cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh0957398.10fu
title: SH0957398.10FU

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: 10.15156/bio/sh0957399.10fu
title: SH0957399.10FU

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: 10.15156/bio/sh0957400.10fu
title: SH0957400.10FU

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: 10.15156/bio/sh0957401.10fu
title: SH0957401.10FU

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: 10.15468/dl.74zhrz
title: Occurrence Download

description: A dataset containing 2784315 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pinus L."
 ]
}

 The dataset includes 2784315 records from 2956 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000687-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10681595
title: Homopolymer dataset and results

description: Dataset and results of https://github.com/gael-millot/homopolymer
DOI: 10.6084/m9.figshare.20296404
title: Additional file 1 of Genotyping-by-Sequencing Based Investigation of Population Structure and Genome Wide Association Studies for Seven Agronomically Important Traits in a Set of 346 Oryza rufipogon Accessions

description: Additional file 1: The detailed information of Oryza rufipogon accessions investigated in current study along with their countries of origin.
DOI: 10.6084/m9.figshare.20296410.v1
title: Additional file 3 of Genotyping-by-Sequencing Based Investigation of Population Structure and Genome Wide Association Studies for Seven Agronomically Important Traits in a Set of 346 Oryza rufipogon Accessions

description: Additional file 3: Map positions of genotypic dataset.
DOI: 10.6084/m9.figshare.20296410
title: Additional file 3 of Genotyping-by-Sequencing Based Investigation of Population Structure and Genome Wide Association Studies for Seven Agronomically Important Traits in a Set of 346 Oryza rufipogon Accessions

description: Additional file 3: Map positions of genotypic dataset.
DOI: 10.6084/m9.figshare.13489171.v1
title: Defining the Syrian hamster as a highly susceptible preclinical model for SARS-CoV-2 infection

description: Following emergence in late 2019, SARS-CoV-2 rapidly became pandemic and is presently responsible for millions of infections and hundreds of thousands of deaths worldwide. There is currently no approved vaccine to halt the spread of SARS-CoV-2 and only very few treatment options are available to manage COVID-19 patients. For development of preclinical countermeasures, reliable and well-characterized small animal disease models will be of paramount importance. Here we show that intranasal inoculation of SARS-CoV-2 into Syrian hamsters consistently caused moderate broncho-interstitial pneumonia, with high viral lung loads and extensive virus shedding, but animals only displayed transient mild disease. We determined the infectious dose 50 to be only five infectious particles, making the Syrian hamster a highly susceptible model for SARS-CoV-2 infection. Neither hamster age nor sex had any impact on the severity of disease or course of infection. Finally, prolonged viral persistence in interleukin 2 receptor gamma chain knockout hamsters revealed susceptibility of SARS-CoV-2 to adaptive immune control. In conclusion, the Syrian hamster is highly susceptible to SARS-CoV-2 making it a very suitable infection model for COVID-19 countermeasure development.
DOI: 10.6084/m9.figshare.21353324
title: Naringin regulates mitochondrial dynamics to protect against acetaminophen-induced hepatotoxicity by activating the AMPK/Nrf2 signaling pathway in vitro

description: Naringin (Nar) has been reported to exert potential hepatoprotective effects against acetaminophen (APAP)-induced injury. Mitochondrial dysfunction plays an important role in APAP-induced liver injury. However, the protective mechanism of Nar against mitochondrial damage has not been elucidated. Therefore, the aim of this study was to investigate the hepatoprotective effects of Nar against APAP and the possible mechanisms of actions. Primary rat hepatocytes and HepG2 cells were utilized to establish an in vitro model of APAP-induced hepatotoxicity. The effect of APAP and Nar on cell viability was evaluated by a CCK8 assay and detection of the concentrations of alanine aminotransferase, aspartate aminotransferase, and lactate dehydrogenase. The cellular concentrations of biomarkers of oxidative stress were measured by ELISA. The mRNA expression levels of APAP-related phase II enzymes were determined by real-time PCR. The protein levels of Nrf2, phospho (p)-AMPK/AMPK, and biomarkers of mitochondrial dynamics were determined by western blot analysis. The mitochondrial membrane potential (MMP) was measured by high-content analysis and confocal microscopy. JC-1 staining was performed to evaluate mitochondrial depolarization. Nar pretreatment notably prevented the marked APAP-induced hepatocyte injury, increases in oxidative stress marker expression, reductions in the expression of phase II enzymes, significant loss of MMP, mitochondrial depolarization, and mitochondrial fission in vitro. In conclusion, Nar alleviated APAP-induced hepatocyte and mitochondrial injury by activating the AMPK/Nrf2 pathway to reduce oxidative stress in vitro. Applying Nar for the treatment of APAP-induced liver injury might be promising.
DOI: 10.6084/m9.figshare.20296257
title: Additional file 2 of An ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactome

description: Additional file 2. Table S1. Proteins containing ubiquitinated sites identified by four previous ubiquitome analyses.
DOI: 10.6084/m9.figshare.20296260
title: Additional file 3 of An ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactome

description: Additional file 3. Table S2. Ubiquitinated substrates and their corresponding E3s.
DOI: 10.6084/m9.figshare.20296266
title: Additional file 4 of An ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactome

description: Additional file 4. Table S3. Ubiquitin E3-encoding ORFs retaining full-length CDS.
DOI: 10.6084/m9.figshare.20296266.v1
title: Additional file 4 of An ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactome

description: Additional file 4. Table S3. Ubiquitin E3-encoding ORFs retaining full-length CDS.
DOI: 10.21410/7e4/svvkcc
title: Expériences et perception des forces de l'ordre - vague 2 (ELIPSS 2023)

description: L'objectif de ce questionnaire est de cerner les perceptions et les expériences ordinaires et concrètes que les citoyens entretiennent à l'égard des forces de l'ordre, tout en mesurant ces dernières à l'aune des variables sociodémographiques présentes dans le tronc commun d'ELIPSS. Le questionnaire vise, d'une part, à analyser l'effet des expériences sur les représentations, et d'autre part, à évaluer le poids de la position sociale des sondés sur leur perception des forces de l'ordre et sur les interactions concrètes qu'ils entretiennent avec elles. Comment les sondés perçoivent-ils les forces de l'ordre et comment interagissent-ils concrètement avec ces dernières ? Dans quelle mesure la position dans l'espace social des sondés détermine-t-elle les représentations et les rapports différenciés qu'ils entretiennent avec les forces de l'ordre ? En quoi ces interactions concrètes sont-elles génératrices de représentations des forces de l'ordre et, plus globalement, d'une socialisation à l'État ? À travers cette analyse des perceptions et des expériences socialement différenciées vis-à-vis des forces de l'ordre (notamment selon le genre, le lieu de résidence, le diplôme, la profession, le niveau de revenu, le positionnement politique ou encore le sentiment d'appartenance à une religion), le questionnaire vise à produire des données originales sur la sociologie de la police et du rapport à l'autorité publique.
DOI: 10.6084/m9.figshare.21358539
title: Differences in methanogenic pathways and communities in paddy soils under three typical cropping modes

description: Differences in methanogenic pathways and communities in paddy soils under three typical cropping modes
DOI: 10.6084/m9.figshare.20296272
title: Additional file 6 of An ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactome

description: Additional file 6. Table S5. E3-type interactors screened from the rice UbE3 library.
DOI: 10.6084/m9.figshare.20296272.v1
title: Additional file 6 of An ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactome

description: Additional file 6. Table S5. E3-type interactors screened from the rice UbE3 library.
DOI: 10.25402/epi.15067131
title: Supplementary Table 1 epi-2020-0377

description: Supplementary table 1: Primer sequences for RT-qPCR
DOI: 10.6084/m9.figshare.12440588.v1
title: Additional file 3 of Evolutionary significance of amino acid permease transporters in 17 plants from Chlorophyta to Angiospermae

description: Additional file 3. The information of duplication and collinearity gene pairs and their Ka/Ks rations.
DOI: 10.6084/m9.figshare.12440582.v1
title: Additional file 2 of Evolutionary significance of amino acid permease transporters in 17 plants from Chlorophyta to Angiospermae

description: Additional file 2. The data of motifs for all AAPs and specific information for 10 motifs.
DOI: 10.6084/m9.figshare.20296407
title: Additional file 2 of Genotyping-by-Sequencing Based Investigation of Population Structure and Genome Wide Association Studies for Seven Agronomically Important Traits in a Set of 346 Oryza rufipogon Accessions

description: Additional file 2: Genotypic data of studied 346 accessions.
DOI: 10.6084/m9.figshare.12440588
title: Additional file 3 of Evolutionary significance of amino acid permease transporters in 17 plants from Chlorophyta to Angiospermae

description: Additional file 3. The information of duplication and collinearity gene pairs and their Ka/Ks rations.
DOI: 10.6084/m9.figshare.12440636.v1
title: Additional file 2 of Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria

description: Additional file 2: Supplementary Table 1. Information of α-Proteobacterial metagenome-assembled genomes (MAGs).
DOI: 10.17632/tn5gtswhgz.1
title: Rvision of Interactions between Vitamin D Binding Protein Variants and Major Dietary Patterns on Mental Health Status

description: This data was random sample of adult participants (n=265 and 18–55 years old) in Tehran. Major dietary patterns were determined using principal component analysis (PCA) method on 24 food groups, using a valid and reliable 147-item food frequency questionnaire (FFQ). DBP genotypes were determined by polymerase chain reactions - restriction fragment length polymorphism (PCR-RFLP). Data about the mental health status were collected using the Depression Anxiety, Stress Score (DASS-21).
DOI: 10.6084/m9.figshare.12440549.v1
title: Additional file 10 of Evolutionary significance of amino acid permease transporters in 17 plants from Chlorophyta to Angiospermae

description: Additional file 10. The numbers and location of Aa_trans and transmembrane domain.
DOI: 10.6084/m9.figshare.12440567.v1
title: Additional file 13 of Evolutionary significance of amino acid permease transporters in 17 plants from Chlorophyta to Angiospermae

description: Additional file 13.. The result of NCBI-CDD which include the mainly domain in each protein.
DOI: 10.6084/m9.figshare.12440582
title: Additional file 2 of Evolutionary significance of amino acid permease transporters in 17 plants from Chlorophyta to Angiospermae

description: Additional file 2. The data of motifs for all AAPs and specific information for 10 motifs.
DOI: 10.6084/m9.figshare.12440567
title: Additional file 13 of Evolutionary significance of amino acid permease transporters in 17 plants from Chlorophyta to Angiospermae

description: Additional file 13.. The result of NCBI-CDD which include the mainly domain in each protein.
DOI: 10.6084/m9.figshare.12440597.v1
title: Additional file 5 of Evolutionary significance of amino acid permease transporters in 17 plants from Chlorophyta to Angiospermae

description: Additional file 5. Enrichment and integration of GO annotation information refer to the analysis of Blast2GO.
DOI: 10.17632/y8dntyxhzc.1
title: AI in PSVC/PVC diagnosis

description: The diagnostic efficiency of artificial intelligence based 2 hours Holter monitoring in premature ventricular and supraventricular contractions detection.
DOI: 10.6084/m9.figshare.12440594.v1
title: Additional file 4 of Evolutionary significance of amino acid permease transporters in 17 plants from Chlorophyta to Angiospermae

description: Additional file 4. Ka, Ks and Ka/Ks ratios in AAP gene for each plant species.
DOI: 10.6084/m9.figshare.12440597
title: Additional file 5 of Evolutionary significance of amino acid permease transporters in 17 plants from Chlorophyta to Angiospermae

description: Additional file 5. Enrichment and integration of GO annotation information refer to the analysis of Blast2GO.
DOI: 10.17632/3cfhv5ztnw.1
title: comparing the effects of aquatic exercises and land-based movements on cardiovascular fitness

description: detailed searching process
DOI: 10.6084/m9.figshare.5625097
title: AKT-mediated phosphorylation of ATG4B impairs mitochondrial activity and enhances the Warburg effect in hepatocellular carcinoma cells

description: Phosphorylation is a major type of post-translational modification, which can influence the cellular physiological function. ATG4B, a key macroautophagy/autophagy-related protein, has a potential effect on the survival of tumor cells. However, the role of ATG4B phosphorylation in cancers is still unknown. In this study, we identified a novel phosphorylation site at Ser34 of ATG4B induced by AKT in HCC cells. The phosphorylation of ATG4B at Ser34 had little effect on autophagic flux, but promoted the Warburg effect including the increase of L-lactate production and glucose consumption, and the decrease of oxygen consumption in HCC cells. The Ser34 phosphorylation of ATG4B also contributed to the impairment of mitochondrial activity including the inhibition of F<sub>1</sub>Fo-ATP synthase activity and the elevation of mitochondrial ROS in HCC cells. Moreover, the phosphorylation of ATG4B at Ser34 enhanced its mitochondrial location and the subsequent colocalization with F<sub>1</sub>Fo-ATP synthase in HCC cells. Furthermore, recombinant human ATG4B protein suppressed the activity of F<sub>1</sub>Fo-ATP synthase in MgATP submitochondrial particles from patient-derived HCC tissues in vitro. In brief, our results demonstrate for the first time that the phosphorylation of ATG4B at Ser34 participates in the metabolic reprogramming of HCC cells via repressing mitochondrial function, which possibly results from the Ser34 phosphorylation-induced mitochondrial enrichment of ATG4B and the subsequent inhibition of F<sub>1</sub>Fo-ATP synthase activity. Our findings reveal a noncanonical working pattern of ATG4B under pathological conditions, which may provide a scientific basis for developing novel strategies for HCC treatment by targeting ATG4B and its Ser34 phosphorylation.
DOI: 10.6084/m9.figshare.8246567
title: MOESM1 of Metabolic engineering to enhance biosynthesis of both docosahexaenoic acid and odd-chain fatty acids in Schizochytrium sp. S31

description: Additional file 1: Fig. S1. Comparison of acetyl-CoA carboxylase activity after adding C16-CoA into cell-free extract of Schizochytrium sp. S31. 0 represents adding 0 μM of C16-CoA; 50 represents adding 50 μM of C16-CoA; 100 represents adding 100 μM of C16-CoA. * indicated p &lt; 0.05. ** indicated p &lt; 0.01. Fig. S2. Expression of a codon-optimized ELO3 gene from Mortierella alpina in Schizochytrium. A) Schematic map of the ELO3 gene expression cassette, with the indicated primers. 1: 18s upstream; 2: CaMV 35s promoter; 3: ELO3 gene; 4: Nos terminator; 5: α tubulin promoter from Schizochytrium; 6: bleomycin resistance gene; 7: CYC1 terminator; 8: 18s downstream; B) Genomic PCR detection with primer 1 and primer 2. M: 1 kb marker from Vazyme company; 1: S-E strain; 2: wild type. C) RT-PCR detection with primer 3 and primer 4. M: 1 kb marker from Thermo Scientific company; 1: S-E strain; 2: wild type. Fig. S3. Expression of a malic enzyme gene from C. cohnii in Schizochytrium. A) Schematic map of the malic enzyme expression cassette, with the indicated primers. 1: 18s upstream; 2: CaMV 35s promoter; 3: neomycin resistance gene; 4: CaMV poly(A) terminator; 5: malic enzyme gene; 6: 18s downstream; B) Genomic PCR detection with primer 5 and primer 6. M: 1kb marker; 1: water; 2: wild type; 3: S-M strain; C) RT-PCR detection with primer 7 and primer 8. 1: water; 2: wild type; 3 S-M strain. Fig. S4. Malic enzyme activity and NADPH content in the wild type and S-M strains. A) The malic enzyme activity. Blue: wild type; Purple: S-M strain. * indicated p &lt; 0.05; B) NADPH content. Blue: wild type; Purple: S-M strain. * indicated p &lt; 0.05, **indicated p &lt; 0.01. Fig. S5. Expression of a codon-optimized ELO3 gene from M. alpina in S-M strain. A) Schematic map of the ELO3 gene expression cassette, with the indicated primers. 1: CaMV 35s promoter; 2: ELO3 gene; 3: Nos terminator; 4: α tubulin promoter from Schizochytrium; 5: bleomycin resistance gene 6: CYC1 terminator; B) Genomic PCR detection with primer 1 and primer 2. M: 1 kb marker; 1: S-M-E strain; 2: S-M strain; C) RT-PCR detection with primer 3 and primer 4. M: 1 kb marker; 1: S-M strain; 2: S-M-E strain. Fig. S6. MS spectrums of methyl fatty acids detected among strains. Fig. S7. Principal component analysis of LC–MS targeted metabolomics of S-M and S-M-E strains. A) 48 h; B) 72 h. Purple: S-M strain; Green: S-M-E strain.
DOI: 10.6084/m9.figshare.12440576
title: Additional file 1 of Evolutionary significance of amino acid permease transporters in 17 plants from Chlorophyta to Angiospermae

description: Additional file 1. A part of information about all AAPs. The table includes protein length, location of Aa_trans, number of tranmembrane domains and exons, gene name, duplication events and group of each gene.
DOI: 10.17632/k3gzy92c77.1
title: Raw-data-Lauber-et-al-2024

description: Raw data (Unprocessed photos of immunoblots, southern blots and HR presented in the following study : Bacterial host adaptation through sequence and structural variations of a single type III effector gene, by Lauber et al.)