cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12441650.v1
title: Additional file 1 of Comparative analysis of microbial community structure between healthy and Aeromonas veronii-infected Yangtze finless porpoise

description: Additional file 1: Table S1. The OTUs classification of all samples at different levels.
DOI: 10.5281/zenodo.10683732
title: System Architecture Optimization Experiments Dataset

description: This dataset contains experimental results for testing system architecture optimization algorithms. The results have been generated with https://github.com/jbussemaker/ArchitectureOptimizationExperiments/tree/hidden-constraints.

The results correspond to the following blocks of results:



01_sampling_*: hierarchical sampling and correction algorithms

02_hier_*: hierarchical integration strategies

03_hc_07_*: engine architecture optimization application case
DOI: 10.5281/zenodo.10683733
title: System Architecture Optimization Experiments Dataset

description: This dataset contains experimental results for testing system architecture optimization algorithms. The results have been generated with https://github.com/jbussemaker/ArchitectureOptimizationExperiments/tree/hidden-constraints.

The results correspond to the following blocks of results:



01_sampling_*: hierarchical sampling and correction algorithms

02_hier_*: hierarchical integration strategies

03_hc_07_*: engine architecture optimization application case
DOI: 10.6084/m9.figshare.15058101.v1
title: Additional file 4 of Analysis of immune cell components and immune-related gene expression profiles in peripheral blood of patients with type 1 diabetes mellitus

description: Additional file 4. KEGG pathway
DOI: 10.6084/m9.figshare.15058098
title: Additional file 3 of Analysis of immune cell components and immune-related gene expression profiles in peripheral blood of patients with type 1 diabetes mellitus

description: Additional file 3. GO terms
DOI: 10.6084/m9.figshare.15058104.v1
title: Additional file 5 of Analysis of immune cell components and immune-related gene expression profiles in peripheral blood of patients with type 1 diabetes mellitus

description: Additional file 5. Distribution of immune cells
DOI: 10.5281/zenodo.10512459
title: Discovering and exploring the hidden diversity of the human gut viruses using highly enriched virome samples.

description: Discovering and exploring the hidden diversity of the human gut viruses using highly enriched virome samples

Viruses are crucially important in the human microbiome. By leveraging enriched Viral-Like Particle (VLP) viromes, through metagenomic assembly and sequence clustering, we retrieved thousands of viral contigs by from viromes and metagenomes.This upload contains the public collection of > 162,000 viral sequnces we retrieved. Sequences are clustered into 3,944 VSCs (Viral Sequence Clusters) that are labelled as known (kVSCs) or unknown (uVSCs), and further grouped into 1,345 Viral Sequence Groups (VSGs).

Files




File
Description


VSC5_rep_fnas_nr99_45k_metaphlanDB.fna.gz
The 45,872 representative sequences (dereplicated at 99% identity), included in the MetaPhlan 4.1 module, in FASTA format.


VSCs_groups.csv
Metadata of the 45,872 representative sequences included in the MetaPhlan 4.1 module.


VSC5_rep_fnas_full_47k.fna.gz
The non-dereplicated set of  47,820 representative sequences.


VSC5_complete_162k_labelled.fna.gz


The complete set of 162,876 sequences of potential viral origin extracted from metagenomes and viromes:



5651 Highly Enriched Virome Contigs (HEVC)

126,894 contigs from the unbinned metagenomes of Pasolli et al.

30,331 contigs from viromes 






CRISPR_VSG-to-species.csv

CRISPR_VSG-to-SGBs.csv



The  host-associations of each VSG group (each line is a match between VSG-species and VSG-SGB).





VSC_profiling_examples.zip



An archive containing a test / tutorial subsampled dataset.





Supplementary Data

See Supplementary Figures and Tables in the original biorxiv publication.

Citation

Discovering and exploring the hidden diversity of the human gut viruses using highly enriched virome samples - bioRxiv 2024

Moreno Zolfo,  Andrea Silverj, Aitor Blanco-Míguez, Paolo Manghi, Omar Rota-Stabelli, Vitor Heidrich, Jordan Jensen, Sagun Maharjan, Eric Franzosa, Cristina Menni, Alessia Visconti, Federica Pinto, Matteo Ciciani, Curtis Huttenhower, Anna Cereseto, Francesco Asnicar, Hiroaki Kitano, Takuji Yamada, Nicola Segata.
DOI: 10.5281/zenodo.10512460
title: Discovering and exploring the hidden diversity of the human gut viruses using highly enriched virome samples.

description: Discovering and exploring the hidden diversity of the human gut viruses using highly enriched virome samples

Viruses are crucially important in the human microbiome. By leveraging enriched Viral-Like Particle (VLP) viromes, through metagenomic assembly and sequence clustering, we retrieved thousands of viral contigs by from viromes and metagenomes.This upload contains the public collection of > 162,000 viral sequnces we retrieved. Sequences are clustered into 3,944 VSCs (Viral Sequence Clusters) that are labelled as known (kVSCs) or unknown (uVSCs), and further grouped into 1,345 Viral Sequence Groups (VSGs).

Files




File
Description


VSC5_rep_fnas_nr99_45k_metaphlanDB.fna.gz
The 45,872 representative sequences (dereplicated at 99% identity), included in the MetaPhlan 4.1 module, in FASTA format.


VSCs_groups.csv
Metadata of the 45,872 representative sequences included in the MetaPhlan 4.1 module.


VSC5_rep_fnas_full_47k.fna.gz
The non-dereplicated set of  47,820 representative sequences.


VSC5_complete_162k_labelled.fna.gz


The complete set of 162,876 sequences of potential viral origin extracted from metagenomes and viromes:



5651 Highly Enriched Virome Contigs (HEVC)

126,894 contigs from the unbinned metagenomes of Pasolli et al.

30,331 contigs from viromes 






CRISPR_VSG-to-species.csv

CRISPR_VSG-to-SGBs.csv



The  host-associations of each VSG group (each line is a match between VSG-species and VSG-SGB).





VSC_profiling_examples.zip



An archive containing a test / tutorial subsampled dataset.





Supplementary Data

See Supplementary Figures and Tables in the original biorxiv publication.

Citation

Discovering and exploring the hidden diversity of the human gut viruses using highly enriched virome samples - bioRxiv 2024

Moreno Zolfo,  Andrea Silverj, Aitor Blanco-Míguez, Paolo Manghi, Omar Rota-Stabelli, Vitor Heidrich, Jordan Jensen, Sagun Maharjan, Eric Franzosa, Cristina Menni, Alessia Visconti, Federica Pinto, Matteo Ciciani, Curtis Huttenhower, Anna Cereseto, Francesco Asnicar, Hiroaki Kitano, Takuji Yamada, Nicola Segata.
DOI: 10.6084/m9.figshare.15058146
title: Additional file 1 of Significance of initial, interim and end-of-therapy 18F-FDG PET/CT for predicting transformation risk in follicular lymphoma

description: Additional file 1. The original data.
DOI: 10.6084/m9.figshare.15058257
title: Additional file 1 of Dissecting indirect genetic effects from peers in laboratory mice

description: Additional file 1: Table S1. Cages for all mice across their time at the phenotyping facility.
DOI: 10.6084/m9.figshare.15058257.v1
title: Additional file 1 of Dissecting indirect genetic effects from peers in laboratory mice

description: Additional file 1: Table S1. Cages for all mice across their time at the phenotyping facility.
DOI: 10.6084/m9.figshare.15058207.v1
title: Additional file 5 of DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell

description: Additional file 5: Table S3. The statistics of predicted TAD-like domains using three methods with Li’s data.
DOI: 10.6084/m9.figshare.24494110.v1
title: Additional file 1 of Rare variants in GPR3 in POI patients: a case series with review of literature

description: Additional file 1: Supplementary table 1. Filtering steps of two WES data processing. Supplementary table 2. Primers used for Sanger sequencing. Supplementary table 3. List of 101 known POI causative genes. Supplementary table 4. List of 92 POI candidate genes.
DOI: 10.6084/m9.figshare.15058266.v1
title: Additional file 4 of Dissecting indirect genetic effects from peers in laboratory mice

description: Additional file 4: Table S3. Genome-wide significant IGE associations (per-phenotype FDR &lt; 10%).
DOI: 10.6084/m9.figshare.15058266
title: Additional file 4 of Dissecting indirect genetic effects from peers in laboratory mice

description: Additional file 4: Table S3. Genome-wide significant IGE associations (per-phenotype FDR &lt; 10%).
DOI: 10.6073/pasta/3a3f8c4f4e87dcf4607fccb1b695e91a
title: Meteorological measurements at Key Largo Ranger Station, South Florida (FCE) for July 2001 to August 2001

description: Basic radiation data, including Infra-red canopy temperatures, collected as 1 minute averages from a 5 m tower at Key Largo Ranger Station, South Florida, near Everglades National Park.
DOI: 10.6084/m9.figshare.15058095
title: Additional file 2 of Analysis of immune cell components and immune-related gene expression profiles in peripheral blood of patients with type 1 diabetes mellitus

description: Additional file 2. The 124 down-regulated genes
DOI: 10.6084/m9.figshare.15058098.v1
title: Additional file 3 of Analysis of immune cell components and immune-related gene expression profiles in peripheral blood of patients with type 1 diabetes mellitus

description: Additional file 3. GO terms
DOI: 10.6084/m9.figshare.15058101
title: Additional file 4 of Analysis of immune cell components and immune-related gene expression profiles in peripheral blood of patients with type 1 diabetes mellitus

description: Additional file 4. KEGG pathway
DOI: 10.5281/zenodo.10684580
title: Relationship among Connectivity of the Frontal Aslant Tract, Executive Functions, and Speech and Language Impairment in Children with Childhood Apraxia of Speech

description: Data for Tables and Figures sources for "Bombonato C, Cipriano E, Pecini C, Casalini C, Bosco P, Podda I, Tosetti M, Biagi L., Chilosi AM. “Relationship among Connectivity of the Frontal Aslant Tract, Executive Functions, and Speech and Language Impairment in Children with Childhood Apraxia of Speech” Brain Sciences 2023, 13 Article number 78.
DOI: 10.5281/zenodo.10684581
title: Relationship among Connectivity of the Frontal Aslant Tract, Executive Functions, and Speech and Language Impairment in Children with Childhood Apraxia of Speech

description: Data for Tables and Figures sources for "Bombonato C, Cipriano E, Pecini C, Casalini C, Bosco P, Podda I, Tosetti M, Biagi L., Chilosi AM. “Relationship among Connectivity of the Frontal Aslant Tract, Executive Functions, and Speech and Language Impairment in Children with Childhood Apraxia of Speech” Brain Sciences 2023, 13 Article number 78.
DOI: 10.5281/zenodo.10255267
title: NEP models for PTAF including PES and dipole

description: (This version is identical to the previous version 10.5281/zenodo.10255268 with the only change that the nep.txt files are added separately to provide easier interfacing with parsing scripts.)

NEP models used in https://doi.org/10.48550/arXiv.2311.09739 and https://doi.org/10.48550/arXiv.2312.05233.

The DFT data is obtained using the ASE ORCA interface with the following parameters:

calc = ORCA(label='orcacalc', maxiter=500, charge=-1, mult=1, orcasimpleinput='PBE def2-TZVP TIGHTSCF engrad')

train.xyz collects the relevant structures with associated information to train the NEP models on.

pes.zip and dipole.zip include inputs (nep.in), final NEP models (nep.txt), as well as loss and scatter plots.
DOI: 10.5281/zenodo.10255268
title: NEP models for PTAF including PES and dipole

description: NEP models used in https://doi.org/10.48550/arXiv.2311.09739 and https://doi.org/10.48550/arXiv.2312.05233.

The DFT data is obtained using the ASE ORCA interface with the following parameters:

calc = ORCA(label='orcacalc', maxiter=500, charge=-1, mult=1, orcasimpleinput='PBE def2-TZVP TIGHTSCF engrad')

train.xyz collects the relevant structures with associated information to train the NEP models on.

pes.zip and dipole.zip include inputs (nep.in), final NEP models (nep.txt), as well as loss and scatter plots.
DOI: 10.5281/zenodo.10684562
title: NEP models for PTAF including PES and dipole

description: (This version is identical to the previous version 10.5281/zenodo.10255268 with the only change that the nep.txt files are added separately to provide easier interfacing with parsing scripts.)

NEP models used in https://doi.org/10.48550/arXiv.2311.09739 and https://doi.org/10.48550/arXiv.2312.05233.

The DFT data is obtained using the ASE ORCA interface with the following parameters:

calc = ORCA(label='orcacalc', maxiter=500, charge=-1, mult=1, orcasimpleinput='PBE def2-TZVP TIGHTSCF engrad')

train.xyz collects the relevant structures with associated information to train the NEP models on.

pes.zip and dipole.zip include inputs (nep.in), final NEP models (nep.txt), as well as loss and scatter plots.
DOI: 10.6084/m9.figshare.15058146.v1
title: Additional file 1 of Significance of initial, interim and end-of-therapy 18F-FDG PET/CT for predicting transformation risk in follicular lymphoma

description: Additional file 1. The original data.
DOI: 10.5281/zenodo.10684654
title: Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile

description: Supporting data for AFProfile

casp15.tar.zst - predicted structures and MSAs for the CASP15 setnative_afm_2_6_bench.tar.zst - native cif files for all complexes with ranking confidence <0.75 in the AFM 2-6 chains benchmark ( https://doi.org/10.1093/bioinformatics/btad424)pred_top_models_afm_2_6_bench.tar.zst - predicted top ranked models and scores for all 100 samples.afm_opt_metrics.csv - the best models, confidences and MMscores for the AFProfile run on the AFM 2-6 chains benchmark (n=427 structures)msa_shapes.csv - the shape of the MSA as input to AFM for each structuredirected.tar.zst - contains all models for the AFProfile run on the AFM 2-6 chains benchmark (n=42700 samples)

The directories are compressed with zstd: https://github.com/facebook/zstdUncompress:tar --use-compress-program full/path/to/zstd -xvf file.tar.zst
DOI: 10.5281/zenodo.8108748
title: Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile

description: Supporting data for AFProfile

casp15.tar.zst - predicted structures and MSAs for the CASP15 setnative_afm_2_6_bench.tar.zst - native cif files for all complexes with ranking confidence <0.75 in the AFM 2-6 chains benchmark ( https://doi.org/10.1093/bioinformatics/btad424)pred_top_models_afm_2_6_bench.tar.zst - predicted top ranked models and scores for all 100 samples.afm_opt_metrics.csv - the best models, confidences and MMscores for the AFProfile run on the AFM 2-6 chains benchmark (n=427 structures)msa_shapes.csv - the shape of the MSA as input to AFM for each structuredirected.tar.zst - contains all models for the AFProfile run on the AFM 2-6 chains benchmark (n=42700 samples)

The directories are compressed with zstd: https://github.com/facebook/zstdUncompress:tar --use-compress-program full/path/to/zstd -xvf file.tar.zst
DOI: 10.5281/zenodo.8108749
title: Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile

description: Supporting data for AFProfile casp15.tar.zst - predicted structures and MSAs afm_2_6_bench_models.tar.zst - predicted structures
DOI: 10.6084/m9.figshare.19776420
title: Additional file 4 of Endocrine-disrupting chemicals and the risk of gestational diabetes mellitus: a systematic review and meta-analysis

description: Additional file 4: Datasets.
DOI: 10.6084/m9.figshare.15058204.v1
title: Additional file 4 of DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell

description: Additional file 4: Table S2. The statistics of predicted TAD-like domains using three methods with Flyamer’s data.
DOI: 10.25934/pr00008877
title: Antithrombotic therapies for secondary prevention in patients with cryptogenic stroke: a systematic review and network meta-analysis with individual participant data

description: Stroke is a life‐threatening medical condition in which brain tissue is damaged. Ischemic stroke is caused by a clot blocking the blood supply to part of the brain. There are ischemic strokes without a known origin of the clot, called cryptogenic. Because approximately 1 in 4 stroke survivors will likely have another stroke event, finding the cause of the stroke helps clinicians to select the most effective and safe pharmacological treatment to lower the likelihood of another cerebrovascular event (secondary prevention). Antithrombotic are blood thinning medicines that prevent clots from forming and growing and therefore are used to prevent the recurrence of stroke. There are two classes of antithrombotic agents, anticoagulants that slow down clotting and antiplatelets that prevent platelets from clumping. In the case of cryptogenic stroke, there is uncertainty about the best approach.
We aim to conduct a systematic review, a research project to collect, extract and interpret data from published studies on the topic, with network meta-analysis, a statistical technique that allows the quantitative comparisons of the effects interventions (medicines) that were not investigated by the same study.
DOI: 10.5281/zenodo.10684565
title: 4. Supplementary material--mortality vs density plots by species

description: Data and script to create additional, species-specific plots visualizing mortality vs. density.
DOI: 10.5281/zenodo.10684566
title: 4. Supplementary material--mortality vs density plots by species

description: Data and script to create additional, species-specific plots visualizing mortality vs. density.
DOI: 10.6084/m9.figshare.21228906.v1
title: Additional file 1 of Descriptive study of foodborne disease using disease monitoring data in Zhejiang Province, China, 2016–2020

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.15058272.v1
title: Additional file 5 of Dissecting indirect genetic effects from peers in laboratory mice

description: Additional file 5: Table S4. Genome-wide significant DGE associations (per-phenotype FDR &lt; 10%).
DOI: 10.6084/m9.figshare.20499829
title: Additional file 8 of Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes

description: Additional file 8: Table S3. Environment compounds used in this study. Concentrations of 1000 random environments that constitute the environment ball (see Methods). These concentrations are set as upper bounds to the metabolic models of the pan-reactomes.
DOI: 10.5281/zenodo.5097580
title: Data set related to the manuscript "Mesoscopic simulations of the in situ NMR spectra of porous carbon based supercapacitors: Electronic structure and adsorbent reorganisation effects"

description: Graphical files in the agr format for all the figures in the manuscript entitled "Mesoscopic simulations of the in situ NMR spectra of porous carbon based supercapacitors: Electronic structure and adsorbent reorganisation effects". Examples of input files for the lattice simulations are also provided.
DOI: 10.5281/zenodo.5097581
title: Data set related to the manuscript "Mesoscopic simulations of the in situ NMR spectra of porous carbon based supercapacitors: Electronic structure and adsorbent reorganisation effects"

description: Graphical files in the agr format for all the figures in the manuscript entitled "Mesoscopic simulations of the in situ NMR spectra of porous carbon based supercapacitors: Electronic structure and adsorbent reorganisation effects". Examples of input files for the lattice simulations are also provided.
DOI: 10.6084/m9.figshare.19776420.v1
title: Additional file 4 of Endocrine-disrupting chemicals and the risk of gestational diabetes mellitus: a systematic review and meta-analysis

description: Additional file 4: Datasets.
DOI: 10.15468/dl.ew4ckl
title: Occurrence Download

description: A dataset containing 251 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Chacophrys Reig & Limeses, 1963"
 ]
}

 The dataset includes 251 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004427-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ojopot
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Schefflera polybotrya (Miq.) R.Vig."
 ]
}

 The dataset includes 36 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033777-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.362y7w
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "TaxonKey is Osmoderma eremita (Scopoli, 1763)",
 "Year 2013-2023"
 ]
}

 The dataset includes 33 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025488-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v0yfif
title: Occurrence Download

description: A dataset containing 2647 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Otis tarda Linnaeus, 1758"
 ]
}

 The dataset includes 2647 records from 86 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004428-150316153013904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nr7ccd
title: Occurrence Download

description: A dataset containing 1999 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Composición florística y estructura de una parcela permanente en transición de bosques húmedos tropicales con bosques secos tropicales del municipio de Lebrija, Santander (Primer censo)"
 ]
}

 The dataset includes 1999 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017452-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6qq348
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alchemilla legionensis S.E.Fröhner"
 ]
}

 The dataset includes 21 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026175-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xbx2nq
title: Occurrence Download

description: A dataset containing 90 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Late Albian Col de Palluel (SE France, Niveau Breistroffer): results from planktic foraminifera"
 ]
}

 The dataset includes 90 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004428-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x2bc3v
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Guatemala",
 "TaxonKey is Glaucomys volans (Linnaeus, 1758)"
 ]
}

 The dataset includes 8 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066200-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.