cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3603383_d1.v1
title: Additional file 7: of High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)

description: SNP results from PELE-sequencing of wild and lab-adapted C. remanei populations. Rare SNPs in the wild and lab-adapted C. remanei populations were detected with PELE-Seq at 2000Ă  OPE read depth. Alleles present in both populations are listed, as well as those found in either the wild or lab-adapted population alone. Read pileups are listed for SNPs are absent in one population (putative de novo SNPs and SNPs lost during lab-adaptation). (XLSX 722 kb)
DOI: 10.6084/m9.figshare.c.3603362_d5.v1
title: Additional file 2: of Physiological and transcriptional analyses of developmental stages along sugarcane leaf

description: Fasta file with the assembly. Transcript assembly as obtained by trinity and submitted to the TSA at NCBI. (BZ2 57956 kb)
DOI: 10.6084/m9.figshare.c.3603362_d6.v1
title: Additional file 10: of Physiological and transcriptional analyses of developmental stages along sugarcane leaf

description: This Additional File is an Excel File containing 6 spreadsheets (Additional Tables 4–9) with the results of our gene ontology analysis for each leaf segment. Table S4. Enriched gene ontology terms for genes over-expressed at B0 identified on the contrast B-B0. Table S5. Enriched gene ontology terms for genes over-expressed at B identified on the contrast B-B0. Table S6. Enriched gene ontology terms for genes over-expressed at B identified on the contrast M-B. Table S7. Enriched gene ontology terms for genes over-expressed at M identified on the contrast M-B. Table S8. Enriched gene ontology terms for genes over-expressed at M identified on the contrast T-M. Table S9. Enriched gene ontology terms for genes over-expressed at T identified on the contrast T-M. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.c.3603383_d4.v1
title: Additional file 6: of High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)

description: Recommended PELE-Seq workflow and SNP-calling parameters. An overview of the PELE-Seq analysis pipeline is outlined and optimized variant-calling parameters are provided for various read depths. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3603362_d7.v1
title: Additional file 6: of Physiological and transcriptional analyses of developmental stages along sugarcane leaf

description: Table with the list of orthologous genes between the five species: Sorghum bicolor (Abbreviation: SBIC), Setaria italica (Abbreviation: SITA), Saccharum sp. SP80–3280 (Abbreviation: SACC), Oryza sativa (Abbreviation: OSAT) and Zea mays (Abbreviation: ZMAY). Groups of orthologous genes were identified by OrthoMCL with an inflation value of 1.5. (BZ2 1258 kb)
DOI: 10.6084/m9.figshare.c.3603386_d1.v1
title: Additional file 2 of Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints

description: Code S1. This zip-file contains the MATLAB code used for the simulation example (conversion process) and the application examples (NGF-induced Erk signaling in primary sensory neurons and Raf/MEK/ERK signaling in HeLa cells after release from S-phase arrest) presented in the paper. We provide implementations for the hybrid optimization and simulation-based optimization methods, the models and the optimization. In addition to the implementation, also all data and result files (.mat,.csv) are included. (ZIP 25965 kb)
DOI: 10.6084/m9.figshare.c.3603383_d6.v1
title: Additional file 8: of High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)

description: Basic PELE-seq SNP-calling scripts. The basic commands used for PELE-Seq analysis are provided as a shell script. (TXT 11 kb)
DOI: 10.6084/m9.figshare.c.3603362_d8.v1
title: Additional file 7: of Physiological and transcriptional analyses of developmental stages along sugarcane leaf

description: This Additional File is an Excel File containing 3 spreadsheets (Additional Tables 1–3) with the results of our differential expression analysis contrasting two leaf segments. Table S1. Differentially expressed genes between the contrast B-B0. Table S2. Differentially expressed genes between the contrast M-B. Table S3. Differentially expressed genes between the contrast T-M. (XLSX 150 kb)
DOI: 10.15468/dl.6xv8dh
title: Occurrence Download

description: A dataset containing 57 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Schoenoplectus heterochaetus (Chase) Soják",
 "BasisOfRecord is one of (Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Continent is North America"
 ]
}

 The dataset includes 57 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0175172-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kmmznc
title: Occurrence Download

description: A dataset containing 95 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Panama",
 "TaxonKey is Porthidium lansbergii (Schlegel, 1841)"
 ]
}

 The dataset includes 95 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027158-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s58baf
title: Occurrence Download

description: A dataset containing 164915 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Observation",
 "BasisOfRecord is Machine Observation"
 ]
 },
 "Geometry POLYGON((-74.03687 42.9725,-74.12476 41.22825,-69.73022 40.7639,-69.77417 42.81152,-74.03687 42.9725))",
 "HasCoordinate is true",
 "TaxonKey is Tachycineta bicolor (Vieillot, 1808)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 164915 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027159-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4erv6z
title: Occurrence Download

description: A dataset containing 229 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhynchospora capillacea Torr.",
 "BasisOfRecord is one of (Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Continent is North America"
 ]
}

 The dataset includes 229 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0175141-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9b7c6c
title: Occurrence Download

description: A dataset containing 181 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Schoenoplectiella purshiana (Fernald) Lye",
 "BasisOfRecord is one of (Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Continent is North America"
 ]
}

 The dataset includes 181 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0175162-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pcpjvc
title: Occurrence Download

description: A dataset containing 378 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "MediaType is Image",
 "TaxonKey is Anthriscus cerefolium (L.) Hoffm."
 ]
}

 The dataset includes 378 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027161-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dcmrld
title: Occurrence Download

description: A dataset containing 363153 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Poa pratensis L.",
 "HasGeospatialIssue is FALSE",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 363153 records from 562 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027161-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j3sbbm
title: Occurrence Download

description: A dataset containing 941 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Trichophorum cespitosum (L.) Hartm.",
 "BasisOfRecord is one of (Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Continent is North America"
 ]
}

 The dataset includes 941 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0175218-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.l2e6pr
title: Occurrence Download

description: A dataset containing 600384 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Specimen"
 ]
 },
 "Country is Chinese Taipei",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 600384 records from 112 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027161-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z9n9ed
title: Occurrence Download

description: A dataset containing 22760 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carcharhinus perezii (Poey, 1876)"
 ]
}

 The dataset includes 22760 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0175227-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2j9mxf
title: Occurrence Download

description: A dataset containing 87 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Plantago cafra Decne.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 87 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047242-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4r4mxm
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Populus davidiana var. tomentosa (C.K.Schneid.) Nakai"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0150277-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h2wivn
title: Occurrence Download

description: A dataset containing 4511 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-99.29581 25.09964,-98.16971 25.09964,-98.16971 26.31363,-99.29581 26.31363,-99.29581 25.09964))",
 "HasCoordinate is true",
 "TaxonKey is Plantae",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4511 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027161-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3va8vu
title: Occurrence Download

description: A dataset containing 127 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "Geometry POLYGON((-118.37089 21.68313,-108.33729 21.68313,-108.33729 33.94317,-118.37089 33.94317,-118.37089 21.68313))",
 "HasGeospatialIssue is false",
 "TaxonKey is Aquilegia formosa Fisch. ex DC."
 ]
}

 The dataset includes 127 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047243-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y7so9i
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Echinodorus lanceolatus Rataj",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 46 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027162-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m335ea
title: Occurrence Download

description: A dataset containing 104352 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gammaridae",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than 2000"
 ]
}

 The dataset includes 104352 records from 401 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0163425-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.txgawc
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cranoglanis bouderius (Richardson, 1846))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 10 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047244-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gcbawg
title: Occurrence Download

description: A dataset containing 299606 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Machine Observation",
 "BasisOfRecord is Human Observation"
 ]
 },
 "Year 2000-2018",
 "Geometry POLYGON((-180 -52,180 -52,180 52,-180 52,-180 -52))",
 "HasCoordinate is true",
 "TaxonKey is Annelida",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 299606 records from 352 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027163-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15147561
title: Biological modifications of the immune response to COVID-19 vaccine in patients treated with rituximab and immune-checkpoint inhibitors

description: Understanding how immune-modulating therapies affect mRNA vaccine responses is essential for optimizing immunization strategies in cancer and immunocompromised patients. In this work, we investigate the immune response to the third dose of COVID-19 mRNA vaccine in cancer-free individuals, patients with non-Hodgkin lymphoma treated with rituximab (RTX), and patients with solid tumors receiving immune-checkpoint inhibitors (ICI). By integrating blood RNA-sequencing, SARS-CoV-2 serology, and interferon-γ release assessment, we chart the vaccine-induced immunity over a 6 month-time frame. Our findings reveal that RTX patients exhibit profound immune dysfunction, characterized by a blunted type I interferon response, upregulation of transcripts pertaining to regulatory T-cell, and widespread impairment of humoral immunity. In contrast, ICI patients have a preserved vaccine-induced immunity, displaying adaptive B-cell and T-cell responses akin to those of cancer-free volunteers. These results provide critical insights into immunization strategies for immunocompromised populations and may inform future vaccination protocols.
DOI: 10.5281/zenodo.15147562
title: Biological modifications of the immune response to COVID-19 vaccine in patients treated with rituximab and immune-checkpoint inhibitors

description: Understanding how immune-modulating therapies affect mRNA vaccine responses is essential for optimizing immunization strategies in cancer and immunocompromised patients. In this work, we investigate the immune response to the third dose of COVID-19 mRNA vaccine in cancer-free individuals, patients with non-Hodgkin lymphoma treated with rituximab (RTX), and patients with solid tumors receiving immune-checkpoint inhibitors (ICI). By integrating blood RNA-sequencing, SARS-CoV-2 serology, and interferon-γ release assessment, we chart the vaccine-induced immunity over a 6 month-time frame. Our findings reveal that RTX patients exhibit profound immune dysfunction, characterized by a blunted type I interferon response, upregulation of transcripts pertaining to regulatory T-cell, and widespread impairment of humoral immunity. In contrast, ICI patients have a preserved vaccine-induced immunity, displaying adaptive B-cell and T-cell responses akin to those of cancer-free volunteers. These results provide critical insights into immunization strategies for immunocompromised populations and may inform future vaccination protocols.
DOI: 10.13145/bacdive116936.20241212.9.2
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive116936.20251217.10
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0108823.10fu
title: SH0108823.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.13145/bacdive116937.20241212.9.2
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive116937.20251217.10
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0108824.10fu
title: SH0108824.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.25574/28475
title: Chandra X-ray Observatory ObsId 28475

description: AO-25 Observations of the Perseus Cluster
DOI: 10.13145/bacdive116938.20241212.9.2
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive116938.20251217.10
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0108825.10fu
title: SH0108825.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.13145/bacdive116939.20241212.9.2
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0108826.10fu
title: SH0108826.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.