidelines. It provides detailed information about the identification, screening, and inclusion of studies, supporting the methodological rigor of the research.
DOI: 10.15468/dl.jt7qn8
title: Occurrence Download

description: A dataset containing 70 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Spisula sibyllae (Valenciennes, 1858)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 70 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016236-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zu4p8m
title: Occurrence Download

description: A dataset containing 741 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ichthyococcus ovatus (Cocco, 1838)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 741 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016238-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mfr5nn
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cetorhinus maximus (Gunnerus, 1765)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 7 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016239-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a59vvz
title: Occurrence Download

description: A dataset containing 16341 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Marine Species Records from Skomer Marine Conservation Zone (MCZ) Marine Monitoring Programme"
 ]
}

 The dataset includes 16341 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016240-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17608/k6.auckland.25869148
title: Supplementary Data 3 - pairwise distances between isolates for each intron

description: Supplementary Data 3 ReadmeThis datafile contains CSV files showing the pairwise distances between isolates for each intron. Matrix is self-by-self, so numbers down the left edge represent the same isolates named horizontally.
DOI: 10.17608/k6.auckland.25869148.v2
title: Supplementary Data 3 - pairwise distances between isolates for each intron

description: Supplementary Data 3 ReadmeThis datafile contains CSV files showing the pairwise distances between isolates for each intron. Matrix is self-by-self, so numbers down the left edge represent the same isolates named horizontally.
DOI: 10.17608/k6.auckland.25869148.v1
title: Supplementary Data 3 - ancestral state reconstructions of intron presence/absence and their associated phylogenies

description: Supplementary Data 3 ReadmeThis datafile contains the ancestral state reconstruction data. There are six different sets of phylogenies/dendrograms used for the ancestral state reconstructions. These are phylogenies made from the tefA and tubB nuclear genes with hybrids included using one copy of each gene, with hybrids included using both copies of each gene found in the hybrids are included, and with hybrids excluded. Similarly, they are from a concatenation of mitochondrial protein-coding genes with hybrids included and with hybrids excluded. Finally, there is a dendrogram using intron presence-absence as the phylogenetic character. Therefore, these phylogenies have different numbers of tips, including some with more tips than the number of isolates used in this study because of the use of two copies of each gene present in hybrids.For each phylogeny/dendrogram, ancestral state reconstruction outputs from Mesquite and RASP are provided, as are the tables of intron gains/losses inferred from the Mesquite analyses.Note that older names are used for some isolates: E. typhina subspecies Holcus = E. clarkii; E. typhina subspecies poae = E. poae
DOI: 10.15468/dl.8dhxej
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Squalus maximus Gunnerus, 1765",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016242-241126133413365/datasets/export for details.
DOI: 10.15468/dl.b7dz7b
title: Occurrence Download

description: A dataset containing 45 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Quercus mexicana Bonpl."
 ]
}

 The dataset includes 45 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016244-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wwdpz6
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Cameroon",
 "DatasetKey is Global compendium of Aedes aegypti occurrence"
 ]
}

 The dataset includes 55 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001646-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xvyd2g
title: Occurrence Download

description: A dataset containing 12288 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Árboles de Chiapas: registro georreferenciado de los ejemplares depositados en el herbario de la Academia de Ciencias de California (CAS)"
 ]
}

 The dataset includes 12288 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001647-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b9fgcq
title: Occurrence Download

description: A dataset containing 92 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aleurodicus rugioperculatus Martin, 2004",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 92 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001648-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12738577
title: LLM-Generated Software Requirements from GitHub Issues

description: This dataset contains software requirements automatically generated from bug reports and feature requests extracted from the three most popular machine learning repositories on GitHub: Scikit-learn, TensorFlow, and Transformers. The dataset is structured into issue data, generated requirements, and evaluations based on three well-defined criteria.

Dataset Structure



issues.csv: Contains issue titles along with their corresponding repository names and unique identifiers.

Requirements Files: These files store the requirements generated by LLMs for each issue, categorized by different prompting methods:



few_shot_requirements.csv

zero_shot_requirements.csv

expert_requirements.csv

expert_few_shot_requirements.csv



Evaluation Files: These files contain the assessment of the generated requirements based on three key quality criteria: Unambiguity, Understandability, and Singularity. The evaluations are also divided by prompting methods:



few_shot_evaluation.csv

zero_shot_evaluation.csv

expert_evaluation.csv

expert_few_shot_evaluation.csv
DOI: 10.5281/zenodo.12738578
title: Issues Bug / Feature Request Dataset
DOI: 10.5281/zenodo.13655334
title: Issues Bug / Feature Request Dataset
DOI: 10.5281/zenodo.13685804
title: AI-Generated Software requirements from Bug Reports/Feature Request

description: This repository comprehends the dataset and scripts used to generate Software Requirements using LLM from Bug Reports and Feature Requests from the 3 most popular Machine Learning Repositories on Github: Scikit-learn, TensorFlow, and Transformers.Repository Structure:



Issues Dataset



scikit-learn_dataset.csv

tensorflow_dataset.csv

trasnformers_dataset.csv



IPython Notebook Scripts



analyze_requirements.ipynb

generate_requirements.ipynb

extract_issues.ipynb

wordcloud.ipynb



AI-Generated Requirements Dataset



responses_dataset.jsonl
DOI: 10.5281/zenodo.15003631
title: LLM-Generated Software Requirements from GitHub Issues

description: This dataset contains software requirements automatically generated from bug reports and feature requests extracted from the three most popular machine learning repositories on GitHub: Scikit-learn, TensorFlow, and Transformers. The dataset is structured into issue data, generated requirements, and evaluations based on three well-defined criteria.

Dataset Structure



issues.csv: Contains issue titles along with their corresponding repository names and unique identifiers.

Requirements Files: These files store the requirements generated by LLMs for each issue, categorized by different prompting methods:



few_shot_requirements.csv

zero_shot_requirements.csv

expert_requirements.csv

expert_few_shot_requirements.csv



Evaluation Files: These files contain the assessment of the generated requirements based on three key quality criteria: Unambiguity, Understandability, and Singularity. The evaluations are also divided by prompting methods:



few_shot_evaluation.csv

zero_shot_evaluation.csv

expert_evaluation.csv

expert_few_shot_evaluation.csv
DOI: 10.6084/m9.figshare.28571198
title: Supp fig S8 Verification of deletion of the MR from BMDC

description: Verification of deletion of the MR from BMDCs. Western blot for the MR using an antibody raised to the MR N terminus. A band was detected in the wild type sample of the correct size for MR (Lanes 1 and 2) and substantially reduced expression in the Cre recombinase expressing mice (Lanes 3 and 4). Purified MR from mouse kidney (Lane 5) served as control.
DOI: 10.15468/dl.gfmyeg
title: Occurrence Download

description: A dataset containing 162 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eriococcus lagerstroemiae Kuwana, 1907",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 162 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001649-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kd3ncm
title: Occurrence Download

description: A dataset containing 101 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is one of (Capra sibirica (Pallas, 1776), Ovis ammon polii Blyth, 1840)"
 ]
}

 The dataset includes 101 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001651-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5nwtua
title: Occurrence Download

description: A dataset containing 17691 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Amaranthus viridis L."
 ]
}

 The dataset includes 17691 records from 678 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001650-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8x53sq
title: Occurrence Download

description: A dataset containing 570 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Atherigona orientalis Schiner, 1868",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 570 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001652-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48610/87eda8c
title: Raw Data for Co-Cultivation paper

description: Raw data deposited for Co-Cultivation Manuscript
DOI: 10.15468/dl.gsa6rd
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Lithocarpus obscurus C.C.Huang & Y.T.Chang"
 ]
}

 The dataset includes 40 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001655-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cca44s
title: Occurrence Download

description: A dataset containing 936 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Atherigona reversura Villeneuve, 1936",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 936 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001656-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gsye79
title: Occurrence Download

description: A dataset listing the 13 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Amaranthus viridis L."
 ]
}

 The dataset's 13 records were derived from 678 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001654-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xnw6ak
title: Occurrence Download

description: A dataset containing 1348 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Loxodonta cyclotis (Matschie, 1900)"
 ]
}

 The dataset includes 1348 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001658-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.