cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8019259
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Charlotte Nichols Saunders Horner, http://www.wikidata.org/entity/Q95160969. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q95160969
DOI: 10.5281/zenodo.8019258
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Charlotte Nichols Saunders Horner, http://www.wikidata.org/entity/Q95160969. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q95160969
DOI: 10.6084/m9.figshare.23432024
title: The Evolution of Microphysical Structures and Lightning in A Deep Moist Thunderstorm over Nanjing Area

description: Figure data in paper.
DOI: 10.6084/m9.figshare.23432024.v1
title: The Evolution of Microphysical Structures and Lightning in A Deep Moist Thunderstorm over Nanjing Area

description: Figure data in paper.
DOI: 10.6084/m9.figshare.23004563.v1
title: <strong>Diurnal versus nocturnal pollination in a subalpine wetland: from network structure to plant reproduction - Dataset</strong>

description: Dataset associated with the manuscript "<strong>Diurnal versus nocturnal pollination in a subalpine wetland: from network structure to plant reproduction</strong>" (Teng et al. 2023) <br>
DOI: 10.5281/zenodo.7927398
title: Optimising the xWORM Assay for Monitoring Hookworm Larvae Motility

description: Parasitic worms (helminths) infect almost all taxa across the animal kingdom, and pose significant challenges to public health and economies, particularly in developing countries. To address this problem, researchers have developed various tools to measure the motility and viability of helminths. However, the conditions used in anthelmintic screening assays are often not optimised, and they can vary considerably between research teams. These un-optimised conditions can impact new drug screens as little is known about the effect of different conditions on the health of the target parasites. To improve future research this study determined the effect of key assay parameters such as media type, media concentration, in-well parasite density, and assay duration on the infective third-stage larva (L3) of two types of hookworms, <em>Nippostrongylus brasiliensis</em> in rodents and <em>Necator americanus </em>in humans. Conditions were screened over several days using the xWORM assay, a real time impedance-based helminth motility assay using the xCELLigence system with 96-well microplates. While results varied depending on the species and media used, the study found that 500-1000 L3/200µL well volume and a media concentration of 3.13 – 25% generally produced good to excellent assay conditions. This data set provides the outcomes for all conditions tested by this study. This study’s findings can guide future selection of xWORM assay parameters for novel drug trials involving these parasite species and serve as a suggested model for optimising trial conditions for alternate parasite targets and assays.
DOI: 10.5281/zenodo.7927397
title: Optimising the xWORM Assay for Monitoring Hookworm Larvae Motility

description: Parasitic worms (helminths) infect almost all taxa across the animal kingdom, and pose significant challenges to public health and economies, particularly in developing countries. To address this problem, researchers have developed various tools to measure the motility and viability of helminths. However, the conditions used in anthelmintic screening assays are often not optimised, and they can vary considerably between research teams. These un-optimised conditions can impact new drug screens as little is known about the effect of different conditions on the health of the target parasites. To improve future research this study determined the effect of key assay parameters such as media type, media concentration, in-well parasite density, and assay duration on the infective third-stage larva (L3) of two types of hookworms, <em>Nippostrongylus brasiliensis</em> in rodents and <em>Necator americanus </em>in humans. Conditions were screened over several days using the xWORM assay, a real time impedance-based helminth motility assay using the xCELLigence system with 96-well microplates. While results varied depending on the species and media used, the study found that 500-1000 L3/200µL well volume and a media concentration of 3.13 – 25% generally produced good to excellent assay conditions. This data set provides the outcomes for all conditions tested by this study. This study’s findings can guide future selection of xWORM assay parameters for novel drug trials involving these parasite species and serve as a suggested model for optimising trial conditions for alternate parasite targets and assays.
DOI: 10.25340/r4/7zrkqp
title: Related Data for: Ammonia transporter 2 as a molecular marker to elucidate the potentials of ammonia transport in phylotypes of Symbiodinium, Cladocopium and Durusdinium in the fluted giant clam, Tridacna squamosa

description: Giant clams harbor coccoid Symbiodiniaceae dinoflagellates that are phototrophic. These dinoflagellates generally include multiple phylotypes (species) of Symbiodinium, Cladocopium, and Durusdinium in disparate proportions depending on the environmental conditions. The coccoid symbionts can share photosynthate with the clam host, which in return supply them with nutrients containing inorganic carbon, nitrogen and phosphorus. Symbionts can recycle nitrogen by absorbing and assimilating the endogenous ammonia produced by the host. This study aimed to use the transcript levels of ammonia transporter 2 (AMT2) in Symbiodinium (Symb-AMT2), Cladocopium (Clad-AMT2) and Durusdinium (Duru-AMT2) as molecular indicators to estimate the potential of ammonia transport in these three genera of Symbiodiniaceae dinoflagellates in different organs of the fluted giant clam, Tridacna squamosa, obtained from Vietnam. We also determined the transcript levels of form II ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcII) and nitrate transporter 2 (NRT2) in Symbiodinium (Symb-rbcII; Symb-NRT2), Cladocopium (Clad-rbcII; Clad-NRT2) and Durusdinium (Duru-rbcII; Duru-NRT2), in order to examine the potential of ammonia transport with reference to the potentials of phototrophy or NO₃− uptake independent of the quantities and proportion of these Symbiodiniaceae phylotypes. Our results indicated for the first time that phylotypes of Symbiodinium and Cladocopium could have different potentials of ammonia transport, and that phylotypes of Symbiodinium might have higher potential of NO₃− transport than ammonia transport. They also suggested that Symbiodiniaceae phylotypes residing in different organs of T. squamosa could have disparate potentials of ammonia transport, alluding to the functional diversity among phylotypes of coccoid Symbiodinium, Cladocopium, and Durusdinium.
DOI: 10.6084/m9.figshare.23430710
title: Association of IL-17A and IL-17F single nucleotide polymorphisms with atopic dermatitis in Chinese Han Child population

description: These resources are the supporting data for the article.
DOI: 10.6084/m9.figshare.23430710.v1
title: Association of IL-17A and IL-17F single nucleotide polymorphisms with atopic dermatitis in Chinese Han Child population

description: These resources are the supporting data for the article.
DOI: 10.6084/m9.figshare.23432066
title: Enhanced glacial weathering records in continental margins and dynamic response to climate and sea-level changes

description: This data set includes concentrations of major and trace elements of silicate components in core MD12-3429 that located in the northern South China Sea since MIS 7. In addition, the Sr-Nd isotopes and chemical weathering intensity were also presented.
DOI: 10.6084/m9.figshare.23432066.v1
title: MD12-3429_SCS Data.xlsx

description: This data set includes concentrations of major and trace elements of silicate components in core MD12-3429 that located in the northern South China Sea since MIS 7. In addition, the Sr-Nd isotopes and chemical weathering intensity were also presented.
DOI: 10.6084/m9.figshare.23432066.v2
title: Enhanced glacial weathering records in continental margins and dynamic response to climate and sea-level changes

description: This data set includes concentrations of major and trace elements of silicate components in core MD12-3429 that located in the northern South China Sea since MIS 7. In addition, the Sr-Nd isotopes and chemical weathering intensity were also presented.
DOI: 10.5281/zenodo.7939273
title: IBHI

description: Metagenomics project
DOI: 10.5281/zenodo.7944952
title: IBHI

description: Metagenomics project
DOI: 10.5281/zenodo.7952569
title: IBHI

description: Metagenomics project
DOI: 10.5281/zenodo.7992584
title: IBHI

description: Metagenomics project
DOI: 10.5281/zenodo.8000402
title: IBHI

description: Metagenomics project
DOI: 10.5281/zenodo.8002360
title: IBHI

description: Metagenomics project
DOI: 10.5281/zenodo.8003738
title: IBHI

description: Metagenomics project
DOI: 10.5281/zenodo.6472024
title: Data for the metaRegulon framework

description: The original data for the metaRegulon framework
DOI: 10.5281/zenodo.6472023
title: Data for the metaRegulon framework

description: The original data for the metaRegulon framework
DOI: 10.5281/zenodo.6472036
title: Data for the metaRegulon framework

description: The original data for the metaRegulon framework
DOI: 10.5281/zenodo.5732557
title: Tissue associated gene regulatory network

description: GRN network with tissue information
DOI: 10.5281/zenodo.5732556
title: Tissue associated gene regulatory network

description: GRN network with tissue information
DOI: 10.6084/m9.figshare.23434908
title: Additional file 1 of Paediatric Cogan´s syndrome - review of literature, case report and practical approach to diagnosis and management

description: Additional file 1.
DOI: 10.6084/m9.figshare.23434908.v1
title: Additional file 1 of Paediatric Cogan´s syndrome - review of literature, case report and practical approach to diagnosis and management

description: Additional file 1.
DOI: 10.6084/m9.figshare.23434921
title: Additional file 1 of TEMPROT: protein function annotation using transformers embeddings and homology search

description: Additional file 1. Analysis of ensemble techniques of TEMPROT and BLASTp.
DOI: 10.6084/m9.figshare.23434921.v1
title: Additional file 1 of TEMPROT: protein function annotation using transformers embeddings and homology search

description: Additional file 1. Analysis of ensemble techniques of TEMPROT and BLASTp.
DOI: 10.6084/m9.figshare.23434923.v1
title: Additional file 1 of Protein length distribution is remarkably uniform across the tree of life

description: Additional file 1: Table S1. Per species protein length data summary and BUSCO results.
DOI: 10.6084/m9.figshare.23434923
title: Additional file 1 of Protein length distribution is remarkably uniform across the tree of life

description: Additional file 1: Table S1. Per species protein length data summary and BUSCO results.
DOI: 10.6084/m9.figshare.23434929
title: Additional file 3 of Protein length distribution is remarkably uniform across the tree of life

description: Additional file 3: Table S3. Mapping of species in our original dataset to the species in Hug et al., 2016 [19], and associated data used in MvMorph.
DOI: 10.6084/m9.figshare.23434929.v1
title: Additional file 3 of Protein length distribution is remarkably uniform across the tree of life

description: Additional file 3: Table S3. Mapping of species in our original dataset to the species in Hug et al., 2016 [19], and associated data used in MvMorph.
DOI: 10.6084/m9.figshare.23434932
title: Additional file 4 of Protein length distribution is remarkably uniform across the tree of life

description: Additional file 4: Table S4. Aggregated results of tests for different models of evolution for each evaluated genomic feature. Parameters of the models, maximum likelihood estimation and model ranking according to AICw are reported
DOI: 10.6084/m9.figshare.23434932.v1
title: Additional file 4 of Protein length distribution is remarkably uniform across the tree of life

description: Additional file 4: Table S4. Aggregated results of tests for different models of evolution for each evaluated genomic feature. Parameters of the models, maximum likelihood estimation and model ranking according to AICw are reported
DOI: 10.6084/m9.figshare.23434935
title: Additional file 5 of Protein length distribution is remarkably uniform across the tree of life

description: Additional file 5: Table S5. BUSCO quality score for every species dataset and Mean KS of protein length distribution according to their taxonomic Domain. Proteomes labeled as outlier in this current species are also reported.
DOI: 10.6084/m9.figshare.23434935.v1
title: Additional file 5 of Protein length distribution is remarkably uniform across the tree of life

description: Additional file 5: Table S5. BUSCO quality score for every species dataset and Mean KS of protein length distribution according to their taxonomic Domain. Proteomes labeled as outlier in this current species are also reported.
DOI: 10.6084/m9.figshare.23434938
title: Additional file 6 of Protein length distribution is remarkably uniform across the tree of life

description: Additional file 6: Table S6. Report of assessed features for proteins in the Drosophila genome, whether they are deprecated in the most recent annotationor not.
DOI: 10.6084/m9.figshare.23434938.v1
title: Additional file 6 of Protein length distribution is remarkably uniform across the tree of life

description: Additional file 6: Table S6. Report of assessed features for proteins in the Drosophila genome, whether they are deprecated in the most recent annotationor not.
DOI: 10.6084/m9.figshare.23434941
title: Additional file 7 of Protein length distribution is remarkably uniform across the tree of life

description: Additional file 7: Table S7. List of complete proteomes with atypical distribution and comparisons with other annotation sets.
DOI: 10.6084/m9.figshare.14516552
title: Additional file 12 of Ten-eleven translocation protein 1 modulates medulloblastoma progression

description: Additional file 12: Table S11. Motif analysis results of mouse 5hmC gain.
DOI: 10.6084/m9.figshare.14516576.v1
title: Additional file 2 of Ten-eleven translocation protein 1 modulates medulloblastoma progression

description: Additional file 2: Table S1. Summary of GEO datasets.
DOI: 10.6084/m9.figshare.14516561
title: Additional file 15 of Ten-eleven translocation protein 1 modulates medulloblastoma progression

description: Additional file 15: Table S14. DhMRs bound by both Tet1 and Nanog.
DOI: 10.6084/m9.figshare.15041071
title: Additional file 2 of Methylation status of nc886 epiallele reflects periconceptional conditions and is associated with glucose metabolism through nc886 RNAs

description: Additional file 2. Supplementary Tables S4-10.
DOI: 10.6084/m9.figshare.14516564.v1
title: Additional file 16 of Ten-eleven translocation protein 1 modulates medulloblastoma progression

description: Additional file 16: Table S15. Summary of 5hmdC and dC in human normal cerebella (n = 5) and human MBs (n = 24).
DOI: 10.6084/m9.figshare.14516579
title: Additional file 3 of Ten-eleven translocation protein 1 modulates medulloblastoma progression

description: Additional file 3: Table S2. MB sample summary.
DOI: 10.6084/m9.figshare.14516567
title: Additional file 17 of Ten-eleven translocation protein 1 modulates medulloblastoma progression

description: Additional file 17: Table S16. Summary of all the key reagents.
DOI: 10.6084/m9.figshare.14516585.v1
title: Additional file 5 of Ten-eleven translocation protein 1 modulates medulloblastoma progression

description: Additional file 5: Table S4. Summary of annotation using 5hmC gain and 5hmC loss regions.
DOI: 10.6084/m9.figshare.14516591
title: Additional file 7 of Ten-eleven translocation protein 1 modulates medulloblastoma progression

description: Additional file 7: Table S6. Summary of MSigPathway results (GREAT analysis).
DOI: 10.6084/m9.figshare.19759493
title: Additional file 4 of Sustained correction of hippocampal neurogenic and cognitive deficits after a brief treatment by Nutlin-3 in a mouse model of fragile X syndrome

description: Additional file 4: Table S1. Primer sequences for qPCR.
DOI: 10.6084/m9.figshare.19759733
title: Additional file 1 of Identification of a novel autophagy-related prognostic signature and small molecule drugs for glioblastoma by bioinformatics

description: Additional file 1. ARGs selected in this study.
DOI: 10.6084/m9.figshare.19759496
title: Additional file 5 of Sustained correction of hippocampal neurogenic and cognitive deficits after a brief treatment by Nutlin-3 in a mouse model of fragile X syndrome

description: Additional file 5: Table S2. Result of RNA-seq read alignment.
DOI: 10.57745/eperqm
title: DATABASE_LICENSE.txt

description: license ODbL_v1.0
DOI: 10.57745/iohwr1
title: CADO_airplane_database_v1.0.tab

description: Full database with legends and colors
DOI: 10.57745/1hhhd9
title: CADO_airplane_database_v1.0.csv

description: Full database in CSV format
DOI: 10.6084/m9.figshare.19759562
title: Additional file 2 of C-terminal mini-PEGylation of a marine peptide N6 had potent antibacterial and anti-inflammatory properties against Escherichia coli and Salmonella strains in vitro and in vivo

description: Additional file 2. (XLSX 89 kb)
DOI: 10.6084/m9.figshare.19759562.v1
title: Additional file 2 of C-terminal mini-PEGylation of a marine peptide N6 had potent antibacterial and anti-inflammatory properties against Escherichia coli and Salmonella strains in vitro and in vivo

description: Additional file 2. (XLSX 89 kb)
DOI: 10.6084/m9.figshare.19759733.v1
title: Additional file 1 of Identification of a novel autophagy-related prognostic signature and small molecule drugs for glioblastoma by bioinformatics

description: Additional file 1. ARGs selected in this study.
DOI: 10.5281/zenodo.17000263
title: Dataset for GM3 ganglioside employs amplified competition and membrane reorganization to control EGFR signaling

description: # EGFR-GM3 Molecular Dynamics Trajectories


## Dataset Description


This dataset contains molecular dynamics simulation trajectories investigating the inhibitory mechanism of GM3 ganglioside on EGFR (Epidermal Growth Factor Receptor) activation. The simulations reveal how GM3 prevents EGFR dimerization through competitive binding and membrane reorganization.


## File Contents


### Trajectory Files

- `with_GM3.xtc` - Trajectory of EGFR TM-JM peptides in GM3-containing membrane (8-10 μs)

- `without_GM3.xtc` - Trajectory of EGFR TM-JM peptides in GM3-free ordered membrane (8-10 μs)


### Structure Files

- `with_GM3.psf` - Protein structure file for GM3-containing system

- `without_GM3.psf` - Protein structure file for GM3-free system


## Simulation Details


### System Composition

- **Membrane dimensions**: 40 × 40 nm

- **Proteins**: 4 EGFR TM-JM peptides (residues 610-659)

- **GM3-free system**: CHOL:DLiPC:SM = 33:33:33 mol% (upper leaflet); CHOL:DLiPC:DOPS = 33:33:33 mol% (lower leaflet)

- **GM3-containing system**: CHOL:DLiPC:SM:GM3 = 33:33:33:1 mol% (upper leaflet); CHOL:DLiPC:DOPS = 33:33:33 mol% (lower leaflet)


### Simulation Parameters

- **Force field**: MARTINI 2.2 coarse-grained

- **Software**: GROMACS 2023.3

- **Temperature**: 298 K

- **Pressure**: 1 bar (semi-isotropic coupling)

- **Salt concentration**: 150 mM NaCl

- **Duration**: 8-10 μs per system


## Usage


These trajectories can be analyzed using standard molecular dynamics analysis tools:


```bash

# Example: Load with MDAnalysis (Python)

import MDAnalysis as mda


# Load GM3-containing system

u_gm3 = mda.Universe('with_GM3.psf', 'with_GM3.xtc')


# Load GM3-free system

u_free = mda.Universe('without_GM3.psf', 'without_GM3.xtc')


# Codes for analyses on the manuscript by Sato and Tamagaki-Asahina


Codes for analyses are available on github, https://github.com/takeshi-sato-dev/
DOI: 10.5281/zenodo.17000264
title: Dataset for GM3 ganglioside employs amplified competition and membrane reorganization to control EGFR signaling

description: # EGFR-GM3 Molecular Dynamics Trajectories


## Dataset Description


This dataset contains molecular dynamics simulation trajectories investigating the inhibitory mechanism of GM3 ganglioside on EGFR (Epidermal Growth Factor Receptor) activation. The simulations reveal how GM3 prevents EGFR dimerization through competitive binding and membrane reorganization.


## File Contents


### Trajectory Files

- `with_GM3.xtc` - Trajectory of EGFR TM-JM peptides in GM3-containing membrane (8-10 μs)

- `without_GM3.xtc` - Trajectory of EGFR TM-JM peptides in GM3-free ordered membrane (8-10 μs)


### Structure Files

- `with_GM3.psf` - Protein structure file for GM3-containing system

- `without_GM3.psf` - Protein structure file for GM3-free system


## Simulation Details


### System Composition

- **Membrane dimensions**: 40 × 40 nm

- **Proteins**: 4 EGFR TM-JM peptides (residues 610-659)

- **GM3-free system**: CHOL:DLiPC:SM = 33:33:33 mol% (upper leaflet); CHOL:DLiPC:DOPS = 33:33:33 mol% (lower leaflet)

- **GM3-containing system**: CHOL:DLiPC:SM:GM3 = 33:33:33:1 mol% (upper leaflet); CHOL:DLiPC:DOPS = 33:33:33 mol% (lower leaflet)


### Simulation Parameters

- **Force field**: MARTINI 2.2 coarse-grained

- **Software**: GROMACS 2023.3

- **Temperature**: 298 K

- **Pressure**: 1 bar (semi-isotropic coupling)

- **Salt concentration**: 150 mM NaCl

- **Duration**: 8-10 μs per system


## Usage


These trajectories can be analyzed using standard molecular dynamics analysis tools:


```bash

# Example: Load with MDAnalysis (Python)

import MDAnalysis as mda


# Load GM3-containing system

u_gm3 = mda.Universe('with_GM3.psf', 'with_GM3.xtc')


# Load GM3-free system

u_free = mda.Universe('without_GM3.psf', 'without_GM3.xtc')


# Codes for analyses on the manuscript by Sato and Tamagaki-Asahina


Codes for analyses are available on github, https://github.com/takeshi-sato-dev/
DOI: 10.15468/dl.cqq82x
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Polyscias scutellaria",
 "Country is Philippines",
 "HasCoordinate is true"
 ]
}

 The dataset includes 11 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014939-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qak43j
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Veronica glauca glauca"
 ]
}

 The dataset includes 46 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014940-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/whit-c170-101127
title: Loyola vs St. Marys football, Los Angeles, Calif.,1939

description: 6 photographs of the football game between Loyola University and St. Mary's College of California in the Los Angeles Memorial Coliseum, Los Angeles, California 1939 December 3. Editor's note: the photographer's job number does not indicate a date.