cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13955415
title: Key Resource Table associated with "Endo-IP and Lyso-IP Toolkit for Endolysosomal Profiling of Human Induced Neurons"

description: This entry contains a Key Resource table associated with: https://doi.org/10.1101/2024.09.24.614704
DOI: 10.5281/zenodo.13955416
title: Key Resource Table associated with "Endo-IP and Lyso-IP Toolkit for Endolysosomal Profiling of Human Induced Neurons"

description: This entry contains a Key Resource table associated with: https://doi.org/10.1101/2024.09.24.614704
DOI: 10.15468/dl.237v3p
title: Occurrence Download

description: A dataset containing 464 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Italy",
 "TaxonKey is Euplagia quadripunctaria (Poda, 1761)",
 "Year 2024-2024"
 ]
}

 The dataset includes 464 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018902-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13885852
title: Source data for Fig. S1F associated with "Endo-IP and Lyso-IP Toolkit for Endolysosomal Profiling of Human Induced Neurons"

description: This entry contains source data and statistical test for plots in Fig. S1F associated with: https://doi.org/10.1101/2024.09.24.614704
DOI: 10.5281/zenodo.13885853
title: Source data for Fig. S1F associated with "Endo-IP and Lyso-IP Toolkit for Endolysosomal Profiling of Human Induced Neurons"

description: This entry contains source data and statistical test for plots in Fig. S1F associated with: https://doi.org/10.1101/2024.09.24.614704
DOI: 10.6084/m9.figshare.27088913
title: Molecular docking and molecular dynamics simulation studies reveal repurposing I-Motif ligand as a promising protease inhibitor against SARS-CoV-2 variants

description: The COVID-19 caused by the SARS-CoV-2 virus has escalated into a global pandemic, urgently necessitating effective treatments. Tremendous research of the SARS-CoV-2 main protease have enabled insight understanding of its mechanism and potential inhibitors. Due to its crucial role in viral replication, the protease is considered an attractive target for antiviral therapy. This study aimed to identify novel potent inhibitors of main protease protein by repurposing i-Motif (iM) binding compounds from the G4LDB database. iM ligands are known for their ability to stabilise iM structures in DNA, and their repurposing as protein inhibitors is an alternative therapeutic approach. To achieve this, we performed <i>in silico</i> studies with six iM binding compounds. Molecular docking, molecular dynamics (MD) simulations and MM/GBSA binding free energy analysis revealed favourable conformational stability and superior binding affinity of the three proposed iM ligands, including iML0042 (−59.91 ± 3.82 kcal/mol), iML0043 (−56.37 ± 3.87 kcal/mol), and iML0094 (−84.68 ± 3.40 kcal/mol), to SARS-CoV-2 Mpro variants compared to the reference inhibitor nirmatrelvir (−34.35 ± 3.74 kcal/mol). The results suggested that repurposing iM ligands as protease inhibitors is a promising strategy. Our findings revealed significant candidate inhibitors and are recommended for further development as potential protease inhibitors against SARS-CoV-2.
DOI: 10.6084/m9.figshare.27088913.v1
title: Molecular docking and molecular dynamics simulation studies reveal repurposing I-Motif ligand as a promising protease inhibitor against SARS-CoV-2 variants

description: The COVID-19 caused by the SARS-CoV-2 virus has escalated into a global pandemic, urgently necessitating effective treatments. Tremendous research of the SARS-CoV-2 main protease have enabled insight understanding of its mechanism and potential inhibitors. Due to its crucial role in viral replication, the protease is considered an attractive target for antiviral therapy. This study aimed to identify novel potent inhibitors of main protease protein by repurposing i-Motif (iM) binding compounds from the G4LDB database. iM ligands are known for their ability to stabilise iM structures in DNA, and their repurposing as protein inhibitors is an alternative therapeutic approach. To achieve this, we performed <i>in silico</i> studies with six iM binding compounds. Molecular docking, molecular dynamics (MD) simulations and MM/GBSA binding free energy analysis revealed favourable conformational stability and superior binding affinity of the three proposed iM ligands, including iML0042 (−59.91 ± 3.82 kcal/mol), iML0043 (−56.37 ± 3.87 kcal/mol), and iML0094 (−84.68 ± 3.40 kcal/mol), to SARS-CoV-2 Mpro variants compared to the reference inhibitor nirmatrelvir (−34.35 ± 3.74 kcal/mol). The results suggested that repurposing iM ligands as protease inhibitors is a promising strategy. Our findings revealed significant candidate inhibitors and are recommended for further development as potential protease inhibitors against SARS-CoV-2.
DOI: 10.15468/dl.ayzr4h
title: Occurrence Download

description: A dataset containing 419 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Astragalus arnacantha M.Bieb."
 ]
}

 The dataset includes 419 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018903-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fke68b
title: Occurrence Download

description: A dataset containing 419 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Astragalus arnacantha M.Bieb."
 ]
}

 The dataset includes 419 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018904-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p62aa4
title: Occurrence Download

description: A dataset containing 544895 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "TaxonKey is Ciconia ciconia (Linnaeus, 1758)"
 ]
}

 The dataset includes 544895 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018906-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hd6b2x
title: Occurrence Download

description: A dataset containing 1974 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Retrophyllum C.N.Page"
 ]
}

 The dataset includes 1974 records from 143 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018908-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dtx9zt
title: Occurrence Download

description: A dataset listing the 487 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "Geometry POLYGON((-73.77047 5.68762,-73.66531 5.70059,-73.66717 5.58204,-73.53874 5.60334,-73.53036 5.76911,-73.48793 5.95536,-73.62567 5.94055,-73.6508 5.81187,-73.77047 5.68762))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Chordata",
 "Year 2000-2024"
 ]
}

 The dataset's 487 records were derived from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018905-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.62662c
title: Occurrence Download

description: A dataset containing 1813330 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is one of (iNaturalist Research-grade Observations, Observation.org, Nature data from around the World)",
 "TaxonKey is Apidae",
 "Year 2000-2024"
 ]
}

 The dataset includes 1813330 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018907-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.je4vew
title: Occurrence Download

description: A dataset containing 4174 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((97.8615 2.86387,99.3939 2.86387,99.3939 4.17736,97.8615 4.17736,97.8615 2.86387))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Animalia",
 "Year 2021-2024"
 ]
}

 The dataset includes 4174 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018910-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s2fctz
title: Occurrence Download

description: A dataset containing 4483 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Vanellus vanellus (Linnaeus, 1758)",
 "Year 2003-2023"
 ]
}

 The dataset includes 4483 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018911-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14014223
title: Data, Pre- and Post- processing scripts for shallow-water photogrammetry applications

description: Description

This repository contains the data and scripts to reproduce the results of Casella et al. (Remote Sensing, 2024). The scripts are in python, two of them are wrapped in Jupyter Notebooks with explanatory notes.Please read the paper for further information on the platform used to collect the data shared in this repository.

Folder structure

The main folder contains two subfolders:



Data: this folder includes all the original data, and the results of the preprocessing and post-processing notebooks. Note that the original photos, included in the "Camera/all_photos" folder must be unzipped before running the preprocessing Jupyter  Notebooks.

Precision_Analysis: this folder includes the digital bathymetric models that were co-registered as described in the paper. The co-registration was done offline with Quantum GIS. In this folder are also stored the results of the "Compare_DBMs.py" script, that makes the precision analysis (differences between co-registered DBMs).


Installation

Refer to the README.md file for a quick installation guide using Anaconda. 

Credits

The code included in this work has been improved with the assistance of ChatGPT, which provided guidance on optimization, debugging, and documentation to enhance clarity and functionality. All the code has been reviewed and supervised by humans to ensure consistency and correctness.
DOI: 10.5281/zenodo.14014224
title: Data, Pre- and Post- processing scripts for shallow-water photogrammetry applications

description: Description

This repository contains the data and scripts to reproduce the results of Casella et al. (Remote Sensing, 2024). The scripts are in python, two of them are wrapped in Jupyter Notebooks with explanatory notes.Please read the paper for further information on the platform used to collect the data shared in this repository.

Folder structure

The main folder contains two subfolders:



Data: this folder includes all the original data, and the results of the preprocessing and post-processing notebooks. Note that the original photos, included in the "Camera/all_photos" folder must be unzipped before running the preprocessing Jupyter  Notebooks.

Precision_Analysis: this folder includes the digital bathymetric models that were co-registered as described in the paper. The co-registration was done offline with Quantum GIS. In this folder are also stored the results of the "Compare_DBMs.py" script, that makes the precision analysis (differences between co-registered DBMs).


Installation

Refer to the README.md file for a quick installation guide using Anaconda. 

Credits

The code included in this work has been improved with the assistance of ChatGPT, which provided guidance on optimization, debugging, and documentation to enhance clarity and functionality. All the code has been reviewed and supervised by humans to ensure consistency and correctness.
DOI: 10.15468/dl.9bukxy
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Artemia franciscana Kellogg, 1906",
 "Country is Spain",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 24 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018913-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u9qf6a
title: Occurrence Download

description: A dataset containing 109 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Russian Federation, Georgia, Türkiye, Armenia, Azerbaijan)",
 "TaxonKey is Lilium kesselringianum Miscz."
 ]
}

 The dataset includes 109 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018915-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wppumj
title: Occurrence Download

description: A dataset containing 76097 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Podocarpus L'Hér. ex Pers."
 ]
}

 The dataset includes 76097 records from 712 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018912-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.93aq4r
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amphipholis laevidisca H.L.Clark, 1909",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 },
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is MANAGED"
 ]
 }
 },
 {
 "not" : {
 "EstablishmentMeans" : [
 "is not null"
 ]
 }
 }
 ]
 },
 {
 "or" : [
 "OccurrenceStatus is Present",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is not null"
 ]
 }
 }
 ]
 }
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040252-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lpsbk1
title: Occurrence Download

description: A dataset containing 270 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "TaxonKey is Theobroma cacao L."
 ]
}

 The dataset includes 270 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009007-170826194755519/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.77n7tr
title: Occurrence Download

description: A dataset containing 1087 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Pulchrana grandocula (Taylor, 1920)"
 ]
}

 The dataset includes 1087 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042854-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mzxu2p
title: Occurrence Download

description: A dataset containing 143 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "DatasetKey is one of (Occurrence dataset of waterbirds in Tiaozini Wetland, the World Nature Heritage, China, 2021_nsmk_biodiversity_observations_bi_eagle_81252, birds-red-river-delta-seawater-reservoir, Occurrence dataset of birds in the Sihong Hongze Lake Wetland National Nature Reserve,Jiangsu, China, 2021_nsmk_biodiversity_observations_bird_136784, Xeno-canto - Bird sounds from around the world, 2021_nsmk_biodiversity_observations_bird_197960, iNaturalist Research-grade Observations, Occurrence dataset of birds in the Xinjizhou National Wetland Park，Nanjing，China)",
 "OccurrenceStatus is Present",
 "StateProvince is Liaoning",
 "TaxonKey is Aves",
 "Year 2019-2023"
 ]
}

 The dataset includes 143 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022849-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.44cx8e
title: Occurrence Download

description: A dataset containing 73 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Diospyros gillespiei (Fosberg) Kosterm."
 ]
}

 The dataset includes 73 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023041-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.spszik
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Protographium thyastes (Drury, 1782)",
 "Country is Brazil"
 ]
}

 The dataset includes 17 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009009-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3fdtwb
title: Occurrence Download

description: A dataset containing 107 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dicksonia lanigera Holttum"
 ]
}

 The dataset includes 107 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021720-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8vygab
title: Occurrence Download

description: A dataset containing 406 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Davallia hookeri (Bedd.) X.C.Zhang"
 ]
}

 The dataset includes 406 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023042-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ws0v04
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Epiactis ritteri Torrey, 1902"
 ]
}

 The dataset includes 29 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009008-150615163101818/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sldjli
title: Occurrence Download

description: A dataset containing 104277 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mammalia",
 "Geometry POLYGON((-102.11 16.59,-102.11 20.37,-95.22 20.37,-95.22 16.59,-102.11 16.59))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 104277 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009008-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mjwjxw
title: Occurrence Download

description: A dataset containing 377 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euphorbia griffithii Hook.f."
 ]
}

 The dataset includes 377 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050400-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.henbkj
title: Occurrence Download

description: A dataset containing 995 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Davallia griffithiana Hook."
 ]
}

 The dataset includes 995 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023031-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.792pd6
title: Occurrence Download

description: A dataset containing 51605 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Amaranthus hybridus L."
 ]
}

 The dataset includes 51605 records from 1012 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021730-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bu62pu
title: Occurrence Download

description: A dataset containing 93650 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Aneuraceae)"
 ]
}

 The dataset includes 93650 records from 594 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023039-240314170635999/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.28280210
title: Socioeconomic status and dental indices

description: The data compares the socioeconomic status with the oral health
DOI: 10.6084/m9.figshare.28280210.v1
title: Socioeconomic status and dental indices

description: The data compares the socioeconomic status with the oral health
DOI: 10.15468/dl.ace8dt
title: Occurrence Download

description: A dataset containing 56 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Country is Italy",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Lithophaga lithophaga (Linnaeus, 1758)",
 "Year 2000-2025"
 ]
}

 The dataset includes 56 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006018-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/mdw38m2wwn
title: Modelling study on estuarine circulation and its effect on turbidity maximum zone in the Yalu River Estuary, China: Dataset

description: Field data (river discharge, water elevation, depth-averaged current velocity, salinity and SSC) and model results in Yalu River Estuary.