cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23632606
title: Additional file 1 of Proteomic profiling of longitudinal changes in kidney function among middle-aged and older men and women: the KORA S4/F4/FF4 study

description: Additional file 1: Table S1. Normalized expressionvalues for proteomic biomarkers at baseline; Table S2. SNPs-traitsassociations retrieved from PhenoScanner V2 for proteins-related SNPs; Table S3. Harmonized summary statisticsused in Mendelian randomization analysis; TableS4. Characteristics of participants over the study period; Table S5. Baseline characteristics forparticipants with and without follow-up information on eGFRcr; Table S6. Longitudinal associationsbetween 233 proteomic biomarkers and the annual rate of change in eGFRcr; Table S7. Longitudinal associations between 233 proteomicbiomarkers and the annual rate of change in CKD-EPI Equation 2009-based andCKD-EPI Equation 2021-based eGFRcr;Table S8. Sensitivity analyses oflongitudinal associations between 66 proteomic biomarkers and the annual rateof change in eGFRcr; Table S9. Sensitivityanalyses of association of 66 proteomic biomarkers with rapid decline in eGFRcrand CKD incidence; Table S10. Associationof 66 proteomic biomarkers with the annual rate of change in eGFRcys and CKDincidence; Table S11. Longitudinalassociations between 233 proteomic biomarkers and the annual rate of change ineGFRcys; Table S12. Longitudinal associationsbetween baseline characteristics and the annual rate of change in eGFRcr andeGFRcys; Table S13. Association of 21 proteomic biomarkers with UACR; Table S14. Summary of druggable targetsand their corresponding disease of the 21 identified proteins; Table S15. Proteomic biomarkersassociated with kidney function and/or chronic kidney disease in previouscross-sectional or longitudinal proteomic studies; Table S16. Evaluation of bias due to participant overlap intwo-sample Mendelian randomization analysis; Table S17. STROBEStatement—checklist of items in reports of observational studies; Table S18. STROBE-MR checklist of recommended items in reports of Mendelianrandomization studies.
DOI: 10.6084/m9.figshare.18393509
title: Additional file 8 of Proteome evaluation of homolog abundance patterns in Arachis hypogaea cv. Tifrunner

description: Additional file 8: Table S3. The paralogous and homeologous protein pairs with differential abundances in the leaf. The differential abundance was estimated between leaf and root tissues.
DOI: 10.6084/m9.figshare.18393509.v1
title: Additional file 8 of Proteome evaluation of homolog abundance patterns in Arachis hypogaea cv. Tifrunner

description: Additional file 8: Table S3. The paralogous and homeologous protein pairs with differential abundances in the leaf. The differential abundance was estimated between leaf and root tissues.
DOI: 10.6084/m9.figshare.18393506.v1
title: Additional file 7 of Proteome evaluation of homolog abundance patterns in Arachis hypogaea cv. Tifrunner

description: Additional file 7: Table S2. The paralogous and homeologous protein pairs with abundances in the leaf and root tissues.
DOI: 10.6084/m9.figshare.18393503.v1
title: Additional file 6 of Proteome evaluation of homolog abundance patterns in Arachis hypogaea cv. Tifrunner

description: Additional file 6: Table S1. Proteins with abundances were detected using the tandem mass tag technology.
DOI: 10.6084/m9.figshare.18393512.v1
title: Additional file 9 of Proteome evaluation of homolog abundance patterns in Arachis hypogaea cv. Tifrunner

description: Additional file 9: Table S4. The paralogous and homeologous protein pairs with differential abundances in the root. The differential abundance was estimated between leaf and root tissues.
DOI: 10.6084/m9.figshare.23632653
title: Additional file 1 of Growth hormone treatment improves the development of follicles and oocytes in prepubertal lambs

description: Addition file 1. DEGs in GC transcriptome between control and GH treatment groups.
DOI: 10.6084/m9.figshare.8956637.v1
title: TAp73 expression and P1 promoter methylation, a potential marker for chemoresponsiveness to cisplatin therapy and survival in muscle-invasive bladder cancer (MIBC)

description: Intrinsic and/or acquired resistance to cisplatin is a significant obstacle in the treatment of muscle-invasive bladder cancer. p73, a p53 homolog and determinant of chemosensitivity, is rarely mutated in bladder cancer (BC). However p73 expression and therefore function can be repressed through epigenetic changes. In this study, we sought to identify DNA methylation status of p73, expression of TAp73 isoform, and their role in cisplatin sensitivity in BC. Primary tumor samples from 338 bladder cancer patients showed decreased TAp73 expression in MIBC compared to superficial BC. Low TAp73 protein expression was associated with shorter overall survival. To investigate if the loss of expression was methylation dependent, we utilized Illumina 450K methylation arrays to interrogate over 150 BC patient samples. We found 12 distinct CpGs in the p73 gene locus that were hypermethylated in tumors compared to adjacent normal tissues. Patients with high p73 promoter methylation specifically at CpG site cg07382920 had worse survival. <i>In vitro</i>, treatment with a DNA demethylating agent, decitabine (DAC), decreased TAp73 methylation and upregulated expression in both CR-T24 (cisplatin resistant T24 cells) and wild type T24 cells. Furthermore, treatment with DAC increased cisplatin response in wild type T24 and CR-T24. Our studies indicate that TAp73 expression and P1 promoter methylation, specifically at the cg073892920 site, may have prognostic and diagnostic value in MIBC. In the setting of P1 promoter hypermethylation, DAC could be used as a potentiating agent of cisplatin-based chemotherapy.
DOI: 10.6084/m9.figshare.14723615
title: Mining of linear B cell epitopes of SARS-CoV-2 ORF8 protein from COVID-19 patients

description: Given the on-going SARS-CoV-2 pandemic, identification of immunogenic targets against the viral protein will provide crucial advances towards the development of sensitive diagnostic tools and vaccination strategies. Our previous study has found that ORF8 protein of SARS-CoV-2 is highly immunogenic and shows high sensitivity in identifying COVID-19 disease. In this study, by employing overlapping linear peptides, we characterized the IgG immunodominant regions on SARS-CoV-2 ORF8 protein that are seropositive in the sera from SARS-CoV-2-infected patients. The major immunogenic epitopes are localized at (1) N-termini alpha helix, (2) the resides spanning beta 2 and 3 sheets, and (3) the loop between beta 4 and 5 sheets. Additionally, hamster model infected by SARS-CoV-2 further validates the seropositivity of the linear epitopes <i>in vivo</i>, demonstrating a potential application of the linear peptide-based immunization strategy. Taken together, identification and validation of these B-cell linear epitopes will provide insights into the design of serological diagnostics and peptide-based vaccination approach against this pandemic virus of high priority.
DOI: 10.6084/m9.figshare.12102555
title: Monte Carlo Simulation Source Code from On the use of random graphs in analysing resource utilization in urban systems

description: The file contains source code used in the generation of the Monte Carlo samples.
DOI: 10.6084/m9.figshare.14723615.v1
title: Mining of linear B cell epitopes of SARS-CoV-2 ORF8 protein from COVID-19 patients

description: Given the on-going SARS-CoV-2 pandemic, identification of immunogenic targets against the viral protein will provide crucial advances towards the development of sensitive diagnostic tools and vaccination strategies. Our previous study has found that ORF8 protein of SARS-CoV-2 is highly immunogenic and shows high sensitivity in identifying COVID-19 disease. In this study, by employing overlapping linear peptides, we characterized the IgG immunodominant regions on SARS-CoV-2 ORF8 protein that are seropositive in the sera from SARS-CoV-2-infected patients. The major immunogenic epitopes are localized at (1) N-termini alpha helix, (2) the resides spanning beta 2 and 3 sheets, and (3) the loop between beta 4 and 5 sheets. Additionally, hamster model infected by SARS-CoV-2 further validates the seropositivity of the linear epitopes <i>in vivo</i>, demonstrating a potential application of the linear peptide-based immunization strategy. Taken together, identification and validation of these B-cell linear epitopes will provide insights into the design of serological diagnostics and peptide-based vaccination approach against this pandemic virus of high priority.
DOI: 10.5281/zenodo.6016719
title: 3Cnet: pathogenicity prediction of human variants using multitask learning with evolutionary constraints

description: Dataset needed to train and evaluate 3Cnet.

See github repository for source code.

https://github.com/KyoungYeulLee/3Cnet
DOI: 10.5281/zenodo.6016720
title: 3Cnet: pathogenicity prediction of human variants using multitask learning with evolutionary constraints

description: Dataset needed to train and evaluate 3Cnet. See github repository for source code. https://github.com/KyoungYeulLee/3Cnet
DOI: 10.6084/m9.figshare.12102555.v1
title: Monte Carlo Simulation Source Code from On the use of random graphs in analysing resource utilization in urban systems

description: The file contains source code used in the generation of the Monte Carlo samples.
DOI: 10.6084/m9.figshare.23632686.v1
title: Additional file 6 of CircGNB1 facilitates the malignant phenotype of GSCs by regulating miR-515-5p/miR-582-3p-XPR1 axis

description: Additional file 6. Table S3: The expression of GNB1 originated circRNAs in GSE146463.
DOI: 10.6084/m9.figshare.13671047
title: Additional file 3 of A multilayered post-GWAS assessment on genetic susceptibility to pancreatic cancer

description: Additional file 3: Table S5. List of the 76 SNPs overlapping with a chromatin interaction region (bait regions) and their 54 targets.
DOI: 10.6084/m9.figshare.17869956.v1
title: Additional file 7 of Transcriptional analysis of Bemisia tabaci MEAM1 cryptic species under the selection pressure of neonicotinoids imidacloprid, acetamiprid and thiamethoxam

description: Additional file 7.
DOI: 10.6084/m9.figshare.13671044
title: Additional file 2 of A multilayered post-GWAS assessment on genetic susceptibility to pancreatic cancer

description: Additional file 2: Table S4. List of the 510 SNPs prioritized according to their Local Moran Index (LMI).
DOI: 10.6084/m9.figshare.17869956
title: Additional file 7 of Transcriptional analysis of Bemisia tabaci MEAM1 cryptic species under the selection pressure of neonicotinoids imidacloprid, acetamiprid and thiamethoxam

description: Additional file 7.
DOI: 10.6084/m9.figshare.13671053
title: Additional file 4 of A multilayered post-GWAS assessment on genetic susceptibility to pancreatic cancer

description: Additional file 4: Table S6. Annotation and functional in silico analysis of the 143 prioritized SNPs.
DOI: 10.6084/m9.figshare.23632536.v1
title: Additional file 1 of Oral-microbiome-derived signatures enable non-invasive diagnosis of laryngeal cancers

description: Additional file 1: Table S1. Statistical P values of alpha diversity indices among different groups. Table S2. Percentage values and statistical P values of genera among different groups.
DOI: 10.6084/m9.figshare.23632536
title: Additional file 1 of Oral-microbiome-derived signatures enable non-invasive diagnosis of laryngeal cancers

description: Additional file 1: Table S1. Statistical P values of alpha diversity indices among different groups. Table S2. Percentage values and statistical P values of genera among different groups.
DOI: 10.6084/m9.figshare.17869962.v1
title: Additional file 9 of Transcriptional analysis of Bemisia tabaci MEAM1 cryptic species under the selection pressure of neonicotinoids imidacloprid, acetamiprid and thiamethoxam

description: Additional file 9.
DOI: 10.6084/m9.figshare.17869983
title: Additional file 12 of Gene regulation network analyses of pistil development in papaya

description: Additional file 12. Statistics information of each node in the network from six gene regulation networks.
DOI: 10.6084/m9.figshare.17869992
title: Additional file 15 of Gene regulation network analyses of pistil development in papaya

description: Additional file 15. The expression information of important genes at different developmental stages in this study.
DOI: 10.6084/m9.figshare.17869995
title: Additional file 16 of Gene regulation network analyses of pistil development in papaya

description: Additional file 16. Summary statistics of RNA-Seq data from papaya male and female flowers.
DOI: 10.6084/m9.figshare.17869992.v1
title: Additional file 15 of Gene regulation network analyses of pistil development in papaya

description: Additional file 15. The expression information of important genes at different developmental stages in this study.
DOI: 10.6084/m9.figshare.23632608
title: Additional file 1 of Effects of editing DFR genes on flowers, leaves, and roots of tobacco

description: Additional file 1: Figure S1. Anthocyanin chromatograms of the flower samples. Table S1. Non-targeted metabolome detection using LC-MS/MS of all samples. Table S2. Gene number and corresponding names.
DOI: 10.6084/m9.figshare.8956700
title: Autophagy induction by the pathogen receptor NECTIN4 and sustained autophagy contribute to peste des petits ruminants virus infectivity

description: Macroautophagy/autophagy is an essential cellular response in the fight against intracellular pathogens. Although some viruses can escape from or utilize autophagy to ensure their own replication, the responses of autophagy pathways to viral invasion remain poorly documented. Here, we show that peste des petits ruminants virus (PPRV) infection induces successive autophagic signalling in host cells via distinct and uncoupled molecular pathways. Immediately upon invasion, PPRV induced a first transient wave of autophagy via a mechanism involving the cellular pathogen receptor NECTIN4 and an AKT-MTOR-dependent pathway. Autophagic detection showed that early PPRV infection not only increased the amounts of autophagosomes and LC3-II but also downregulated the phosphorylation of AKT-MTOR. Subsequently, we found that the binding of viral protein H to NECTIN4 ultimately induced a wave of autophagy and inactivated the AKT-MTOR pathway, which is a critical step for the control of infection. Soon after infection, new autophagic signalling was initiated that required viral replication and protein expression. Interestingly, expression of IRGM and HSPA1A was significantly upregulated following PPRV replication. Strikingly, knockdown of IRGM and HSPA1A expression using small interfering RNAs impaired the PPRV-induced second autophagic wave and viral particle production. Moreover, IRGM-interacting PPRV-C and HSPA1A-interacting PPRV-N expression was sufficient to induce autophagy through an IRGM-HSPA1A-dependent pathway. Importantly, syncytia formation could facilitate sustained autophagy and the replication of PPRV. Overall, our work reveals distinct molecular pathways underlying the induction of self-beneficial sustained autophagy by attenuated PPRV, which will contribute to improving the use of vaccines for therapy. <b>Abbreviations:</b> ACTB: actin beta; ANOVA: analysis of variance; ATG: autophagy-related; BECN1: beclin 1; CDV: canine distemper virus; Co-IP: coimmunoprecipitation; FIP: fusion inhibitory peptide; GFP: green fluorescent protein; GST: glutathione S-transferase; HMOX1: heme oxygenase 1; hpi: hours post infection; HSPA1A: heat shock protein family A (Hsp70) member 1A; HSP90AA1: heat shock protein 90 kDa alpha (cytosolic), class A member 1; IFN: interferon; IgG: immunoglobulin G; INS: insulin; IRGM: immunity related GTPase M; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MeV: measles virus; MOI: multiplicity of infection; MTOR: mechanistic target of rapamycin kinase; PI3K: phosphoinositide-3 kinase; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; SDS: sodium dodecyl sulfate; siRNA: small interfering RNA; SQSTM1/p62: sequestosome 1; UV: ultraviolet.
DOI: 10.6084/m9.figshare.17870049.v1
title: Additional file 12 of Genome-wide identification and functional analysis of circRNAs in Trichophyton rubrum conidial and mycelial stages

description: Additional file 12: Table S11. KEGG pathways analysis of target genes for DE-circRNAs.
DOI: 10.6084/m9.figshare.23632653.v1
title: Additional file 1 of Growth hormone treatment improves the development of follicles and oocytes in prepubertal lambs

description: Addition file 1. DEGs in GC transcriptome between control and GH treatment groups.
DOI: 10.6084/m9.figshare.17870058.v1
title: Additional file 14 of Genome-wide identification and functional analysis of circRNAs in Trichophyton rubrum conidial and mycelial stages

description: Additional file 14: Table S13. Primers used in this study.
DOI: 10.15468/dl.vuxdy7
title: Occurrence Download

description: A dataset containing 124 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is Malaysia",
 "OccurrenceStatus is Present",
 "TaxonKey is Castanopsis megacarpa Gamble"
 ]
}

 The dataset includes 124 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021342-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m9yxa5
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Maerua mungaii Beentje"
 ]
}

 The dataset includes 31 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051983-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.funcxk
title: Occurrence Download

description: A dataset containing 4948 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Cavendishia bracteata (Ruiz & Pav. ex A.St.-Hil.) Hoerold"
 ]
}

 The dataset includes 4948 records from 109 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051979-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2bmn44
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mallotus lauterbachianus (Pax & K.Hoffm.) Pax & K.Hoffm."
 ]
}

 The dataset includes 15 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051984-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pydy2r
title: Occurrence Download

description: A dataset containing 448 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Atlapetes pallidiceps (Sharpe, 1900)"
 ]
}

 The dataset includes 448 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051985-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bdhjeb
title: Occurrence Download

description: A dataset containing 28418 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euphorbia heterophylla L."
 ]
}

 The dataset includes 28418 records from 653 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051971-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f9v6qq
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Merwilla dracomontana (Hilliard & B.L.Burtt) Speta"
 ]
}

 The dataset includes 44 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051986-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d8hjj7
title: Occurrence Download

description: A dataset containing 6381641 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Geothlypis trichas (Linnaeus, 1766)"
 ]
}

 The dataset includes 6381641 records from 245 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051947-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qpqfan
title: Occurrence Download

description: A dataset containing 58 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Melastoma pentapetalum (Toyoda) T.Yamaz. & Toyoda"
 ]
}

 The dataset includes 58 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051989-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x6k566
title: Occurrence Download

description: A dataset containing 3025 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dermacentor albipictus Packard, 1869"
 ]
}

 The dataset includes 3025 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051987-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.feff47
title: Occurrence Download

description: A dataset containing 18907 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Atlapetes pallidinucha (Boissonneau, 1840)"
 ]
}

 The dataset includes 18907 records from 135 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051988-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q5kaw9
title: Occurrence Download

description: A dataset containing 1911 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Medicago intertexta (L.) Mill."
 ]
}

 The dataset includes 1911 records from 149 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051990-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dnctee
title: Occurrence Download

description: A dataset containing 685 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lysimachia pentapetala Bunge"
 ]
}

 The dataset includes 685 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051991-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a6ubrf
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Maerua nana R.A.Graham ex Polhill"
 ]
}

 The dataset includes 10 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051992-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.