cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.12099119
title: Supplementary Data and Code: Different traits dominate evolution at early and late stages of adaptive radiation

description: Supplementary Data and R code for phylogenetic analyses for manuscript entitled Different traits dominate evolution at early and late stages of adaptive radiation. 

Code.zip contains all R scripts and data needed for analyses in the paper. It is divided in two parts, DECOUPLED DIVERSIFICATION (folder 1) and STATES-DEPENDENT SPECIATION AND EXTINCTION (folder 2).

1) DECOUPLED DIVERSIFICATION

"data" folder contains phyogeny, morpho and eco data, species by clades, and RDS with imputed values for missing traits.

Niphargus_trait_evolution.rmd file runs neccessary packages and scripts and outputs results. Note that working directory and "result" folder need to be defined before you run the script.

00_data.R: import and data manipulation, including imputation of missing values to morpho ds. All variables needed in later analyses are defined here, including subsets, subclades, etc.00_functions.R: all custom functions01_figure1_phylogeny.R: plots half-circle phylogeny02_regression_PCA.R: runs phylogenetic regression and PCA, and saves results03_kmeans.R: calculates k-means and saves results04_modeling.R: runs modeling, ancestral trait reconstruction and morphospace expansion through time, simulations and comparison of morphospace expansion of real and simulated data.

2) STATES-DEPENDENT SPECIATION AND EXTINCTION

This folder includes data and code used for sec_sse analysis. The analysis was run on whole genus and three major clades. Additionally, trophic trait classes were compared with habitat trait class (trophicD and trophicP), so overall, 8 combinations of model comparisons were performed. The folder is thus divided into "clades" and "whole_genus" subfolders. Data and R scripts for model setup, launching the analysis and calculation of AIC values are provided.
DOI: 10.5281/zenodo.12099120
title: Supplementary Data and Code: Different traits dominate evolution at early and late stages of adaptive radiation

description: Supplementary Data and R code for phylogenetic analyses for manuscript entitled Different traits dominate evolution at early and late stages of adaptive radiation. 

Code.zip contains all R scripts and data needed for analyses in the paper. It is divided in two parts, DECOUPLED DIVERSIFICATION (folder 1) and STATES-DEPENDENT SPECIATION AND EXTINCTION (folder 2).

1) DECOUPLED DIVERSIFICATION

"data" folder contains phyogeny, morpho and eco data, species by clades, and RDS with imputed values for missing traits.

Niphargus_trait_evolution.rmd file runs neccessary packages and scripts and outputs results. Note that working directory and "result" folder need to be defined before you run the script.

00_data.R: import and data manipulation, including imputation of missing values to morpho ds. All variables needed in later analyses are defined here, including subsets, subclades, etc.00_functions.R: all custom functions01_figure1_phylogeny.R: plots half-circle phylogeny02_regression_PCA.R: runs phylogenetic regression and PCA, and saves results03_kmeans.R: calculates k-means and saves results04_modeling.R: runs modeling, ancestral trait reconstruction and morphospace expansion through time, simulations and comparison of morphospace expansion of real and simulated data.

2) STATES-DEPENDENT SPECIATION AND EXTINCTION

This folder includes data and code used for sec_sse analysis. The analysis was run on whole genus and three major clades. Additionally, trophic trait classes were compared with habitat trait class (trophicD and trophicP), so overall, 8 combinations of model comparisons were performed. The folder is thus divided into "clades" and "whole_genus" subfolders. Data and R scripts for model setup, launching the analysis and calculation of AIC values are provided.
DOI: 10.15468/dl.gerpwm
title: Occurrence Download

description: A dataset containing 44458 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Helianthus tuberosus L."
 ]
}

 The dataset includes 44458 records from 786 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0105997-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13382792
title: Structural Insights into Tryptamine Psychedelics: The Role of Hydroxyl Indole Ring Site in 5-HT2A Receptor Activation and Psychedelic-like Activity
DOI: 10.5281/zenodo.13382793
title: Structural Insights into Tryptamine Psychedelics: The Role of Hydroxyl Indole Ring Site in 5-HT2A Receptor Activation and Psychedelic-like Activity
DOI: 10.5281/zenodo.13382820
title: TTV Data Extraction

description: This data set contains TTV (threats to validity) analysis extracted from 91 studies.
DOI: 10.15468/dl.bz7m7k
title: Occurrence Download

description: A dataset containing 6640 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Helenium flexuosum Raf."
 ]
}

 The dataset includes 6640 records from 161 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0105999-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4cg9qa
title: Occurrence Download

description: A dataset containing 59771 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Mustela erminea Linnaeus, 1758",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 59771 records from 478 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0106001-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mhjcrw
title: Occurrence Download

description: A dataset containing 13533 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Helenium autumnale L."
 ]
}

 The dataset includes 13533 records from 311 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0106004-240626123714530/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.13323746
title: Additional file 5 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 5. Centered log2(fpkm+1) gene expression clusters of NEC and EC callus. Gene expression profiles of quantile normalized FPKM values for genes that were clustered by k-means clustering in NEC and EC callus.
DOI: 10.6084/m9.figshare.13323998.v1
title: Additional file 11 of Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

description: Additional file 11: Supplementary Data 11. Candidate regions and genes in these regions with KEGG and GO results for dressing percentage.
DOI: 10.6084/m9.figshare.7558937.v1
title: Additional file 4: of A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication

description: Table S3. SNVs detected by mapping RNA-seq of 19 barley accessions against either Morex HCâ +â LC or CWA. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.13324004
title: Additional file 2 of Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

description: Additional file 2: Supplementary Data 2. Significant GWAS results for each phenotype.
DOI: 10.6084/m9.figshare.13324001.v1
title: Additional file 1 of Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

description: Additional file 1: Supplementary Data 1. Breed phenotypes.
DOI: 10.6084/m9.figshare.13324004.v1
title: Additional file 2 of Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

description: Additional file 2: Supplementary Data 2. Significant GWAS results for each phenotype.
DOI: 10.6084/m9.figshare.19093578.v1
title: Transcriptome profiling provides preliminary molecular insights into adventitious bud formation in herbaceous peony (<i>Paeonia ×</i> ‘Coral Charm’)

description: Herbaceous peony is a kind of perennial herbaceous flowering plant and most varieties are highly dependent on ramet propagation. Some varieties, such as <i>Paeonia ×</i> ‘Coral Charm’, have characteristics of relatively easy root cutting propagation. However, underlying adventitious buds of root cutting, the molecular mechanisms are still not completely understood. Here, we collected four key stages of adventitious bud formation of <i>P. ×</i> ‘Coral Charm’ for transcriptome sequencing, and assembled and annotated 326,139 transcripts. By carrying out weighted gene co-expression network analysis, three functional modules and several biological and metabolic pathways related to the adventitious bud formation were identified. Finally, we determined six transcription factors in the MYB, HD-ZIP, C2H2 and bZIP gene family that may play a key role in the adventitious bud formation. These results provided insights into the adventitious bud formation of herbaceous peony, and laid a theoretical foundation for the rapid propagation of <i>Paeonia</i>.
DOI: 10.6084/m9.figshare.13323743
title: Additional file 4 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 4. Gene Ontology enrichment of genes downregulated EC (&gt;=1 fold change). Gene ontology classification results of genes that are downregulated at least 1FC in embryogenic callus when compared to nonembryogenic callus.
DOI: 10.6084/m9.figshare.12277970
title: tumor_IKK.m is used to reproduce what happens after inhibiting the activation rate of IKK. from Mathematical modelling of the role of GADD45<i>β</i> in the pathogenesis of multiple myeloma

description: Multiple myeloma (MM) is an incurable disease with relatively high morbidity and mortality rates. Great efforts were made to develop nuclear factor-kappa B (NF-κB)-targeted therapies against MM disease. However, these treatments influence MM cells as well as normal cells, inevitably causing serious side effects. Further research showed that NF-κB signalling promotes the survival of MM cells by interacting with JNK signalling through growth arrest and DNA damage-inducible beta (GADD45β), the downstream module of NF-κB signalling. The GADD45β-targeted intervention was suggested to be an effective and MM cell-specific treatment. However, the underlying mechanism through which GADD45β promotes the survival of MM cells is usually ignored in the previous models. A mathematical model of MM is built in this paper to investigate how NF-κB signalling acts along with JNK signalling through GADD45β and MKK7 to promote the survival of MM cells. The model cannot only mimic the variations in bone cells, the bone volume and MM cells with time, but it can also examine how the NF-κB pathway acts with the JNK pathway to promote the development of MM cells. In addition, the model also investigates the efficacies of GADD45β<i>-</i> and NF-κB-targeted treatments, suggesting that GADD45β-targeted therapy is more effective but has no apparent side effects. The simulation results match the experimental observations. It is anticipated that this model could be employed as a useful tool to initially investigate and even explore potential therapies involving the NF-κB and JNK pathways in the future.
DOI: 10.6084/m9.figshare.13323725
title: Additional file 10 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 10. Transcription factors with differential expression profiles in NEC and EC callus. A list of all annotated transcription factors in the v2.0 of Gossypium hirsutum reference assembly with logFC values in EC.
DOI: 10.6084/m9.figshare.13323749
title: Additional file 6 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 6. Subcluster 1 GO enrichment. Gene ontology enrichment of subcluster 1 as determined by k-means clustering
DOI: 10.6084/m9.figshare.13323725.v1
title: Additional file 10 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 10. Transcription factors with differential expression profiles in NEC and EC callus. A list of all annotated transcription factors in the v2.0 of Gossypium hirsutum reference assembly with logFC values in EC.
DOI: 10.6084/m9.figshare.13323731.v1
title: Additional file 12 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 12. Gene expression evaluation by RT-qPCR. The expression pattern of all the selected genes in embryogenic cells (EC) vs. non-embryogenic cells (NEC) confirmed the RNAseq results.
DOI: 10.6084/m9.figshare.13323752
title: Additional file 7 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 7. Subcluster 2 GO enrichment. Gene ontology enrichment of subcluster 2 as determined by k-means clustering
DOI: 10.6084/m9.figshare.12277973.v1
title: Equation_Tumor1.m represents the condition with the introduction of MM cells. from Mathematical modelling of the role of GADD45<i>β</i> in the pathogenesis of multiple myeloma

description: Multiple myeloma (MM) is an incurable disease with relatively high morbidity and mortality rates. Great efforts were made to develop nuclear factor-kappa B (NF-κB)-targeted therapies against MM disease. However, these treatments influence MM cells as well as normal cells, inevitably causing serious side effects. Further research showed that NF-κB signalling promotes the survival of MM cells by interacting with JNK signalling through growth arrest and DNA damage-inducible beta (GADD45β), the downstream module of NF-κB signalling. The GADD45β-targeted intervention was suggested to be an effective and MM cell-specific treatment. However, the underlying mechanism through which GADD45β promotes the survival of MM cells is usually ignored in the previous models. A mathematical model of MM is built in this paper to investigate how NF-κB signalling acts along with JNK signalling through GADD45β and MKK7 to promote the survival of MM cells. The model cannot only mimic the variations in bone cells, the bone volume and MM cells with time, but it can also examine how the NF-κB pathway acts with the JNK pathway to promote the development of MM cells. In addition, the model also investigates the efficacies of GADD45β<i>-</i> and NF-κB-targeted treatments, suggesting that GADD45β-targeted therapy is more effective but has no apparent side effects. The simulation results match the experimental observations. It is anticipated that this model could be employed as a useful tool to initially investigate and even explore potential therapies involving the NF-κB and JNK pathways in the future.
DOI: 10.6084/m9.figshare.12277982.v1
title: parameters.m represents the parameters in the NF-kB pathway. from Mathematical modelling of the role of GADD45<i>β</i> in the pathogenesis of multiple myeloma

description: Multiple myeloma (MM) is an incurable disease with relatively high morbidity and mortality rates. Great efforts were made to develop nuclear factor-kappa B (NF-κB)-targeted therapies against MM disease. However, these treatments influence MM cells as well as normal cells, inevitably causing serious side effects. Further research showed that NF-κB signalling promotes the survival of MM cells by interacting with JNK signalling through growth arrest and DNA damage-inducible beta (GADD45β), the downstream module of NF-κB signalling. The GADD45β-targeted intervention was suggested to be an effective and MM cell-specific treatment. However, the underlying mechanism through which GADD45β promotes the survival of MM cells is usually ignored in the previous models. A mathematical model of MM is built in this paper to investigate how NF-κB signalling acts along with JNK signalling through GADD45β and MKK7 to promote the survival of MM cells. The model cannot only mimic the variations in bone cells, the bone volume and MM cells with time, but it can also examine how the NF-κB pathway acts with the JNK pathway to promote the development of MM cells. In addition, the model also investigates the efficacies of GADD45β<i>-</i> and NF-κB-targeted treatments, suggesting that GADD45β-targeted therapy is more effective but has no apparent side effects. The simulation results match the experimental observations. It is anticipated that this model could be employed as a useful tool to initially investigate and even explore potential therapies involving the NF-κB and JNK pathways in the future.
DOI: 10.6084/m9.figshare.12277985.v1
title: tumor_GADD45B.m is used to reproduce what happens after inhibiting the formation rate of GADD45B|MKK7 complex. from Mathematical modelling of the role of GADD45<i>β</i> in the pathogenesis of multiple myeloma

description: Multiple myeloma (MM) is an incurable disease with relatively high morbidity and mortality rates. Great efforts were made to develop nuclear factor-kappa B (NF-κB)-targeted therapies against MM disease. However, these treatments influence MM cells as well as normal cells, inevitably causing serious side effects. Further research showed that NF-κB signalling promotes the survival of MM cells by interacting with JNK signalling through growth arrest and DNA damage-inducible beta (GADD45β), the downstream module of NF-κB signalling. The GADD45β-targeted intervention was suggested to be an effective and MM cell-specific treatment. However, the underlying mechanism through which GADD45β promotes the survival of MM cells is usually ignored in the previous models. A mathematical model of MM is built in this paper to investigate how NF-κB signalling acts along with JNK signalling through GADD45β and MKK7 to promote the survival of MM cells. The model cannot only mimic the variations in bone cells, the bone volume and MM cells with time, but it can also examine how the NF-κB pathway acts with the JNK pathway to promote the development of MM cells. In addition, the model also investigates the efficacies of GADD45β<i>-</i> and NF-κB-targeted treatments, suggesting that GADD45β-targeted therapy is more effective but has no apparent side effects. The simulation results match the experimental observations. It is anticipated that this model could be employed as a useful tool to initially investigate and even explore potential therapies involving the NF-κB and JNK pathways in the future.
DOI: 10.6084/m9.figshare.10184534
title: MOESM11 of Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species

description: Additional file 11: Table S7. List of the differentially expressed genes between the 3 Prunus mira fruit types (PMHF, PMHR and PMHY) representing the â core transcriptomeâ and their functional annotation. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.10184534.v1
title: MOESM11 of Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species

description: Additional file 11: Table S7. List of the differentially expressed genes between the 3 Prunus mira fruit types (PMHF, PMHR and PMHY) representing the â core transcriptomeâ and their functional annotation. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.19092729
title: Additional file 1 of Subtyping of sarcomas based on pathway enrichment scores in bulk and single cell transcriptomes

description: Additional file 1: Table S1. A summary of the datasets analyzed.
DOI: 10.6084/m9.figshare.19092732.v1
title: Additional file 2 of Subtyping of sarcomas based on pathway enrichment scores in bulk and single cell transcriptomes

description: Additional file 2: Table S2. Pathways, immune signatures, and biological processes and their marker genes.
DOI: 10.6084/m9.figshare.10184549
title: MOESM13 of Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species

description: Additional file 13: Table S8. List of the differentially expressed genes between the 3 Prunus mira fruit types (PMHF, PMHR and PMHY) mapped to the terpernoid-carotenoid pathways and phenylpropanoid-flavonoid pathways and their expression level during the fruit ripening stage (C). (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7034792.v3
title: CASP4/caspase-11 promotes autophagosome formation in response to bacterial infection

description: CASP4/caspase-11-dependent inflammasome activation is important for the clearance of various Gram-negative bacteria entering the host cytosol. Additionally, CASP4 modulates the actin cytoskeleton to promote the maturation of phagosomes harboring intracellular pathogens such as <i>Legionella pneumophila</i> but not those enclosing nonpathogenic bacteria. Nevertheless, this non-inflammatory role of CASP4 regarding the trafficking of vacuolar bacteria remains poorly understood. Macroautophagy/autophagy, a catabolic process within eukaryotic cells, is also implicated in the elimination of intracellular pathogens such as <i>Burkholderia cenocepacia</i>. Here we show that CASP4-deficient macrophages exhibit a defect in autophagosome formation in response to <i>B. cenocepacia</i> infection. The absence of CASP4 causes an accumulation of the small GTPase RAB7, reduced colocalization of <i>B. cenocepacia</i> with LC3 and acidic compartments accompanied by increased bacterial replication <i>in vitro</i> and <i>in vivo</i>. Together, our data reveal a novel role of CASP4 in regulating autophagy in response to <i>B. cenocepacia</i> infection.
DOI: 10.6084/m9.figshare.10184549.v1
title: MOESM13 of Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species

description: Additional file 13: Table S8. List of the differentially expressed genes between the 3 Prunus mira fruit types (PMHF, PMHR and PMHY) mapped to the terpernoid-carotenoid pathways and phenylpropanoid-flavonoid pathways and their expression level during the fruit ripening stage (C). (XLSX 11 kb)