cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.sejt36
title: Occurrence Download

description: A dataset containing 11424 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Herpestes javanicus (É.Geoffroy Saint-Hilaire, 1818)"
 ]
}

 The dataset includes 11424 records from 118 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001003-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.13466845.v1
title: Additional file 8 of CircCDKN2B-AS1 interacts with IMP3 to stabilize hexokinase 2 mRNA and facilitate cervical squamous cell carcinoma aerobic glycolysis progression

description: Additional file 8: Table S4. All proteins verified by mass spectrometry analysis.
DOI: 10.6084/m9.figshare.13466935.v1
title: Additional file 3 of CircRNA_0000392 promotes colorectal cancer progression through the miR-193a-5p/PIK3R3/AKT axis

description: Additional file 3. CircRNA Expression Profiling in this study (please see the attached excel spreadsheet).
DOI: 10.6084/m9.figshare.20282217.v1
title: Additional file 1 of Multiplex immunohistochemistry defines the tumor immune microenvironment and immunotherapeutic outcome in CLDN18.2-positive gastric cancer

description: Additional file 1: Table S1. Details of antibodies used for multiple immunohistochemistry. Table S2. The clinical, pathological, and molecular characteristics of groups with higher or lower CLDN18 expression in TCGA cohorts. Table S3. The clinical, pathological, and molecular characteristics of CLDN18.2 positive or negative gastric cancer patients receiving immunotherapy. Table S4. The expression proportion of cell markers in CLDN18.2 positive and negative tumor tissues. Table S5. The effective score of cell markers in CLDN18.2 positive and negative tumor tissues. Table S6. The effective percent of cell markers in CLDN18.2 positive and negative tumor tissues. Table S7. The expression proportion of cell markers in CLDN18.2 positive and negative normal tissues. Table S8. The effective score of cell markers in CLDN18.2 positive and negative normal tissues. Table S9. The effective percent of cell markers in CLDN18.2 positive and negative normal tissues.
DOI: 10.6084/m9.figshare.7175573
title: Additional file 1: of Genome-wide analysis of the plant-specific PLATZ proteins in maize and identification of their general role in interaction with RNA polymerase III complex

description: Table S1. Primer list. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.11894175
title: Reevaluating Cryphonectriaceae and allied families in Diaporthales

description: The Diaporthales (Sordariomycetes) includes many important families of plant pathogenic fungi, such as the notorious Cryphonectriaceae. The aim of the present study was to reevaluate this family, along with other families in Diaporthales. Based on phylogenetic analyses using combined sequence data of the internal transcribed spacer (ITS) region, large subunit of the nrDNA (28S), and the translation elongation factor 1-alpha (<i>tef1-α</i>) and DNA-directed RNA polymerase II second largest subunit (<i>rpb2</i>) genes, Cryphonectriaceae is separated into two subclades, comprising 21 genera and 55 species. Foliocryphiaceae, fam. nov., is morphologically and phylogenetically its closest relative but is distinct due to its phylogeny and dimorphic conidia. Mastigosporellaceae, fam. nov., is distinguished from other families in Diaporthales by owning apical conidial appendages. <i>Neocryphonectria</i>, gen. nov., within the family Foliocryphiaceae, with two species associated with <i>Carpinus</i> canker in China, is characterized by fusoid, aseptate macroconidia. Additionally, two new combinations are proposed, namely, <i>Cryphonectria citrine</i>, based on <i>Chromendothia citrine</i>, and <i>Cytospora viridistroma</i>, based on <i>Endothia viridistoma</i>. Based on results obtained in this study, 31 families are accepted into Diaporthales.
DOI: 10.6084/m9.figshare.7175573.v1
title: Additional file 1: of Genome-wide analysis of the plant-specific PLATZ proteins in maize and identification of their general role in interaction with RNA polymerase III complex

description: Table S1. Primer list. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7175588
title: Additional file 2: of Genome-wide analysis of the plant-specific PLATZ proteins in maize and identification of their general role in interaction with RNA polymerase III complex

description: File S1. cDNA sequences of 17 ZmPLATZs. (TXT 12 kb)
DOI: 10.6084/m9.figshare.7175642.v1
title: Additional file 5: of Genome-wide analysis of the plant-specific PLATZ proteins in maize and identification of their general role in interaction with RNA polymerase III complex

description: File S2. Protein sequences of 17 ZmPLATZs. (TXT 4 kb)
DOI: 10.6084/m9.figshare.11894175.v1
title: Reevaluating Cryphonectriaceae and allied families in Diaporthales

description: The Diaporthales (Sordariomycetes) includes many important families of plant pathogenic fungi, such as the notorious Cryphonectriaceae. The aim of the present study was to reevaluate this family, along with other families in Diaporthales. Based on phylogenetic analyses using combined sequence data of the internal transcribed spacer (ITS) region, large subunit of the nrDNA (28S), and the translation elongation factor 1-alpha (<i>tef1-α</i>) and DNA-directed RNA polymerase II second largest subunit (<i>rpb2</i>) genes, Cryphonectriaceae is separated into two subclades, comprising 21 genera and 55 species. Foliocryphiaceae, fam. nov., is morphologically and phylogenetically its closest relative but is distinct due to its phylogeny and dimorphic conidia. Mastigosporellaceae, fam. nov., is distinguished from other families in Diaporthales by owning apical conidial appendages. <i>Neocryphonectria</i>, gen. nov., within the family Foliocryphiaceae, with two species associated with <i>Carpinus</i> canker in China, is characterized by fusoid, aseptate macroconidia. Additionally, two new combinations are proposed, namely, <i>Cryphonectria citrine</i>, based on <i>Chromendothia citrine</i>, and <i>Cytospora viridistroma</i>, based on <i>Endothia viridistoma</i>. Based on results obtained in this study, 31 families are accepted into Diaporthales.
DOI: 10.6084/m9.figshare.20282176.v1
title: Additional file 10 of Genome-wide identification, phylogenetic analysis, and expression profiles of trihelix transcription factor family genes in quinoa (Chenopodium quinoa Willd.) under abiotic stress conditions

description: Additional file 10: Table S7. Primer sequences of 10 selected CqTH genes and reference genes for qPCR.
DOI: 10.4121/627b66bc-d686-4607-9c36-51975fbde36c
title: Data underlying a conceptual framework for the analysis of engineering and socio-ecological resilience of urban drainage systems

description: Although resilience contributes to improving the sustainability of urban drainage systems (UDSs), in general, it is not considered in UDS management; furthermore, when it is considered, usually it is considered either as engineering (ER) or as socio-ecological (SER) resilience. This article proposes and discusses a conceptual framework that can analyse ER and SER through a comprehensive resilience (CR) index in a UDS with a focus on floods, considering national and international experiences and methodologies related to resilience analyses and is applicable to UDSs. The framework was evaluated in the Southern Drainage System (SDS) of the city of Cali, Colombia, obtaining moderate values of ER and the CR index, and low values of SER. This conceptual framework can be useful for decision-makers in UDSs management and should be evaluated considering different threat scenarios and mitigation strategies.
DOI: 10.4121/627b66bc-d686-4607-9c36-51975fbde36c.v1
title: Data underlying a conceptual framework for the analysis of engineering and socio-ecological resilience of urban drainage systems

description: Although resilience contributes to improving the sustainability of urban drainage systems (UDSs), in general, it is not considered in UDS management; furthermore, when it is considered, usually it is considered either as engineering (ER) or as socio-ecological (SER) resilience. This article proposes and discusses a conceptual framework that can analyse ER and SER through a comprehensive resilience (CR) index in a UDS with a focus on floods, considering national and international experiences and methodologies related to resilience analyses and is applicable to UDSs. The framework was evaluated in the Southern Drainage System (SDS) of the city of Cali, Colombia, obtaining moderate values of ER and the CR index, and low values of SER. This conceptual framework can be useful for decision-makers in UDSs management and should be evaluated considering different threat scenarios and mitigation strategies.
DOI: 10.6084/m9.figshare.7700438
title: Measurements of the High Temperature Ignition Delay Times and Kinetic Modeling Study on Oxidation of Nitromethane

description: Ignition delay times of the nitromethane (NM)/O<sub>2</sub>/Ar mixtures were measured behind reflected shock waves in the temperature range of 1200–2000 K, pressures of 2.0 and 10.0 atm, equivalence ratios of 0.5, 1.0, and 2.0, and fuel concentrations of 0.5%, 1.0%, and 2.0%. OH emission intensity and pressure evolution were used for the ignition delay time determination. Two-stage ignition behavior was observed in the experiments. The ignition delay time decreases sharply with pressure increasing and equivalence ratio decreasing. In addition, a sub-model including 24 updated reactions for nitromethane oxidation was proposed based on <i>ab initio</i> calculation with CCSD(T)/CBS//B3LYP/6–311 + G(3DF, 3P) level. The present model and the Mathieu’s model (Mathieu et al. Fuel 182(2016): 597) were then validated against present measured ignition delay times, as well as some laminar flame speed data and ignition data in the literature. The present model shows better or comparable predictions with the experimental data. The main species concentration evolution and reaction analysis were presented, based on which the experimentally observed two-stage ignition behavior was interpreted.
DOI: 10.6084/m9.figshare.7700438.v1
title: Measurements of the High Temperature Ignition Delay Times and Kinetic Modeling Study on Oxidation of Nitromethane

description: Ignition delay times of the nitromethane (NM)/O<sub>2</sub>/Ar mixtures were measured behind reflected shock waves in the temperature range of 1200–2000 K, pressures of 2.0 and 10.0 atm, equivalence ratios of 0.5, 1.0, and 2.0, and fuel concentrations of 0.5%, 1.0%, and 2.0%. OH emission intensity and pressure evolution were used for the ignition delay time determination. Two-stage ignition behavior was observed in the experiments. The ignition delay time decreases sharply with pressure increasing and equivalence ratio decreasing. In addition, a sub-model including 24 updated reactions for nitromethane oxidation was proposed based on <i>ab initio</i> calculation with CCSD(T)/CBS//B3LYP/6–311 + G(3DF, 3P) level. The present model and the Mathieu’s model (Mathieu et al. Fuel 182(2016): 597) were then validated against present measured ignition delay times, as well as some laminar flame speed data and ignition data in the literature. The present model shows better or comparable predictions with the experimental data. The main species concentration evolution and reaction analysis were presented, based on which the experimentally observed two-stage ignition behavior was interpreted.
DOI: 10.6084/m9.figshare.12943339
title: Anatomy of a New Specimen of <i>Piscivorenantiornis Inusitatus</i> (Aves: Enantiornithes) from the Lower Cretaceous Jehol Biota

description: We describe a new enantiornithine specimen from the Lower Cretaceous Jiufotang Formation of the Jehol Biota, northeastern China, which can be assigned to the species <i>Piscivorenantiornis inusitatus</i>. The new specimen confirms the presence of the unusual articulation of the cervical vertebrae that characterizes <i>P. inusitatus</i>. The disarticulated bony elements in the new specimen, some of which are preserved in different views or completely missing from the holotype, enable a more comprehensive morphological reconstruction and a refined phylogenetic assessment of <i>P. inusitatus</i>. The new fossil demonstrates that the occipitals are recessed by a pair of fossae lateral to the foramen magnum, a feature otherwise unknown among Mesozoic and extant birds. Our phylogenetic analysis tentatively resolves <i>P. inusitatus</i> as the sister taxon to the clade consisting of <i>Pterygornis dapingfangensis</i> and <i>Mirusavis parvus</i>, which is recovered deeply nested within the Enantiornithes. We hypothesize that the craniolateral processes of the sternum are a derived feature in enantiornithines.
DOI: 10.6084/m9.figshare.12943339.v2
title: Anatomy of a New Specimen of <i>Piscivorenantiornis Inusitatus</i> (Aves: Enantiornithes) from the Lower Cretaceous Jehol Biota

description: We describe a new enantiornithine specimen from the Lower Cretaceous Jiufotang Formation of the Jehol Biota, northeastern China, which can be assigned to the species <i>Piscivorenantiornis inusitatus</i>. The new specimen confirms the presence of the unusual articulation of the cervical vertebrae that characterizes <i>P. inusitatus</i>. The disarticulated bony elements in the new specimen, some of which are preserved in different views or completely missing from the holotype, enable a more comprehensive morphological reconstruction and a refined phylogenetic assessment of <i>P. inusitatus</i>. The new fossil demonstrates that the occipitals are recessed by a pair of fossae lateral to the foramen magnum, a feature otherwise unknown among Mesozoic and extant birds. Our phylogenetic analysis tentatively resolves <i>P. inusitatus</i> as the sister taxon to the clade consisting of <i>Pterygornis dapingfangensis</i> and <i>Mirusavis parvus</i>, which is recovered deeply nested within the Enantiornithes. We hypothesize that the craniolateral processes of the sternum are a derived feature in enantiornithines.
DOI: 10.6084/m9.figshare.13466973
title: Additional file 1 of Mutation screening of the UBE3A gene in Chinese Han population with autism

description: Additional file 1: Table S1. The allele and genotype distributions of rs71127053 and rs150331504 in ASD patients and healthy controls.
DOI: 10.6084/m9.figshare.9797624
title: MOESM2 of A genetic tool for production of GFP-expressing Rhodopseudomonas palustris for visualization of bacterial colonization

description: Additional file 2. The sequences of gene of gfpmut3a and pckA.
DOI: 10.6084/m9.figshare.9797624.v1
title: MOESM2 of A genetic tool for production of GFP-expressing Rhodopseudomonas palustris for visualization of bacterial colonization

description: Additional file 2. The sequences of gene of gfpmut3a and pckA.
DOI: 10.6084/m9.figshare.9797630
title: MOESM3 of A genetic tool for production of GFP-expressing Rhodopseudomonas palustris for visualization of bacterial colonization

description: Additional file 3. The sequence of recombinant plasmid pBBR1-pckAPT-gfp.
DOI: 10.6084/m9.figshare.9797630.v1
title: MOESM3 of A genetic tool for production of GFP-expressing Rhodopseudomonas palustris for visualization of bacterial colonization

description: Additional file 3. The sequence of recombinant plasmid pBBR1-pckAPT-gfp.
DOI: 10.6084/m9.figshare.20282179.v1
title: Additional file 1 of Genome-wide identification, phylogenetic analysis, and expression profiles of trihelix transcription factor family genes in quinoa (Chenopodium quinoa Willd.) under abiotic stress conditions

description: Additional file 1: Table S1. The physicochemical properties, cds and protein sequences of the 47 CqTH genes identified in this study.
DOI: 10.6084/m9.figshare.20282182.v1
title: Additional file 2 of Genome-wide identification, phylogenetic analysis, and expression profiles of trihelix transcription factor family genes in quinoa (Chenopodium quinoa Willd.) under abiotic stress conditions

description: Additional file 2: Table S2. Analysis and distribution of the conserved motifs in CqTH proteins.
DOI: 10.6084/m9.figshare.7175642
title: Additional file 5: of Genome-wide analysis of the plant-specific PLATZ proteins in maize and identification of their general role in interaction with RNA polymerase III complex

description: File S2. Protein sequences of 17 ZmPLATZs. (TXT 4 kb)
DOI: 10.6084/m9.figshare.7175660
title: Additional file 7: of Genome-wide analysis of the plant-specific PLATZ proteins in maize and identification of their general role in interaction with RNA polymerase III complex

description: File S3. Protein sequences of AtPLATZs and OsPLATZs. (TXT 4 kb)
DOI: 10.6084/m9.figshare.7175660.v1
title: Additional file 7: of Genome-wide analysis of the plant-specific PLATZ proteins in maize and identification of their general role in interaction with RNA polymerase III complex

description: File S3. Protein sequences of AtPLATZs and OsPLATZs. (TXT 4 kb)
DOI: 10.6084/m9.figshare.24760734
title: Decoupled terrestrial temperature and hydroclimate in the East Asian Monsoonal region since the late Miocene

description: The GDGT indices of XA3 drill core and the reconstructed temperature of XA3 drill core (this study) and the tropical and midlatitude from West Pacific since 6.0 Ma
DOI: 10.6084/m9.figshare.24760734.v1
title: Decoupled terrestrial temperature and hydroclimate in the East Asian Monsoonal region since the late Miocene

description: The GDGT indices of XA3 drill core and the reconstructed temperature of XA3 drill core (this study) and the tropical and midlatitude from West Pacific since 6.0 Ma
DOI: 10.6084/m9.figshare.7700528
title: A novel location-routing problem in electric vehicle transportation with stochastic demands

description: This is the experimental data of the manuscript entitled "A novel location-routing problem in electric vehicle transportation with stochastic demands". All data are saved in the file with txt format.
DOI: 10.6084/m9.figshare.9797690
title: Additional file 2: of Genome-wide effects of social status on DNA methylation in the brain of a cichlid fish, Astatotilapia burtoni

description: Table S1. Characteristics of individual DMRs and DMR genes. Table S2. Multi-gene DMRs and multi-DMR genes. Table S3. Differentially expressed genes within 50kb of a DMR. Table S4. DMR genes overlapping lncRNAs. Table S5. GO categories and canonical molecular pathways enriched in the DMR genes. Table S6. DMR genes associated with cell-type markers in other studies. Table S7. Molecular interactions enriched in the DMR genes. Table S8. Functions enriched in DMR genes oligodendrocyte progenitor cell coexpression clusters. Table S9. Disease-associated genes enriched in the DMR genes. Table S10. BS-Seq information. (XLSX 925 kb)
DOI: 10.6084/m9.figshare.9797690.v1
title: Additional file 2: of Genome-wide effects of social status on DNA methylation in the brain of a cichlid fish, Astatotilapia burtoni

description: Table S1. Characteristics of individual DMRs and DMR genes. Table S2. Multi-gene DMRs and multi-DMR genes. Table S3. Differentially expressed genes within 50kb of a DMR. Table S4. DMR genes overlapping lncRNAs. Table S5. GO categories and canonical molecular pathways enriched in the DMR genes. Table S6. DMR genes associated with cell-type markers in other studies. Table S7. Molecular interactions enriched in the DMR genes. Table S8. Functions enriched in DMR genes oligodendrocyte progenitor cell coexpression clusters. Table S9. Disease-associated genes enriched in the DMR genes. Table S10. BS-Seq information. (XLSX 925 kb)
DOI: 10.6084/m9.figshare.9797723
title: MOESM1 of Identification of candidate genes controlling oil content by combination of genome-wide association and transcriptome analysis in the oilseed crop Brassica napus

description: Additional file 1: Table S1. Seed oil content (SOC, % of seed weight) phenotypes of 588 accessions for GWAS analysis. 2016CQ, 2017CQ and 2018CQ refer to the three environments, CQ refers to Chongqing. BLUP represents the SOC phenotypic value obtained by the best linear unbiased prediction in three environments. Missing data are replaced by ‘− 999’. Table S2. The quality statistics of RNA sequencing data. Table S3. The number of differential genes is counted under HO/LO accessions. Table S4. Common differential lipid metabolism genes in four tested tissues under CQ24/CQ46 and CQ52/CQ46 based on KEGG pathway analysis. Table S5. All genes within the confidence interval of significant related SNPs with SOC. Table S6. Summary of gene expression of TAG biosynthesis and assembly pathway in all four tissues among LO (CQ46) and HO (CQ24, CQ52) Brassica napus lines. Table S7. Primer sequences for qRT-PCR verification in this study.
DOI: 10.6084/m9.figshare.9797723.v1
title: MOESM1 of Identification of candidate genes controlling oil content by combination of genome-wide association and transcriptome analysis in the oilseed crop Brassica napus

description: Additional file 1: Table S1. Seed oil content (SOC, % of seed weight) phenotypes of 588 accessions for GWAS analysis. 2016CQ, 2017CQ and 2018CQ refer to the three environments, CQ refers to Chongqing. BLUP represents the SOC phenotypic value obtained by the best linear unbiased prediction in three environments. Missing data are replaced by ‘− 999’. Table S2. The quality statistics of RNA sequencing data. Table S3. The number of differential genes is counted under HO/LO accessions. Table S4. Common differential lipid metabolism genes in four tested tissues under CQ24/CQ46 and CQ52/CQ46 based on KEGG pathway analysis. Table S5. All genes within the confidence interval of significant related SNPs with SOC. Table S6. Summary of gene expression of TAG biosynthesis and assembly pathway in all four tissues among LO (CQ46) and HO (CQ24, CQ52) Brassica napus lines. Table S7. Primer sequences for qRT-PCR verification in this study.
DOI: 10.6084/m9.figshare.13467027.v1
title: Additional file 8 of Loss of exosomal miR-146a-5p from cancer-associated fibroblasts after androgen deprivation therapy contributes to prostate cancer metastasis

description: Additional file 8: Table S1. Sequences of primers for PCR and reverse transcript.
DOI: 10.6084/m9.figshare.13466701
title: Additional file 1 of Adiposity, metabolites, and colorectal cancer risk: Mendelian randomization study

description: Additional file 1: Table S1. Genetic variants used to instrument BMI, WHR and metabolites. Table S2. Assesment of instrument strength. Table S3. Colorectal cancer case distributions by study, sex and site. Table S4. LogOR colorectal cancer per SD higher BMI or WHR. Table S5. Beta change in NMR-detected metabolite per SD higher BMI or WHR. Table S6. LogOR colorectal cancer per SD higher BMI or WHR-driven NMR-detected metabolite. Table S7. Risk of overall colorectal cancer per SD higher adipose or metabolite trait, estimated using multivariable Mendelian randomization. Table S8. Posthoc investigations.
DOI: 10.6084/m9.figshare.13466701.v1
title: Additional file 1 of Adiposity, metabolites, and colorectal cancer risk: Mendelian randomization study

description: Additional file 1: Table S1. Genetic variants used to instrument BMI, WHR and metabolites. Table S2. Assesment of instrument strength. Table S3. Colorectal cancer case distributions by study, sex and site. Table S4. LogOR colorectal cancer per SD higher BMI or WHR. Table S5. Beta change in NMR-detected metabolite per SD higher BMI or WHR. Table S6. LogOR colorectal cancer per SD higher BMI or WHR-driven NMR-detected metabolite. Table S7. Risk of overall colorectal cancer per SD higher adipose or metabolite trait, estimated using multivariable Mendelian randomization. Table S8. Posthoc investigations.