cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.ldnzb8
title: Occurrence Download

description: A dataset containing 217 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Angola",
 "Country is Namibia",
 "Country is Botswana"
 ]
 },
 "Geometry POLYGON((14.36426 -22.03269,23.59277 -22.03269,23.59277 -12.21977,14.36426 -12.21977,14.36426 -22.03269))",
 {
 "or" : [
 "TaxonKey is Giraffa giraffa (von Schreber, 1784)",
 "TaxonKey is Cephalophus silvicultor (Afzelius, 1815)"
 ]
 },
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 217 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020452-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4m2hdv
title: Occurrence Download

description: A dataset containing 93 species occurrences available in GBIF matching the query:
{
 "or" : [
 "TaxonKey is Oestlundia ligulata (La Llave & Lex.) Soto Arenas",
 "TaxonKey is Oestlundia cyanocolumna (Ames, F.T.Hubb. & C.Schweinf.) W.E.Higgins"
 ]
}

 The dataset includes 93 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011537-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f50kuv
title: Occurrence Download

description: A dataset containing 126760 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tinca tinca (Linnaeus, 1758)"
 ]
}

 The dataset includes 126760 records from 240 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013829-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vu7nbu
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((147.792331 -34.475792, 147.792331 -34.48253, 147.799069 -34.48253, 147.799069 -34.478038, 147.794577 -34.478038, 147.794577 -34.475792, 147.792331 -34.475792))"
 ]
}

 The dataset includes 11 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071500-240626123714530/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.26751434
title: Additional file 3 of A single viral amino acid shapes the root system architecture of a plant host upon virus infection

description: Supplementary Material 3.
DOI: 10.6084/m9.figshare.26751431.v1
title: Additional file 2 of A single viral amino acid shapes the root system architecture of a plant host upon virus infection

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.23799907
title: Reconstruction of the unbinding pathways of new inhibitors of the SARS-CoV-2 papain-like protease using molecular dynamics simulation

description: Developing novel antiviral drugs against the SARS-CoV-2 virus and COVID-19 disease is imperative as the vaccines may not offer absolute protection. PLpro plays a crucial role in the viral life cycle, making it an attractive target for drug development. Several PLpro inhibitors have been developed, and their 3D structures in complex with PLpro are available. In this work, we employed Supervised Molecular Dynamics (SuMD), a specific Unbiased Molecular Dynamics (UMD) method, to investigate unbinding pathways of the novel inhibitors of PLpro (PDB IDs: 7LBR, 7RZC, 7SDR and 7E35) and GRL0617 (PDB ID: 7JRN) as a reference. We conducted three simulations for each ligand and achieved unbinding events in the nanosecond timescale in all simulations. We found that unbinding events are commonly affected by altering the conformation of the BL2 loop, which is caused by the natural fluctuations of the loop that are required to trap the substrate and throw out the product. BL2 loop is crucial for keeping the ligand and unbinding and acts as a double-edged sword. Any inhibitor designed to be effective must prevent the loop’s natural fluctuations. We perceived that increasing ligands interactions with the binding pocket interior and the BL2 loop will help prevent natural fluctuation of the BL2 loop, Although the interactions with the binding pocket’s inner side are more critical than the BL2 loop. These findings may be helpful in developing more potent inhibitors against SARS-CoV-2. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.23791826.v1
title: Computational analysis of spike protein of SARS-CoV-2 (Omicron variant) for development of peptide-based therapeutics and diagnostics

description: In the last few years, the worldwide population has suffered from the SARS-CoV-2 pandemic. The WHO dashboard indicated that around 504,079,039 people were infected and 6,204,155 died from COVID-19 caused by different variants of SARS-CoV-2. Recently, a new variant of SARS-CoV-2 (B.1.1.529) was reported by South Africa known as Omicron. The high transmissibility rate and resistance towards available anti-SARS-CoV-2 drugs/vaccines/monoclonal antibodies, make Omicron a variant of concern. Because of various mutations in spike protein, available diagnostic and therapeutic treatments are not reliable. Therefore, the present study explored the development of some therapeutic peptides that can inhibit the SARS-CoV-2 virus interaction with host ACE2 receptors and can also be used for diagnostic purposes. The screened linear B cell epitopes derived from receptor-binding domain of spike protein of Omicron variant were evaluated as peptide inhibitor/vaccine candidates through different bioinformatics tools including molecular docking and simulation to analyze the interaction between Omicron peptide and human ACE2 receptor. Overall, <i>in-silico</i> studies revealed that Omicron peptides OP1-P12, OP14, OP20, OP23, OP24, OP25, OP26, OP27, OP28, OP29, and OP30 have the potential to inhibit Omicron interaction with ACE2 receptor. Moreover, Omicron peptides OP20, OP22, OP23, OP24, OP25, OP26, OP27, and OP30 have shown potential antigenic and immunogenic properties that can be used in design and development vaccines against Omicron. Although the <i>in-silico</i> validation was performed by comparative analysis with the control peptide inhibitor, further validation through wet lab experimentation is required before its use as therapeutic peptides. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.23799907.v1
title: Reconstruction of the unbinding pathways of new inhibitors of the SARS-CoV-2 papain-like protease using molecular dynamics simulation

description: Developing novel antiviral drugs against the SARS-CoV-2 virus and COVID-19 disease is imperative as the vaccines may not offer absolute protection. PLpro plays a crucial role in the viral life cycle, making it an attractive target for drug development. Several PLpro inhibitors have been developed, and their 3D structures in complex with PLpro are available. In this work, we employed Supervised Molecular Dynamics (SuMD), a specific Unbiased Molecular Dynamics (UMD) method, to investigate unbinding pathways of the novel inhibitors of PLpro (PDB IDs: 7LBR, 7RZC, 7SDR and 7E35) and GRL0617 (PDB ID: 7JRN) as a reference. We conducted three simulations for each ligand and achieved unbinding events in the nanosecond timescale in all simulations. We found that unbinding events are commonly affected by altering the conformation of the BL2 loop, which is caused by the natural fluctuations of the loop that are required to trap the substrate and throw out the product. BL2 loop is crucial for keeping the ligand and unbinding and acts as a double-edged sword. Any inhibitor designed to be effective must prevent the loop’s natural fluctuations. We perceived that increasing ligands interactions with the binding pocket interior and the BL2 loop will help prevent natural fluctuation of the BL2 loop, Although the interactions with the binding pocket’s inner side are more critical than the BL2 loop. These findings may be helpful in developing more potent inhibitors against SARS-CoV-2. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.26751440.v1
title: Additional file 5 of A single viral amino acid shapes the root system architecture of a plant host upon virus infection

description: Supplementary Material 5.
DOI: 10.15468/dl.3yy8aw
title: Occurrence Download

description: A dataset containing 3777 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Geometry POLYGON((-4.17009 40.42599,-3.85848 40.42599,-3.85848 40.71325,-4.17009 40.71325,-4.17009 40.42599))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 3777 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071501-240626123714530/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.26751350
title: Additional file 2 of An integrated QTL and RNA-seq analysis revealed new petal morphology loci in Brassica napus L.

description: Additional file 2: Table S1. The statistical data of MPA, MPP, PAR, MPL, MPW, and PCD in the KN DH population under six microenvironments, including 17WH, 17YL, 18WH, 18YL, 19WH, and 19YL. Table S2. The Pearson correlation coefficient of MPA, MPP, PAR, MPL, MPW, and PCD in 17WH. The p-value was represented by “*” (p &lt; 0.05, significant) and “**” (p &lt; 0.01, highly significant). Table S3. The Pearson correlation coefficient of MPA, MPP, PAR, MPL, MPW, and PCD in 17YL. The p-value was represented by “*” (p &lt; 0.05, significant) and “**” (p &lt; 0.01, highly significant). Table S4. The Pearson correlation coefficient of MPA, MPP, PAR, MPL, MPW, and PCD in 18WH. The p-value was represented by “*” (p &lt; 0.05, significant) and “**” (p &lt; 0.01, highly significant). Table S5. The Pearson correlation coefficient of MPA, MPP, PAR, MPL, MPW, and PCD in 18YL. The p-value was represented by “*” (p &lt; 0.05, significant) and “**” (p &lt; 0.01, highly significant). Table S6. The Pearson correlation coefficient of MPA, MPP, PAR, MPL, MPW, and PCD in 19WH. The p-value was represented by “*” (p &lt; 0.05, significant) and “**” (p &lt; 0.01, highly significant). Table S7. The Pearson correlation coefficient of MPA, MPP, PAR, MPL, MPW, and PCD in 19YL. The p-value was represented by “*” (p &lt; 0.05, significant) and “**” (p &lt; 0.01, highly significant). Table S8. The detailed information of all identified QTLs detected in the present study. The “position”, “from”, and “to” were presented by the genetic distance. Table S9. The detailed information of all consensus QTLs detected in the present study, and the “position”, “from”, and “to” were presented by the genetic distance. Table S10. The detailed information of all unique QTLs detected in the present study, and the “position”, “from”, and “to” were presented by the genetic distance. Table S11. All PDRs collected in the present study. Table S12. The detailed information of each RNA-seq sample. Table S13. The primers used in the present study. Table S14. The detailed information of candidate genes and high-confidence candidate genes. Table S15. The sequence variations of candidate genes. Table S16. The expression profile (presented by FPKM) of 152 candidate PDRs expressed in the flower stage petals (B ~ J) and their log2(FC) between different petal samples (K ~ P). The zero values of FPKMs were replaced by 0.01 to avoid invalid parameters. Table S17. The expression profile (presented by FPKM) of 168 candidate PDRs expressed in the bud stage petals (B ~ J) and their log2(FC) between different petal samples (K ~ P). The zero values of FPKMs were replaced by 0.01 to avoid invalid parameters. Table S18. The previously reported petal size QTLs of B. napus that are consistent with the petal morphology QTLs detected in the present study.
DOI: 10.6084/m9.figshare.26759279.v1
title: Additional file 6 of Integrated analysis of spatial transcriptomics and CT phenotypes for unveiling the novel molecular characteristics of recurrent and non-recurrent high-grade serous ovarian cancer

description: Supplementary Material 6: Table S4A. Significant ligand-receptor crosstalk of recurrent HGSOC. Table S4B. Significant ligand-receptor crosstalk of non-recurrent HGSOC
DOI: 10.15468/dl.7k7bsj
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.272932 -34.475792, 148.272932 -34.48253, 148.275178 -34.48253, 148.275178 -34.475792, 148.272932 -34.475792))"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071502-240626123714530/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.26751359.v1
title: Additional file 2 of Unraveling the metabolomic architecture of autism in a large Danish population-based cohort

description: Additional file 2: Table S1. All metabolites associated with autism (p &lt; 0.05) in logistic regression model 1, adjusted for age at sampling, season of birth and gestational age. Proof of annotations from GNPS, SIRIUS, MS2LDA and notes for manual annotations are presented. Table S2. Odds ratios and p-values for logistic regression model 1, model 2 and model 3. All significant (p &lt; 0.05) metabolites in model 1 are shown. Table S3. Associations with autism stratified by age of diagnosis. Early indicates autism diagnosis &lt; 6 years old and late &gt;  = 6 years old. Results are from logistic regression model 1. Table S4. Autism associations for cyclic dipeptides cyclo(Leu-Pro) and cyclo(Pro-Val) when included as covariates in the same logistic regression model (model 1). Table S5. Metabolite class enrichment analysis. P-values are calculated using Fisher's exact test. Table S6. Baseline characteristics description of participants from the Malmö Diet and Cancer Study (MDC) and the Malmö Offspring Study (MOS). Table S7. Correlations between 5-AVAB and dietary intake in the Malmö Diet and Cancer Study (MDC) and the Malmö Offspring Study (MOS) stratifed by sex. Table S8. Top 500 SNPs from genomewide association study of 5-AVAB in the Malmö Diet and Cancer Study. Table S9. Relative standard deviations (%) in repeated injections of quality control (QC) samples for 16 metabolites. QC samples consist of pooled adult blood spotted on filter paper. Table S10. Top 500 SNPs from genomewide association study of 5-AVAB in the neonatal cohort. Table S11. Top 500 SNPs from genomewide association study of cLP in the neonatal cohort.
DOI: 10.6084/m9.figshare.26751359
title: Additional file 2 of Unraveling the metabolomic architecture of autism in a large Danish population-based cohort

description: Additional file 2: Table S1. All metabolites associated with autism (p &lt; 0.05) in logistic regression model 1, adjusted for age at sampling, season of birth and gestational age. Proof of annotations from GNPS, SIRIUS, MS2LDA and notes for manual annotations are presented. Table S2. Odds ratios and p-values for logistic regression model 1, model 2 and model 3. All significant (p &lt; 0.05) metabolites in model 1 are shown. Table S3. Associations with autism stratified by age of diagnosis. Early indicates autism diagnosis &lt; 6 years old and late &gt;  = 6 years old. Results are from logistic regression model 1. Table S4. Autism associations for cyclic dipeptides cyclo(Leu-Pro) and cyclo(Pro-Val) when included as covariates in the same logistic regression model (model 1). Table S5. Metabolite class enrichment analysis. P-values are calculated using Fisher's exact test. Table S6. Baseline characteristics description of participants from the Malmö Diet and Cancer Study (MDC) and the Malmö Offspring Study (MOS). Table S7. Correlations between 5-AVAB and dietary intake in the Malmö Diet and Cancer Study (MDC) and the Malmö Offspring Study (MOS) stratifed by sex. Table S8. Top 500 SNPs from genomewide association study of 5-AVAB in the Malmö Diet and Cancer Study. Table S9. Relative standard deviations (%) in repeated injections of quality control (QC) samples for 16 metabolites. QC samples consist of pooled adult blood spotted on filter paper. Table S10. Top 500 SNPs from genomewide association study of 5-AVAB in the neonatal cohort. Table S11. Top 500 SNPs from genomewide association study of cLP in the neonatal cohort.
DOI: 10.6084/m9.figshare.26751425.v1
title: Additional file 1 of Screening for genetic variability in photosynthetic regulation provides insights into salt performance traits in forage sorghum under salt stress

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.26751431
title: Additional file 2 of A single viral amino acid shapes the root system architecture of a plant host upon virus infection

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.26751434.v1
title: Additional file 3 of A single viral amino acid shapes the root system architecture of a plant host upon virus infection

description: Supplementary Material 3.
DOI: 10.6084/m9.figshare.26751437.v1
title: Additional file 4 of A single viral amino acid shapes the root system architecture of a plant host upon virus infection

description: Supplementary Material 4.
DOI: 10.6084/m9.figshare.26751329
title: Additional file 3 of Genome-wide identification and molecular evolution of Dof gene family in Camellia oleifera

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.26751332.v1
title: Additional file 4 of Genome-wide identification and molecular evolution of Dof gene family in Camellia oleifera

description: Supplementary Material 4
DOI: 10.15468/dl.yh4hsg
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.439122 -34.475792, 148.439122 -34.48253, 148.443613 -34.48253, 148.443613 -34.484776, 148.450351 -34.484776, 148.450351 -34.475792, 148.439122 -34.475792))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071503-240626123714530/datasets/export for details.
DOI: 10.6084/m9.figshare.26759474.v1
title: Additional file 2 of READv2: advanced and user-friendly detection of biological relatedness in archaeogenomics

description: Additional file 2. READv2 results for the Rivollat data [22]. Explanations of the columns can be found in the second tab. This table also represents an example of the output of READv2.
DOI: 10.15468/dl.w3v5fa
title: Occurrence Download

description: A dataset containing 65 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "MULTIPOLYGON (((148.580607 -34.475792, 148.587344 -34.475792, 148.587344 -34.478038, 148.58959 -34.478038, 148.58959 -34.473547, 148.580607 -34.473547, 148.580607 -34.475792)), ((148.580607 -34.475792, 148.576115 -34.475792, 148.576115 -34.48253, 148.580607 -34.48253, 148.580607 -34.475792)))"
 ]
}

 The dataset includes 65 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071504-240626123714530/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.26751473
title: Additional file 1 of Rumen and hindgut microbiome regulate average daily gain of preweaning Holstein heifer calves in different ways

description: Additional file 1: Table S1. Nutrient content of Starter and milk replacer (DM basis, %). Table S2. Composition of PYG medium. Table S3. Comparison of physiological parameters and rumen fermentation characteristics between LADG and HADG calves. Table S4. Summary of sequence data generated from rumen samples of 8 LADG and 8 HADG calves. Table S5. Wilcoxon rank sum test was used to compare the rumen microbial domain. Table S6. The relative abundances of the top 10 rumen bacterial phyla, genera and species between HADG and LADG calves. Table S7. The significant differences in rumen bacterial phyla, genera, and species between HADG and LADG calves. Table S8. The relative abundances of ruminal KEGG pathways between HADG and LADG calves. Table S9. Significantly different rumen metabolites between HADG and LADG calves. Table S10. ADG-associated metabolites in rumen. Table S11. Summary of sequence data generated from fecal samples of 8 LADG and 8 HADG calves. Table S12. Wilcoxon rank sum test was used to compare the fecal microbial domain. Table S13. The relative abundances of the top 10 feces bacterial phyla, genera and species between HADG and LADG calves. Table S14. The Significant differences in fecal bacterial genera and species between HADG and LADG calves. Table S15. Significantly different fecal metabolites between HADG and LADG calves. Table S16. ADG-associated metabolites in feces. Table S17. Significantly different plasma metabolites between HADG and LADG calves. Table S18. ADG-associated metabolites in plasme. Table S20. Differential metabolites due to by Acidaminococcus fermentans P41 fermentation.
DOI: 10.15468/dl.wge32x
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euphrasia hachijoensis Nakai ex Furumi"
 ]
}

 The dataset includes 34 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047854-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hhjf8q
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Berberis hypokerina Airy Shaw"
 ]
}

 The dataset includes 7 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055352-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lf5tvt
title: Occurrence Download

description: A dataset containing 2801 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tayassu pecari (Link, 1795)"
 ]
}

 The dataset includes 2801 records from 105 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000935-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vz3g67
title: Occurrence Download

description: A dataset containing 2861 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Calvatia gigantea (Batsch) Lloyd, Calvatia gigantea (Batsch) Rostk.)"
 ]
}

 The dataset includes 2861 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047849-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.