cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20787118.v1
title: Additional file 1 of A gene expression profile for the lower osteogenic potent of bone-derived MSCs from osteoporosis with T2DM and the potential mechanism

description: Additional file 1: Table S1. The expression alteration of all DEGs in T2DM-BMSC.
DOI: 10.6084/m9.figshare.22362375
title: Comprehensive deep mutational scanning reveals the pH induced stability and binding differences between SARS-CoV-2 spike RBD and human ACE2

description: The SARS-CoV-2 spike (S) glycoprotein with its mobile receptor-binding domain (RBD), binds to the human ACE2 receptor and thus facilitates virus entry through low-pH-endosomal pathways. The high degree of SARS-CoV-2 mutability has raised concern among scientists and medical professionals because it created doubt about the effectiveness of drugs and vaccinations designed specifically for COVID-19. In this study, we used computational saturation mutagenesis approach, including structure-based free energy calculations to analyse the effects of the missense mutations on the SARS-CoV-2 S-RBD stability and the S-RBD binding affinity with ACE2 at three different pH (pH 4.5, pH 6.5, and pH 7.4). A total of 3705 mutations in the S-RBD protein were analyzed, and we discovered that most of these mutations destabilize the RBD protein. Specifically, residues G404, G431, G447, A475, and G526 were important for RBD protein stability. In addition, RBD residues Y449, Y489, Y495, Q498, and N487 were critical for the RBD-ACE2 interaction. Next, we found that the distribution of the mean stability changes and mean binding energy changes of RBD due to mutations at both serological and endosomal pH correlated well, indicating the similar effects of mutations. Overall, this computational analysis is useful for understanding the effects of missense mutations in SARS-CoV-2 pathogenesis at different pH. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22362375.v1
title: Comprehensive deep mutational scanning reveals the pH induced stability and binding differences between SARS-CoV-2 spike RBD and human ACE2

description: The SARS-CoV-2 spike (S) glycoprotein with its mobile receptor-binding domain (RBD), binds to the human ACE2 receptor and thus facilitates virus entry through low-pH-endosomal pathways. The high degree of SARS-CoV-2 mutability has raised concern among scientists and medical professionals because it created doubt about the effectiveness of drugs and vaccinations designed specifically for COVID-19. In this study, we used computational saturation mutagenesis approach, including structure-based free energy calculations to analyse the effects of the missense mutations on the SARS-CoV-2 S-RBD stability and the S-RBD binding affinity with ACE2 at three different pH (pH 4.5, pH 6.5, and pH 7.4). A total of 3705 mutations in the S-RBD protein were analyzed, and we discovered that most of these mutations destabilize the RBD protein. Specifically, residues G404, G431, G447, A475, and G526 were important for RBD protein stability. In addition, RBD residues Y449, Y489, Y495, Q498, and N487 were critical for the RBD-ACE2 interaction. Next, we found that the distribution of the mean stability changes and mean binding energy changes of RBD due to mutations at both serological and endosomal pH correlated well, indicating the similar effects of mutations. Overall, this computational analysis is useful for understanding the effects of missense mutations in SARS-CoV-2 pathogenesis at different pH. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.16595223
title: An extended spatiotemporal exposure index for urban racial segregation

description: The Segregation Index quantifies the degree of segregation of social groups or classes. Because of the increasing use of fine-grained spatiotemporal activity and flow data, the conventional segregation measurements’ inclusiveness is challenged. We add population flow to the conventional place-based spatial exposure index to identify spatiotemporal segregation changes. Specifically, we considered the population-flow network, hierarchical structure, and time. In Chicago’s demonstration case study, we first used the time-dependent Twitter Origin-Destination flow matrices and their hierarchical structure information to estimate interactions between areal units at the neighborhood level. Then we computed the new population composition of units based on their interactions with other units and estimated the proposed spatiotemporal exposure index for different times. Finally, we systematically compared their differences with the conventional indices at global and local scales to see how population-flow patterns affect the exposure index. The results show that the population-flow patterns reflect valuable information in neighborhood interactions in temporal and spatial dimensions, but it is missing information in the conventional segregation computations. Furthermore, we emphasize that the hierarchical structures of flow patterns and the choice of appropriate parameters are also important factors for a rational segregation evaluation.
DOI: 10.34740/kaggle/dsv/7655840
title: Diabetes Prediction
DOI: 10.6084/m9.figshare.20787172
title: Additional file 5 of Antioxidant activation, cell wall reinforcement, and reactive oxygen species regulation promote resistance to waterlogging stress in hot pepper (Capsicum annuum L.)

description: Additional file 5: Table S2. Statistical of RNA-seq base information.
DOI: 10.6084/m9.figshare.20787145
title: Additional file 12 of Antioxidant activation, cell wall reinforcement, and reactive oxygen species regulation promote resistance to waterlogging stress in hot pepper (Capsicum annuum L.)

description: Additional file 12: Table S9. The KEGG enrichment of clusters 2 and 5 genes in Fig. 6B.
DOI: 10.6084/m9.figshare.20787169.v1
title: Additional file 4 of Antioxidant activation, cell wall reinforcement, and reactive oxygen species regulation promote resistance to waterlogging stress in hot pepper (Capsicum annuum L.)

description: Additional file 4: Table S1. Data filtering statistics.
DOI: 10.6084/m9.figshare.20787139.v1
title: Additional file 10 of Antioxidant activation, cell wall reinforcement, and reactive oxygen species regulation promote resistance to waterlogging stress in hot pepper (Capsicum annuum L.)

description: Additional file 10: Table S7. The KEGG enrichment of 1,989 specific DEGs compared the control and treatment samples taken at the same time point.
DOI: 10.6084/m9.figshare.19738606.v1
title: Additional file 2 of Identification of miRNA-mRNA-TF regulatory networks in peripheral blood mononuclear cells of type 1 diabetes

description: Additional file 2.
DOI: 10.6084/m9.figshare.20787142
title: Additional file 11 of Antioxidant activation, cell wall reinforcement, and reactive oxygen species regulation promote resistance to waterlogging stress in hot pepper (Capsicum annuum L.)

description: Additional file 11: Table S8. The KEGG enrichment of the intersection genes in the trend of S and T gene expression analysis.
DOI: 10.6084/m9.figshare.20787148
title: Additional file 13 of Antioxidant activation, cell wall reinforcement, and reactive oxygen species regulation promote resistance to waterlogging stress in hot pepper (Capsicum annuum L.)

description: Additional file 13: Table S10. The DEG transcription factor list.
DOI: 10.6084/m9.figshare.20787181.v1
title: Additional file 8 of Antioxidant activation, cell wall reinforcement, and reactive oxygen species regulation promote resistance to waterlogging stress in hot pepper (Capsicum annuum L.)

description: Additional file 8: Table S5. The mapping region statistics.
DOI: 10.6084/m9.figshare.20787175.v1
title: Additional file 6 of Antioxidant activation, cell wall reinforcement, and reactive oxygen species regulation promote resistance to waterlogging stress in hot pepper (Capsicum annuum L.)

description: Additional file 6: Table S3. The ribosome mapping statistics.
DOI: 10.6084/m9.figshare.20787184
title: Additional file 9 of Antioxidant activation, cell wall reinforcement, and reactive oxygen species regulation promote resistance to waterlogging stress in hot pepper (Capsicum annuum L.)

description: Additional file 9: Table S6. The KEGG enrichment of 3,579 specific DEGs in S10T-vs-T10T and S5T-vsT5T.
DOI: 10.6084/m9.figshare.21311457
title: Tanshinone increases Hemopexin expression in lung cells and macrophages to protect against cigarette smoke-induced COPD and enhance antiviral responses

description: Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory disease, while respiratory infections can elicit exacerbations in COPD patients to mediate increased mortality. Administration of Tanshinones (TS) derivatives has been demonstrated to protect against cigarette smoking (CS) and lipopolysaccharide (LPS)-induced COPD progression. However, the underlying molecular mechanisms and the roles of TS in mitigating the severity of viral-mediated exacerbations of COPD have not been elucidated. Here, we found that TS treatments significantly attenuated lung function decline, inflammatory responses and oxidative stress in CS and LPS-induced COPD mice. Subsequent RNA-seq analysis revealed significantly upregulated Hemopexin expression and enriched interferons (IFNs) signaling pathways in lung tissues of COPD mice upon TS treatments. Moreover, TS administration demonstrated Hemopexin-dependent beneficial roles in BEAS-2B lung cells and RAW264.7 macrophages, which was associated with the suppression of oxidative stress and ERK, NF-κB, and NLRP3 inflammasome signaling pathways-mediated inflammation. Furthermore, TS promoted IFN signaling and rescued impaired antiviral responses in CS and LPS-exposed lung cells that were infected by influenza virus. Notably, hemopexin over-expression in lung cells and macrophages recapitulated the pharmacological activities of TS. Taken together, these results indicate that TS administration is a promising and potential therapeutic strategy for treating COPD and preventing COPD exacerbations.
DOI: 10.6084/m9.figshare.21314016
title: Comparing the isotopic and molecular composition of dissolved organic carbon between the oligotrophic South China Sea and the north Pacific Ocean: signals of biodegradation, conservative mixing, and terrestrial input

description: This data set contains: 1)the sampling information and DOC concentrations of the samples; 2) statistics of DOC concentrations, SPE-DOC concentrations, SPE-DOC Δ14C values, SPE-DOC δ13C values, and carbon extraction efficiencies determined for samples from stations F2 and DC6; 3)Molecular characteristics of DOM throughout two water columns at stations F2 and DC6, including the relative abundance of different compound groups and intensity-weighted indices.
DOI: 10.6084/m9.figshare.22360276
title: PCA 1 with raters from Majestic tigers: personality structure in the great Amur cat

description: PCA sample 1 with raters left in
DOI: 10.6084/m9.figshare.7155707
title: Additional file 1: of Genome-wide analysis of the rice PPR gene family and their expression profiles under different stress treatments

description: Table S1. The general information of PPR genes in rice genome. Table S2. PPR genes subcellular location results in rice by TargetP and Predotar. Table S3. PPR genes as miRNA targets in rice. Table S4. FPKM values of PPR genes in rice various organs and tissues. Table S5. RNA-seq data of PPR genes under different biotic and abiotic stresses. Table S6. Primers used in the study. (ZIP 805 kb)
DOI: 10.6084/m9.figshare.19738555.v1
title: Additional file 2 of Association of the tissue infiltrated and peripheral blood immune cell subsets with response to radiotherapy for rectal cancer

description: Additional file 2. Statistically significant cell types validation with pooled dataset of GSE3493 and GSE35452.
DOI: 10.6084/m9.figshare.19738603
title: Additional file 1 of Identification of miRNA-mRNA-TF regulatory networks in peripheral blood mononuclear cells of type 1 diabetes

description: Additional file 1.
DOI: 10.6084/m9.figshare.20787172.v1
title: Additional file 5 of Antioxidant activation, cell wall reinforcement, and reactive oxygen species regulation promote resistance to waterlogging stress in hot pepper (Capsicum annuum L.)

description: Additional file 5: Table S2. Statistical of RNA-seq base information.
DOI: 10.6084/m9.figshare.22360306.v1
title: Procrustes main file from Majestic tigers: personality structure in the great Amur cat

description: We explore individual differences in tiger personality. We first asked—is there evidence of personality dimensions (analogous to the Big Five in human personality research) in the Amur tiger? We then asked, are any discoverable personality dimensions associated with measured outcomes, including group status, health, and mating frequency? 152 of our participating tigers live in the world's largest semi-wild tiger sanctuary in North Eastern China. Our second sample of 96 tigers also lives in a sanctuary. Having two samples allowed us to assess the replicability of the personality dimensions or factors reported in our first sample. We found that two factors (explaining 21% and 17% of the variance among items) which we call, for descriptive ease, Majesty and Steadiness, provide the best fit to the data. Tigers that score higher on Majesty are healthier, eat more live prey, have higher group status (among other tigers as assessed by human raters), and mate more often. We provide some ethological context to put flesh on the quantitative bones of our findings concerning these magnificent and charismatic animals.
DOI: 10.6084/m9.figshare.12923232
title: Additional file 3 of Genome-wide analysis of lncRNA and mRNA expression and endogenous hormone regulation during tension wood formation in Catalpa bungei

description: Additional file 3: Table S3 The annotation of DEGs involved hormone biosynthesis and signal transduction.
DOI: 10.6084/m9.figshare.19738603.v1
title: Additional file 1 of Identification of miRNA-mRNA-TF regulatory networks in peripheral blood mononuclear cells of type 1 diabetes

description: Additional file 1.
DOI: 10.6084/m9.figshare.20787151
title: Additional file 14 of Antioxidant activation, cell wall reinforcement, and reactive oxygen species regulation promote resistance to waterlogging stress in hot pepper (Capsicum annuum L.)

description: Additional file 14: Table S11. The premiers list for qRT-PCR.
DOI: 10.6084/m9.figshare.12923241
title: Additional file 5 of Genome-wide analysis of lncRNA and mRNA expression and endogenous hormone regulation during tension wood formation in Catalpa bungei

description: Additional file 5: Table S4 The annotation of genes regulated by potential lncRNAs through cis regulation. Table S5 The annotation of genes regulated by potential lncRNAs via trans regulation. Table S6 The annotation of genes regulated by potential lncRNAs via antisense regulation.
DOI: 10.6084/m9.figshare.19738609
title: Additional file 3 of Identification of miRNA-mRNA-TF regulatory networks in peripheral blood mononuclear cells of type 1 diabetes

description: Additional file 3.
DOI: 10.6084/m9.figshare.20787169
title: Additional file 4 of Antioxidant activation, cell wall reinforcement, and reactive oxygen species regulation promote resistance to waterlogging stress in hot pepper (Capsicum annuum L.)

description: Additional file 4: Table S1. Data filtering statistics.
DOI: 10.6084/m9.figshare.12923243
title: Additional file 13 of Genome-wide identification and characterization of GRAS genes in soybean (Glycine max)

description: Additional file 13: Table S12. Expression profiles of GmGRAS genes in soybean root during dehydration and salt stresses.
DOI: 10.6084/m9.figshare.12923279.v1
title: Additional file 6 of Genome-wide identification and characterization of GRAS genes in soybean (Glycine max)

description: Additional file 6: Table S5. Gene density of each chromosome or scaffold of the soybean genome.
DOI: 10.6084/m9.figshare.12923288.v1
title: Additional file 9 of Genome-wide identification and characterization of GRAS genes in soybean (Glycine max)

description: Additional file 9: Table S8. Non-redundant GmGRAS gene IDs associated with the syntenic relationships between soybean and the other six species.
DOI: 10.6084/m9.figshare.20787184.v1
title: Additional file 9 of Antioxidant activation, cell wall reinforcement, and reactive oxygen species regulation promote resistance to waterlogging stress in hot pepper (Capsicum annuum L.)

description: Additional file 9: Table S6. The KEGG enrichment of 3,579 specific DEGs in S10T-vs-T10T and S5T-vsT5T.
DOI: 10.6084/m9.figshare.12923244.v1
title: Additional file 6 of Genome-wide analysis of lncRNA and mRNA expression and endogenous hormone regulation during tension wood formation in Catalpa bungei

description: Additional file 6: Table S7 The annotation of genes regulated by lncRNAs and transcription factors in the regulatory network. Table S8 The correlations between the expression of genes and regulators.
DOI: 10.6084/m9.figshare.12923247
title: Additional file 7 of Genome-wide analysis of lncRNA and mRNA expression and endogenous hormone regulation during tension wood formation in Catalpa bungei

description: Additional file 7: Table S9 Primer information.
DOI: 10.6084/m9.figshare.12923258
title: Additional file 18 of Genome-wide identification and characterization of GRAS genes in soybean (Glycine max)

description: Additional file 18: Table S16. Pairwise correlation coefficients between different expressed GmGRAS genes in soybean embryonic axes during seed germination.
DOI: 10.6084/m9.figshare.12923264.v1
title: Additional file 1 of Genome-wide identification and characterization of GRAS genes in soybean (Glycine max)

description: Additional file 1: Table S1. The 117 identified GmGRAS genes in this study.
DOI: 10.6084/m9.figshare.20787178
title: Additional file 7 of Antioxidant activation, cell wall reinforcement, and reactive oxygen species regulation promote resistance to waterlogging stress in hot pepper (Capsicum annuum L.)

description: Additional file 7: Table S4. The statistical of mapping the reference genome.
DOI: 10.6084/m9.figshare.20787178.v1
title: Additional file 7 of Antioxidant activation, cell wall reinforcement, and reactive oxygen species regulation promote resistance to waterlogging stress in hot pepper (Capsicum annuum L.)

description: Additional file 7: Table S4. The statistical of mapping the reference genome.
DOI: 10.6084/m9.figshare.20786765
title: Additional file 1 of Influence of Pleistocene climate fluctuations on the demographic history and distribution of the critically endangered Chinese pangolin (Manis pentadactyla)

description: Additional file 1: Table S1. Best fit MAXENT model based on delta AICc from ENMeval. Table S2. AUC values for each model. Table S3. Sampling site data, gender, distribution clustering, and missing data rate of genetic samples of Chinese pangolins used in this study. Table S4. Estimation of the relative contributions of the environmental variables to the Maxent model. Table S5. Summary of each dataset used for the respective analysis. Table S6. Bioclimatic variable selection for species distribution modelling based on PCA.
DOI: 10.6084/m9.figshare.19738612
title: Additional file 4 of Identification of miRNA-mRNA-TF regulatory networks in peripheral blood mononuclear cells of type 1 diabetes

description: Additional file 4.
DOI: 10.6084/m9.figshare.16590911
title: Additional file 7 of Single-cell analysis of a tumor-derived exosome signature correlates with prognosis and immunotherapy response

description: Additional file 7: Table S1. Tumor-derived exosomes associated genes. Table S2. The top 10 miRNAs inversely correlated with TEXscore. Table S3. Multi-variate Cox regression results of TEXscore in TCGA-LUSC, TCGA-STAD, and TCGA-BLCA cohort. Table S4. Statistical results of Fig. 5B–E. Table S5. Statistical results of Figure S5. Table S6. Statistical results of Figure S6.
DOI: 10.6084/m9.figshare.16590911.v1
title: Additional file 7 of Single-cell analysis of a tumor-derived exosome signature correlates with prognosis and immunotherapy response

description: Additional file 7: Table S1. Tumor-derived exosomes associated genes. Table S2. The top 10 miRNAs inversely correlated with TEXscore. Table S3. Multi-variate Cox regression results of TEXscore in TCGA-LUSC, TCGA-STAD, and TCGA-BLCA cohort. Table S4. Statistical results of Fig. 5B–E. Table S5. Statistical results of Figure S5. Table S6. Statistical results of Figure S6.
DOI: 10.25549/pcra-c14-56563
title: Redemption tidings, vol. 37, nos. 1-52, 1 Jan. - 22 Dec. 1961

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.
DOI: 10.15468/dl.7ftmpc
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aloe microstigma subsp. framesii (L.Bolus) Glen & D.S.Hardy"
 ]
}

 The dataset includes 43 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0380025-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2auabf
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Geometry POLYGON((-48.47168 -29.15216,-46.27441 -26.43123,-47.06543 -23.64452,-48.03223 -21.37124,-53.39355 -21.28937,-55.23926 -23.32208,-56.29395 -25.48295,-55.85449 -27.83908,-53.39355 -30.90222,-50.22949 -31.27855,-48.47168 -29.15216))",
 "Geometry POLYGON((-46.42822 -22.87744,-45.19775 -24.20689,-42.29736 -23.07973,-43.04443 -21.77991,-43.92334 -20.59165,-45.68115 -20.96144,-46.42822 -22.87744))"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Acianthera macropoda (Barb.Rodr.) Pridgeon & M.W.Chase",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 12 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050878-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mw2nud
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mikania rimachioides H.Rob. & W.C.Holmes"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041003-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g6yjfb
title: Occurrence Download

description: A dataset containing 60 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sericulus bakeri (Chapin, 1929)"
 ]
}

 The dataset includes 60 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0380000-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-56551
title: Redemption tidings, vol. 37, nos. 1-52, 1 Jan. - 22 Dec. 1961

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.
DOI: 10.15468/dl.xv8wfd
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-95.11398189060505 15.137089217979238,-91.11398189060505 15.137089217979238,-91.11398189060505 19.137089217979238,-95.11398189060505 19.137089217979238,-95.11398189060505 15.137089217979238))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Atherinella guatemalensis (Günther, 1864)"
 ]
}

 The dataset includes 24 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0100897-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.