cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.82250/3003623
title: Tilletia maclaganii Tm001 NY21 Transcriptome - Tmac_Tm001NY21_culture

description: Tilletia maclaganii Tm001 NY21 Transcriptome; sample from Tm001 NY21 single basidiospore culture challenged with 1ppm PCNB
DOI: 10.15468/dl.nwdt6u
title: Occurrence Download

description: A dataset containing 58 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON((-155.32864 10.26611,-38.57609 10.26611,-38.57609 75.57593,-155.32864 75.57593,-155.32864 10.26611))",
 "TaxonKey is Asclepias ovata"
 ]
}

 The dataset includes 58 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045476-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.82250/3003624
title: Tilletia maclaganii Tm001 NY21 Transcriptome - Tmac_SW_interact

description: Tilletia maclaganii Tm001 NY21 Transcriptome; sample from smut-infected switchgrass (cultivar 'Shawnee') panicles, Ithaca, NY
DOI: 10.82250/3003628
title: Files_used_for_figures

description: This folder includes all the relevant files used to generate the main Figures in the paper.
DOI: 10.5281/zenodo.17650022
title: Data used in "Markov Inequality as a Tool for Linear-Scaling Estimation of Local Observables"
DOI: 10.5281/zenodo.17650023
title: Data used in "Markov Inequality as a Tool for Linear-Scaling Estimation of Local Observables"
DOI: 10.82250/3003625
title: Tilletia maclaganii strain Tm001 NY21, whole genome shotgun sequencing project

description: GenBank: JBQVXD000000000.1
DOI: 10.82250/3003631
title: Pichia sp. KDB-2024a strain:UFMG-CM-Y531 Genome sequencing

description: Pichia senei was isolated from necrotic cactus tissues of Cereus saddianus and Micranthocereus dolichospermaticus, and from water tank (phytotelmata) of the bromeliad species Bromelia karatas, collected in the state of Tocantins, Brazil.
DOI: 10.82250/3003632
title: Teucrium chamaedrys sequencing

description: Genomic sequencing of the medicinal plant Teucrium chamaedrys
DOI: 10.82250/3003636
title: Novosphingobium aromaticivorans DSM 12444 DAP Seq epigenomics

description: DNA affinity purification sequencing (DAP-seq) to identify putative transcriptional regulators of aromatic metabolism in Novosphingobium aromaticivorans
DOI: 10.82250/3003637
title: Using DNA Affinity Purification sequencing (DAP-seq) to identify in vitro binding sites of transcription factors potentially involved in aromatic degradation

description: The genome-wide binding sites of 44 transcription factors from the aromatic metabolizing Alphaproteobacterium Novosphingobium aromaticivorans were identified using DNA Affinity Purification sequencing (DAP-seq). We report 32 of these transcription factors have at least one area of enrichment. These data will be valuable for better understanding of aromatic metabolism.
DOI: 10.82250/3003638
title: Study of the effect of the trancription factor SARO_RS14285 in aromatics degradation in Novosphingobium aromaticivorans

description: Novosphingobium aromaticivorans DSM12444 is a bacterium capable of catabolizing several lignin aromatics. A main degradation pathway for these compounds is the protocatechuate (PCA) meta-cleavage. Nevertheless, the transcriptional regulation of this pathway is still unknown. Immediately upstream of the genes encoding the enzymes for this pathway, the LysR-type transcription factor (LTTF) SARO_RS14285 was identified. To evaluate the functionality of this LTTF, a deletion mutant was constructed. A transcriptomic analysis of the mutant strain cultured in several aromatic compounds is included in this report. Overall design: RNA-seq profiling of the WT and the deletion mutant cultured in minimal medium with glucose and one of the following aromatics: protocatechuic acid (PCA), 4-coumaric acid (4-CA), vanillic acid (VA) or syringic acid (SA).
DOI: 10.82250/3003639
title: Novosphingobium aromaticivorans DSM 12444 lignin transcriptomics
DOI: 10.82250/3003640
title: Pooled whole-genome sequencing in Puccinia novopanici

description: Sori from switchgrass rust infections of plants in nine locations were sequenced to a high depth using whole-genome sequencing, with the goal of determining genetic diversity and divergence across the pathogen's range.
DOI: 10.82250/2584700
title: Sorghum bicolor TX08001 Compendium Set3 Gene Expression Profiling
DOI: 10.82250/3003571
title: Panicum virgatum Raw sequence reads

description: Diversity Sequencing of Panicum virgatum
DOI: 10.82250/3001660
title: Vanderwaltozyma urihicola sp. nov., a yeast species isolated from rotting wood and beetles in a Brazilian Amazonian rainforest biome

description: Vanderwaltozyma sp. isolate UFMG-CM-Y7006 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence
DOI: 10.82250/3003643
title: CRISPRt data studying the physiological role of an Acinetobacter-specific sigma factor

description: Here, we show that SigAb is a metal stress-responsive ECF that appears unique to Acinetobacter species and distinct from RpoE. We combine promoter mutagenesis, motif scanning, and ChIP-seq to define the direct SigAb regulon, which consists of sigAb itself, the stringent response mediator, relA, and the uncharacterized small RNA, "sabS."
DOI: 10.15468/dl.ajujwe
title: Occurrence Download

description: A dataset containing 422 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Waitzia nitida",
 "HasCoordinate is true"
 ]
}

 The dataset includes 422 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045477-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.82250/3001663
title: Vanderwaltozyma urihicola sp. nov., a yeast species isolated from rotting wood and beetles in a Brazilian Amazonian rainforest biome

description: Vanderwaltozyma sp. isolate UFMG-CM-Y7006 internal transcribed spacer 2 and large subunit ribosomal RNA gene, partial sequence
DOI: 10.82250/3003644
title: Physiological Roles of an Acinetobacter-specific σ Factor

description: Genome binding/occupancy profiling by high throughput sequencing, Expression profiling by high throughput sequencing
DOI: 10.82250/2584699
title: A small number of point mutations confer formate tolerance in Shewanella oneidensis

description: Several strains of formate-tolerant Shewanella oneidensis were evolved through continuous subculturing in minimal lactate media with increasing concentrations of formate over time.
DOI: 10.82250/3001665
title: Vanderwaltozyma urihicola sp. nov., a yeast species isolated from rotting wood and beetles in a Brazilian Amazonian rainforest biome

description: Vanderwaltozyma sp. UFMG-CM-Y7006, whole genome shotgun sequencing project
DOI: 10.82250/3001667
title: Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes

description: To investigate the effects of stabilizing G-quadruplexes on Escherichia coli, cells were grown in the presence of the G-quadruplex stabilizing compound, NMM, and RNA-seq was performed. This was done for the control cell strain (MG1655 dtolC) as well as a strain with a decrease in a translation elongation factor (MG1655 dtolC tufA::kan). TPM values were used for differential gene expression analysis between each growth condition. All samples were grown and sequenced in triplicate.
DOI: 10.82250/3001670
title: Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes

description: Genomic DNA from each sample was prepared using the Wizard Genomic DNA Purification Kit (Promega) and after, DNA was quantified using the QuantiFluor ONE dsDNA System (Promega). Genomic DNA underwent shearing to ~200 bp fragments via sonication and the gDNA fragments were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). Bead-based size selection was used to select ~200 bp fragments and the fragments then underwent a splinkerette PCR using a Tn5-enriching forward primer and custom reverse primers for multiplexing. A final bead-based size selection was used to select for the correct length DNA. DNA was sequenced at the University of Michigan Advanced Genomics Core using Illumina sequencing with a custom read primer reading the last 10 nt of the transposon. PhiX174 DNA spike was added to the run to ensure sufficient sequence diversity on the flow cell. Then, a custom index read primer and standard Illumina primer were used to sequence the index reads and PhiX174, respectively.
DOI: 10.82250/3001672
title: Y1000 gene family

description: All relative analysis data and codes used in this study are available on the Figshare data repository. You can also find the codes on the Github repository at https://github.com/vnuii/Y1000_gene_family.
DOI: 10.82250/3001673
title: Long Term Ecological Research Main Cropping System Experiment

description: We leverage the Kellogg Biological Station Long Term Ecological Research Main Cropping System Experiment (KBS MCSE) field experiment to test trade-offs among high growth yield (Y), resource acquisition (A), and stress tolerance (S) traits using metagenomic data from plots with different land use, drought manipulation, and C addition.
DOI: 10.82250/3001678
title: UFMP and CAW Bioreactor Metagenome

description: CSTR anaerobic bioreactors fed UltraFiltered Milk Permeate (UFMP) and Cottage cheese Acid Whey (CAW) were inoculated with acid sludge microbial communities and monitored overtime for lactic acid production. Samples were taken for metagenomics analyses.
DOI: 10.82250/3001679
title: Diazotroph diversity across a land-management gradient

description: Soil diazotrophs are ubiquitous bacteria and archaea responsible for converting atmospheric nitrogen into plant-available ammonium. This process, if properly harnessed, can ameliorate excessive fertilizer inputs in conventional agricultural systems. However, the effect of diazotroph biodiversity on free-living nitrogen fixation (FLNF) is poorly understood. Here, we characterized diazotroph biodiversity across a land-management intensity gradient, determining the interactive effects of land management and diazotroph biodiversity on their ecosystem functioning (FLNF). Subsequently, we evaluated the functional redundancy of diazotroph biodiversity on FLNF in-vitro by performing a biodiversity reduction assay with chloroform fumigation, incubating soils with chloroform for either 24 or 72 hours. We estimated diazotroph biodiversity for both in-situ and chloroform-fumigated samples by preparing and sequencing nifH gene libraries. The raw sequencing data of our nifH library is deposited here.
DOI: 10.82250/3001680
title: Genome assembly PYCC 8100

description: The yeast Torulaspora delbrueckii is gaining importance for biotechnology due to its ability to increase wine sensorial complexity and for enhancing pre-frozen bread dough leavening. However, little is known about its population structure, and variation in gene content, or possible domestication routes have not been investigated. Here, we address these issues and update the circumscription of T. delbrueckii, which is composed of five major clades. Among the three European clades, a lineage associated with the wild arboreal niche is sister to the two other lineages that are linked with anthropic environments, one to wine fermentations and the other one to diverse sources including dairy products and bread dough (Mix- Anthropic clade). Using 62 genomes we identified 5629 genes in the pangenome of T. delbrueckii and 270 genes in the cloud genome. A pangenome tree analysis showed that wine strains have a genome composition were more similar to European wild arboreal strains than to those of the Mix Anthropic clade, in contradiction with the phylogenetic analysis. An association of gene content and ecology gave further support to the hypothesis that the Mix - Anthropic clade has the most specialized genome content and indicated that some of the exclusive genes were implicated in galactose and maltose utilization. More detailed analyses traced the acquisition of a cluster of GAL genes in strains associated with dairy products and the expansion and functional diversification of MAL genes in strains isolated from bread dough. Contrary to S. cerevisiae, domestication in T. delbrueckii is not primed by alcoholic fermentation and appears to be a recent event.
DOI: 10.82250/3001681
title: Genome assembly UWOPS 85-398.1-1

description: The yeast genus Torulaspora (subphylum Saccharomycotina, family Saccharomycetaceae) is mostly known from its type species T. delbrueckii, a frequent colonizer of wine and sourdough bread fermentations. The genus currently contains ten species that are typically found in various natural terrestrial environments in temperate and tropical climates. Here we employ taxogenomic analyses to investigate a large collection of Torulaspora strains obtained in multiple surveys we carried out in Asia, Australasia, North America, South America, and Europe, and to which we added several strains maintained in culture collections. Our analyses detected twelve novel species that are formally described here, thereby more than doubling the species diversity of Torulaspora. We also sketch a genotype-phenotype map for the genus and show how key genes have evolved in concert with the physiological traits they control. This dramatic increase in the number of species in the genus Torulaspora highlights how limited the current inventory of fungal taxa is. It also shows how integrated taxogenomics approaches can foster the assessment of species circumscriptions in fungi, especially when classical approaches relying on DNA barcode regions give inconclusive results.
DOI: 10.82250/3001684
title: Genome assembly UFMG-CM Y6992

description: The yeast genus Torulaspora (subphylum Saccharomycotina, family Saccharomycetaceae) is mostly known from its type species T. delbrueckii, a frequent colonizer of wine and sourdough bread fermentations. The genus currently contains ten species that are typically found in various natural terrestrial environments in temperate and tropical climates. Here we employ taxogenomic analyses to investigate a large collection of Torulaspora strains obtained in multiple surveys we carried out in Asia, Australasia, North America, South America, and Europe, and to which we added several strains maintained in culture collections. Our analyses detected twelve novel species that are formally described here, thereby more than doubling the species diversity of Torulaspora. We also sketch a genotype-phenotype map for the genus and show how key genes have evolved in concert with the physiological traits they control. This dramatic increase in the number of species in the genus Torulaspora highlights how limited the current inventory of fungal taxa is. It also shows how integrated taxogenomics approaches can foster the assessment of species circumscriptions in fungi, especially when classical approaches relying on DNA barcode regions give inconclusive results.
DOI: 10.82250/3001686
title: Genome assembly ASM3058019v1
DOI: 10.82250/3003593
title: Tnseq to identify catabolism of b-5 linked aromatics by Novosphingobium aromaticivorans

description: This study investigates the catabolism of the b-5 linked aromatic dimer dehydrodiconiferyl alcohol (DC-A) by the bacterium Novosphingobium aromaticivorans. We used genome wide screens to identify candidate genes involved in DC-A catabolism. Subsequent in vivo and in vitro analyses of these candidates elucidated a catabolic pathway composed of four required gene products and several partially redundant dehydrogenases that convert DC-A to aromatic monomers that can be funneled into the central aromatic metabolic pathway of N. aromaticivorans.
DOI: 10.82250/3001521
title: Sorghum bicolor BTx623 Regulation of MLG pathway Gene Expression Profiling

description: Genome-transcriptome
DOI: 10.82250/3001522
title: Sorghum bicolor Circadian cycling Gene Expression Profiling

description: Genome-transcriptome
DOI: 10.82250/3001526
title: Sorghum bicolor Della Leaf development Gene Expression Profiling

description: Genome-transcriptome
DOI: 10.82250/3001527
title: Sorghum bicolor R07007 leaf diel cycling Gene Expression Profiling

description: Genome-transcriptome
DOI: 10.82250/3001533
title: Sorghum bicolor Della internode development Gene Expression Profiling

description: Genome-transcriptome
DOI: 10.82250/3001536
title: Sorghum bicolor TX08001 1.Stem V-phase tissues Gene Expression Profiling

description: Genome-transcriptome
DOI: 10.82250/3001539
title: Sorghum bicolor Della diurnal cycling Gene Expression Profiling

description: Genome-transcriptome
DOI: 10.15468/dl.6yrk96
title: Occurrence Download

description: A dataset containing 66659 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-10.57901 47.59192,-11.44927 37.04011,-8.40337 34.86448,-18.19371 22.46339,-15.14783 21.04922,-7.75068 26.59708,3.88893 19.52628,11.93877 23.65998,23.25205 19.19994,24.99255 21.37557,37.71999 22.13704,35.76192 27.79367,38.48145 30.29566,40.43952 33.12397,45.44348 36.93132,44.682 42.58796,29.01746 43.02309,5.08553 54.01002,3.34503 52.48709,-1.93066 50.63236,-10.57901 47.59192))",
 "OccurrenceStatus is Present",
 "TaxonKey is Rutaceae"
 ]
}

 The dataset includes 66659 records from 553 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045422-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5518/345
title: Motion analysis in total joint replacement patients: Data Release 1.

description: This release serves as an example of the data that will be released in coming months. The data collection method and marker protocol can be found in the collection dataset https://doi.org/10.5518/319. This data can be used with motion capture and multibody modelling software such as Anybody Technology Modelling software, where the model built specifically for this data can be found here https://www.anybodytech.com/contact/about-abt/.
DOI: 10.15468/dl.3kj7p6
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "Country is South Africa",
 "OccurrenceStatus is Present",
 "TaxonKey is Urena lobata"
 ]
}

 The dataset includes 30 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045479-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3bfruv
title: Occurrence Download

description: A dataset containing 1652342 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Azorean Biodiversity Portal"
 ]
}

 The dataset includes 1652342 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045431-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17651607
title: Волна и частица – от дуализма к единству

description: Приводятся примеры, когда макроскопический объект проявляет себя и как волна, и как осязаемый объект. Доказывается, что элементарные частицы являются и волнами, и частицами одновременно, а не попеременно. Это доказательство получено, как новые решения уравнений Максвелла. Доказательство не является всеобъемлющим - рассматривается только кубическая,  сферическая и дисковая частицы. Данная публикация – это обзор и дополнение уже опубликованных статей.
DOI: 10.5281/zenodo.17651608
title: Волна и частица – от дуализма к единству

description: Приводятся примеры, когда макроскопический объект проявляет себя и как волна, и как осязаемый объект. Доказывается, что элементарные частицы являются и волнами, и частицами одновременно, а не попеременно. Это доказательство получено, как новые решения уравнений Максвелла. Доказательство не является всеобъемлющим - рассматривается только кубическая,  сферическая и дисковая частицы. Данная публикация – это обзор и дополнение уже опубликованных статей.
DOI: 10.15468/dl.z8w38j
title: Occurrence Download

description: A dataset containing 197 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Spondylus gussonii"
 ]
}

 The dataset includes 197 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045484-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hxcrne
title: Occurrence Download

description: A dataset containing 5407 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "TaxonKey is Psylliodes chrysocephalus"
 ]
}

 The dataset includes 5407 records from 179 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045483-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13140/rg.2.2.19444.00644
title: Served as Chief Guest at the Indira Gandhi Women Leadership and Empowerment Excellence Awards 2025, organized by the National Institute for Research and Development (NIRDI) in association with LKP Academy on 19th November 2025, delivering inspiring insights that added immense value to the event.
DOI: 10.15468/dl.b59xp3
title: Occurrence Download

description: A dataset listing the 2 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is France",
 "TaxonKey is Alosa alosa"
 ]
}

 The dataset's 2 records were derived from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045452-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25345/c5930p793
title: MassIVE MSV000099958 - Rapid optogenetic manipulation of autophagy reveals that the nuclear pore complex is a robust autophagy substrate
title: Autophagy, a conserved recycling process, manages intracellular quality control to mitigate stress. To determine the rapid effects of autophagy perturbation we developed the first optogenetic tool that enables rapid inhibition of autophagy, termed ASAP. ASAP selectively inhibits autophagy within 5 minutes providing a precise and dynamic approach to study autophagy regulation. Proteomic profiling with ASAP revealed the most tightly regulated autophagy substrates along with novel, previously unidentified, substrates including nuclear pore complex (NPC) proteins. Interestingly, autophagy regulates quality control of incomplete NPCs still in the cytoplasm via specific LC3 interacting regions (LIRs), sparing NPCs embedded in the nuclear envelope. Upon rapid autophagy inhibition incomplete NPCs accumulate and instead of undergoing autophagic degradation, cytoplasmic NPCs aggregate in processing bodies. With the use of the first tool to rapidly and specifically inhibit autophagy, these findings reveal that the nuclear pore complex is a tightly regulated autophagy substrate
DOI: 10.7910/dvn/9vtdox
title: Variable-Oriented Quantitative Empirical Research Method for Lossless Knowledge Graph Research Datasets

description: “Variable-oriented quantitative empirical research: systemic framework and procedures” is extracted in this project as a structured knowledge graph, representing the core variables, hypothesized relationships, and analytical steps as nodes and edges, so that they can be easily used for automatic retrieval, modeling, and visual analysis.
DOI: 10.6084/m9.figshare.29830541
title: Supplement Materials, Methods, and Figures

description: Supplemental Information for Murine Partial Tracheal Occlusion Alters Respiratory Dynamics and Potentiates Airspace Injury