cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11341151.v2
title: Genome-wide evolution of wobble base-pairing nucleotides of branchpoint motifs with increasing organismal complexity

description: How have the branchpoint motifs evolved in organisms of different complexity? Here we identified and examined the consensus motifs (R<sub>1</sub>C<sub>2</sub>T<sub>3</sub>R<sub>4</sub>A<sub>5</sub>Y<sub>6</sub>, R: A or G, Y: C or T) of 898 fungal genomes. In Ascomycota unicellular yeasts, the G<sub>4</sub>/A<sub>4</sub> ratio is mostly (98%) below 0.125 but increases sharply in multicellular species by about 40 times on average, and in the more complex Basidiomycota, it increases further by about 7 times. The global G<sub>4</sub> increase is consistent with A<sub>4</sub> to G<sub>4</sub> transitions in evolution. Of the G<sub>4</sub>/A<sub>4</sub>-interacting amino acids of the branchpoint binding protein MSL5 (SF1) and the HSH155 (SF3B1), as well as the 5ʹ splice sites (SS) and <i>U2</i> snRNA genes, the 5ʹ SS G<sup>3</sup>/A<sup>3</sup> co-vary with the G<sub>4</sub> to some extent. However, corresponding increase of the G<sub>4</sub>-complementary GCAGTA-<i>U2</i> gene is rare, suggesting wobble-base pairing between the G<sub>4</sub>-containing branchpoint motif and GTAGTA-<i>U2</i> in most of these species. Interestingly, the G<sub>4</sub>/A<sub>4</sub> ratio correlates well with the abundance of alternative splicing in the two phyla, and G<sub>4</sub> enriched significantly at the alternative 3' SS of genes in RNA metabolism, kinases and membrane proteins. Similar wobble nucleotides also enriched at the 3' SS of multicellular fungi with only thousands of protein-coding genes. Thus, branchpoint motifs have evolved U2-complementarity in unicellular Ascomycota yeasts, but have gradually gained more wobble base-pairing nucleotides in fungi of higher complexity, likely to destabilize branchpoint motif-U2 interaction and/or branchpoint A protrusion for alternative splicing. This implies an important role of relaxing the branchpoint signals in the multicellularity and further complexity of fungi.
DOI: 10.6084/m9.figshare.11341151.v1
title: Genome-Wide Evolution of Wobble Base-Pairing Nucleotides of Branchpoint Motifs with Increasing Organismal Complexity

description: How have the branchpoints evolved in organisms of different complexity? Here we identified and examined the consensus motifs (R<sub>1</sub>C<sub>2</sub>T<sub>3</sub>R<sub>4</sub>A<sub>5</sub>Y<sub>6</sub>, R: A or G, Y: C or T) of 898 fungal genomes. In Ascomycota unicellular yeasts, the G<sub>4</sub>/A<sub>4</sub> ratio is mostly (98%) below 0.125 but increases sharply in multicellular species by about 40 times on average, and in the more complex Basidiomycota it increases further by about 7 times. The global G<sub>4</sub> increase is consistent with A<sub>4</sub> to G<sub>4</sub> transitions in evolution. Of the G<sub>4</sub>/A<sub>4</sub>-interacting amino acids of the branchpoint binding protein MSL5 (SF1) and the HSH155 (SF3B1), as well as the 5ʹ splice sites (SS) and <i>U2</i> snRNA genes, the 5ʹ splice site G<sup>3</sup>/A<sup>3</sup> co-vary with the G<sub>4</sub>. However, corresponding increase of the G<sub>4</sub>-complementary GCAGTA-<i>U2</i> gene is rare, suggesting wobble-base pairing between the branchpoint motif and U2 in most species. Interestingly, the G<sub>4</sub>/A<sub>4</sub> ratio correlates well with the abundance of alternative splicing in the two phyla, and G<sub>4</sub> enriched significantly in the alternative splice sites of genes in RNA metabolism, kinases and membrane proteins. Similar wobble nucleotides also enriched in the splice sites of multicellular fungi with only thousands of protein-coding genes. Thus, branchpoint motifs have evolved U2-complementarity in unicellular Ascomycota yeasts, but have gradually gained more wobble base-pairing nucleotides in fungi of higher complexity, likely to destabilize branchpoint-U2 interaction and/or branchpoint A protrusion for alternative splicing. This implies an important role of the relaxation of branchpoint signals in the multicellularity and further complexity of fungi.
DOI: 10.6084/m9.figshare.11341028
title: MOESM5 of Bidirectional histone-gene promoters in Aspergillus: characterization and application for multi-gene expression

description: Additional file 5. Ph4h3 dendogram distance matrix. Table S2. The distance matrix generated from the alignment of 85 Aspergilli Ph4h3.
DOI: 10.6084/m9.figshare.11341022
title: MOESM3 of Bidirectional histone-gene promoters in Aspergillus: characterization and application for multi-gene expression

description: Additional file 3. Bioinformatic analysis of DNA motifs. Table S3. All results of JASPAR analysis. Table S4. Results of JASPAR analysis with score above 9. Table S5. Best hit of YeTFaSCo Spt10 in each of the 85 Ph4h3 sequences. Table S6. Best eight hits of YeTFaSCo Spt10 in the consensus Ph4h3 sequence. Additional motif results JASPAR analysis in reference fungi.
DOI: 10.6084/m9.figshare.11341022.v1
title: MOESM3 of Bidirectional histone-gene promoters in Aspergillus: characterization and application for multi-gene expression

description: Additional file 3. Bioinformatic analysis of DNA motifs. Table S3. All results of JASPAR analysis. Table S4. Results of JASPAR analysis with score above 9. Table S5. Best hit of YeTFaSCo Spt10 in each of the 85 Ph4h3 sequences. Table S6. Best eight hits of YeTFaSCo Spt10 in the consensus Ph4h3 sequence. Additional motif results JASPAR analysis in reference fungi.
DOI: 10.6084/m9.figshare.11341028.v1
title: MOESM5 of Bidirectional histone-gene promoters in Aspergillus: characterization and application for multi-gene expression

description: Additional file 5. Ph4h3 dendogram distance matrix. Table S2. The distance matrix generated from the alignment of 85 Aspergilli Ph4h3.
DOI: 10.6084/m9.figshare.11341010
title: MOESM2 of Differential impact of malaria control interventions on P. falciparum and P. vivax infections in young Papua New Guinean children

description: Additional file 2: Table S2. Key predictors of the prevalence of infections due to P. falciparum and P. vivax as diagnosed by light microscopy. Multivariate generalised estimating equation (GEE) model-based estimates of the risk of infection detected at each monthly active detection of infection visits via backward selection of significant risk factors. aOverall significance level for the variable estimated using wald chi-squared test. AOR: multivariate adjusted odds ratio. CI95: 95% confidence interval; bExcluding febrile illness at the time of visit; Data for observed positive are %.
DOI: 10.6084/m9.figshare.11341016
title: MOESM1 of Bidirectional histone-gene promoters in Aspergillus: characterization and application for multi-gene expression

description: Additional file 1. Identification of Ph4h3. Table S1. Identification of histone h4.1 and h3 genes in 85 Aspergillus species and reference fungi by BLASTp of A. nidulans H4.1 and H3. Curated usage of gene models and prediction of the Ph4h3 sequence.
DOI: 10.6084/m9.figshare.11341013
title: MOESM1 of Exploring physiological signals on people with Duchenne muscular dystrophy for an active trunk support: a case study

description: Additional file 1. Experimental file data.
DOI: 10.6084/m9.figshare.11341016.v1
title: MOESM1 of Bidirectional histone-gene promoters in Aspergillus: characterization and application for multi-gene expression

description: Additional file 1. Identification of Ph4h3. Table S1. Identification of histone h4.1 and h3 genes in 85 Aspergillus species and reference fungi by BLASTp of A. nidulans H4.1 and H3. Curated usage of gene models and prediction of the Ph4h3 sequence.
DOI: 10.6084/m9.figshare.11341010.v1
title: MOESM2 of Differential impact of malaria control interventions on P. falciparum and P. vivax infections in young Papua New Guinean children

description: Additional file 2: Table S2. Key predictors of the prevalence of infections due to P. falciparum and P. vivax as diagnosed by light microscopy. Multivariate generalised estimating equation (GEE) model-based estimates of the risk of infection detected at each monthly active detection of infection visits via backward selection of significant risk factors. aOverall significance level for the variable estimated using wald chi-squared test. AOR: multivariate adjusted odds ratio. CI95: 95% confidence interval; bExcluding febrile illness at the time of visit; Data for observed positive are %.
DOI: 10.6084/m9.figshare.11341001
title: PfSPZ-Assemblies-Annotations

description: This project contains canu assemblies for four <i>P. falciparum</i> strains used for whole organism malaria vaccination and controlled human malaria infections. You will also find two sets of annotation files: gff3 files generated through gmap, and gff3 files generated through Companion. <br><br>Manuscript describing this work can be found here:<br>doi: https://doi.org/10.1101/684175<br>
DOI: 10.6084/m9.figshare.11341004
title: MOESM1 of Differential impact of malaria control interventions on P. falciparum and P. vivax infections in young Papua New Guinean children

description: Additional file 1: Table S1. Bivariate associations between risk factors and the prevalence, molFOB and clinical incidence. Estimates of bivariate associations calculated via generalised estimating equation (GEE) models for prevalence and molecular force of blood-stage (molFOB) infections and negative binomial regression model used for clinical malaria episodes. Recent antimalarial use was not tested in the model for clinical malaria episodes due to aggregated clinical data. aAge in years at enrolment was used for clinical malaria incidence while at the start of interval was used for molFOB. bComparison group; For multilevel variables, comparison group estimates are presented as odds or incidence rate. PCR: Polymerase chain reaction assay; LM: light microscopy; OR: odds ratio; CI95: 95% confidence interval; IRR: incidence rate ratio.
DOI: 10.6084/m9.figshare.11341013.v1
title: MOESM1 of Exploring physiological signals on people with Duchenne muscular dystrophy for an active trunk support: a case study

description: Additional file 1. Experimental file data.
DOI: 10.6084/m9.figshare.11340965
title: Sample dataset for OnClass

description: Datasets for OnClass
DOI: 10.6084/m9.figshare.11341004.v1
title: MOESM1 of Differential impact of malaria control interventions on P. falciparum and P. vivax infections in young Papua New Guinean children

description: Additional file 1: Table S1. Bivariate associations between risk factors and the prevalence, molFOB and clinical incidence. Estimates of bivariate associations calculated via generalised estimating equation (GEE) models for prevalence and molecular force of blood-stage (molFOB) infections and negative binomial regression model used for clinical malaria episodes. Recent antimalarial use was not tested in the model for clinical malaria episodes due to aggregated clinical data. aAge in years at enrolment was used for clinical malaria incidence while at the start of interval was used for molFOB. bComparison group; For multilevel variables, comparison group estimates are presented as odds or incidence rate. PCR: Polymerase chain reaction assay; LM: light microscopy; OR: odds ratio; CI95: 95% confidence interval; IRR: incidence rate ratio.
DOI: 10.6084/m9.figshare.11340965.v1
title: Sample dataset for OnClass

description: Datasets for OnClass
DOI: 10.6084/m9.figshare.11341001.v2
title: PfSPZ-Assemblies-Annotations

description: This project contains canu assemblies for four <i>P. falciparum</i> strains used for whole organism malaria vaccination and controlled human malaria infections. You will also find two sets of annotation files: gff3 files generated through gmap, and gff3 files generated through Companion. <br><br>Manuscript describing this work can be found here:<br>doi: https://doi.org/10.1101/684175<br>
DOI: 10.6084/m9.figshare.11340926
title: Starrydata_raw_20190816.csv

description: A snapshot of experimental data of thermoelectric materials, stored in Starrydata2 web system. This file contains raw data, as traced from the plot images on the publications.
DOI: 10.6084/m9.figshare.11340935
title: Starrydata thermoelectric data snapshot (interpolated data)

description: This is a snapshot of experimental data on the termperature dependences of thermoelectric properties, recorded in Starrydata. This data was interpolated by the intervals of 100 K.
DOI: 10.6084/m9.figshare.11340869
title: Data

description: point cloud
DOI: 10.6084/m9.figshare.11340926.v1
title: Starrydata_raw_20190816.csv

description: A snapshot of experimental data of thermoelectric materials, stored in Starrydata2 web system. This file contains raw data, as traced from the plot images on the publications.
DOI: 10.6084/m9.figshare.11340935.v1
title: Starrydata thermoelectric data snapshot (interpolated data)

description: This is a snapshot of experimental data on the termperature dependences of thermoelectric properties, recorded in Starrydata. This data was interpolated by the intervals of 100 K.
DOI: 10.6084/m9.figshare.11340863
title: Avoided Affect and Processing Suffering

description: Noticing someone’s pain is the first step to a compassionate response. While past research suggests that the degree to which people want to avoid feeling negative (“avoided negative affect”; ANA) shapes how people respond to someone’s suffering, the present research investigates whether ANA also predicts how people process other’s suffering. In two studies, using complex photographs containing negative aspects (i.e., suffering), we found that the higher people’s ANA, the fewer details of negative aspects they correctly recognized, and the fewer negative words they used in their image descriptions. However, when asked to process negative content, the higher people’s ANA, the more negatively they rated that content. In Study 3, we report cultural differences in people’s sensitivity to notice suffering in an ambiguous image. ANA mediated these cultural differences. Implications for research on compassion are discussed.
DOI: 10.6084/m9.figshare.11340863.v1
title: Avoided Affect and Processing Suffering

description: Noticing someone’s pain is the first step to a compassionate response. While past research suggests that the degree to which people want to avoid feeling negative (“avoided negative affect”; ANA) shapes how people respond to someone’s suffering, the present research investigates whether ANA also predicts how people process other’s suffering. In two studies, using complex photographs containing negative aspects (i.e., suffering), we found that the higher people’s ANA, the fewer details of negative aspects they correctly recognized, and the fewer negative words they used in their image descriptions. However, when asked to process negative content, the higher people’s ANA, the more negatively they rated that content. In Study 3, we report cultural differences in people’s sensitivity to notice suffering in an ambiguous image. ANA mediated these cultural differences. Implications for research on compassion are discussed.
DOI: 10.6084/m9.figshare.11340821
title: Suppl data Gehlert RT metabolome.xlsx

description: Metabolomic analysis of human skeletal muscle after acute and prolonged resistance exercise.
DOI: 10.6084/m9.figshare.11340821.v2
title: Suppl data Gehlert RT metabolome.xlsx

description: Metabolomic analysis of human skeletal muscle after acute and prolonged resistance exercise.
DOI: 10.6084/m9.figshare.11340770
title: global SHR datasets.zip

description: This dataset includes 126 global SHR ensembles.six climate datasets, 3 soil moisture datasets, 7 GPP datasets. randomForest package, R-3.5.2
DOI: 10.6084/m9.figshare.11340821.v1
title: Suppl data Gehlert RT metabolome.xlsx

description: Metabolomic analysis of human skeletal muscle after acute and prolonged resistance exercise.
DOI: 10.6084/m9.figshare.11340203
title: RNA-seq transcriptome of Staphylococcus aureus MRSA at mid-exponential phase

description: <i>Staphylococcus aureus</i> is a known commensal of the human skin microbiome, but it is increasingly recognised as a human pathogen. Specifically, the transformation of this commensal bacterium into a pathogenic species remains enigmatic. More importantly, increasing prevalence of a methicillin resistant strain of <i>S. aureus</i> points to a major clinical need to understand the fundamental biology and pathogenesis mechanisms of this important human pathogen. To this end, this contribution hopes to illuminate the RNA-seq transcriptome of <i>S. aureus</i> MRSA BD02-25 (ArrayExpress accession number: E-GEOD-67344) through processing 0.5 million reads via an in-house MATLAB RNA-seq analysis software. The most highly expressed genes were: clumping factor, formate acetyltransferase, alkaline shock protein 23, pyruvate formate-lyase 1 activating enzyme, transcriptional regulator Spx, anaerobic ribonucleoside triphosphate reductase, DNA-binding protein HU, and ATP-dependent Clp protease ATP-binding subunit. Drugs or antibiotics targeting <i>S. aureus</i> MRSA should ideally identify molecules unique to the bacterium’s physiology. These molecules need not be highly expressed proteins or enzymes, but should play a critical role in <i>S. aureus</i> MRSA physiology and metabolism. Hence, deeper analysis of the presented RNA-seq transcriptome of <i>S. aureus</i> MRSA by the scientific community might offer clues to new molecular targets suitable for drug development, or helping gain additional insights of the pathophysiological process of this important human pathogen. <br><br>
DOI: 10.6084/m9.figshare.11340191
title: RNA-seq transcriptome of Staphylococcus aureus at stationary phase in Tryptic Soy Broth

description: A commensal of the human body, Gram-positive <i>Staphylococcus aureus</i> is also an opportunistic pathogen of increasing concern across the world. Able to grow without oxygen, the bacterium is capable of infecting many types of wounds on different parts of the body. But, chief amongst concerns about the bacterium is its increasing ability to resist a variety of antibiotics. Understanding the physiology of <i>S. aureus</i> provides one avenue for the discovery of drugs able to combat this pathogen, and more fundamentally, provides a glimpse into the biology of this bacterium that has a shared evolution history with humans. In particular, understanding how <i>S. aureus</i> has transformed from a commensal into an opportunistic pathogen with the acquisition of new genetic and physiological repertoire is a fascinating question yet to be fully answered. This contribution hopes to provide some fundamental information that could illuminate the questions posted above. Chiefly, the RNA-seq transcriptome of <i>S. aureus</i> at stationary phase (16 hrs) in Tryptic Soy Broth at 37 <sup>o</sup>C (ArrayExpress accession number: E-GEOD-77242) was analysed by an in-house MATLAB algorithm to yield a transcriptional picture that revealed the importance of DNA and chromosomal maintenance to the cell. Specifically, an ensemble of 0.5 million reads indicated that highly expressed genes were: chromosomal replication initiation protein, lipase, delta-hemolysin, quinol oxidase subunit I, clumping factor, accessory gene regulator protein A, accessory gene regulator protein C, DNA polymerase III subunit beta, quinol oxidase AA3 subunit II, and elongation factor Tu. Overall, understanding the stationary phase gene expression pattern of <i>S. aureus</i> could potentially point us to therapeutic strategies to combat this increasing important human pathogen, that, in some cases, have resisted treatment with our front-line antibiotics. <br><br>
DOI: 10.6084/m9.figshare.11340200
title: Data Availability Statement

description: Data of antioxidant activity, sperm lipidperoxidation, sperm motility, plasma membrane, acrosome membrane, mitochondrial membrane, healthy spermData of statistical analysis<br>
DOI: 10.6084/m9.figshare.11340200.v1
title: Data Availability Statement

description: Data of antioxidant activity, sperm lipidperoxidation, sperm motility, plasma membrane, acrosome membrane, mitochondrial membrane, healthy spermData of statistical analysis<br>
DOI: 10.6084/m9.figshare.11340152
title: Trichogramma evanescens, pooled sequencing PoPoolation and PoPoolation2 for 9 lines

description: This data is supplementary to Chapter 6 of PhD thesis titled, "Know Your Enemy: Genomes of Biological Control Agents" by Kim B. Ferguson and is pooled sequencing data generated for 9 lines of <i>Trichogramma evanescens</i>. This parasitoid is found throughout Europe and is used in biological control of Lepidopteran pests on cabbage and corn.<br>This study will likely be published further, but for now, it is part of a thesis that is accessible through the Wageningen University Library after March 25th, 2020. (DOI: 10.18174/511993)Lines are named. More information on the lines are available in the thesis.<br>This entry contains collected data from PoPoolation and PoPoolation2. For details on the commands used, please refer to the thesis. The PoPoolation data is for Tajima's D and Pi. The PoPoolation2 data also contains Fishers Exact Test P values that correlated to the pairwise comparisons.
DOI: 10.6084/m9.figshare.11340128
title: Diversity score toy data

description: Toy data for the diversity score analysis in Tabula Muris Senis
DOI: 10.6084/m9.figshare.11340104
title: Trichogramma evanescens microsatellite information, wild-caught populations, formatted for GenAlEx

description: This data is supplementary to Chapter 6 of PhD thesis titled, "Know Your Enemy: Genomes of Biological Control Agents" by Kim B. Ferguson and is microsatellite data generated for 10 lines of Trichogramma evanescens. This parasitoid is found throughout Europe and is used in biological control of Lepidopteran pests on cabbage and corn. <br>This study will likely be published further, but for now, it is part of a thesis that is accessible through the Wageningen University Library after March 25th, 2020. (DOI: 10.18174/511993)Lines are named, with regions and putative x and y coordinates, which are an estimate. More information on the lines are available in the thesis.<br><br>For now, additional information for the microsatellite loci is below. Microsatellite data for ten microsatellite loci are available on the ENA under accessions LR758000-LR758009.<br>Microsatellites and primers were mined using a random subsample of T. brassicae reads and MsatCommander/Primer3. More details in thesis.
DOI: 10.6084/m9.figshare.11340152.v1
title: Trichogramma evanescens, pooled sequencing PoPoolation and PoPoolation2 for 9 lines

description: This data is supplementary to Chapter 6 of PhD thesis titled, "Know Your Enemy: Genomes of Biological Control Agents" by Kim B. Ferguson and is pooled sequencing data generated for 9 lines of <i>Trichogramma evanescens</i>. This parasitoid is found throughout Europe and is used in biological control of Lepidopteran pests on cabbage and corn.<br>This study will likely be published further, but for now, it is part of a thesis that is accessible through the Wageningen University Library after March 25th, 2020. (DOI: 10.18174/511993)Lines are named. More information on the lines are available in the thesis.<br>This entry contains collected data from PoPoolation and PoPoolation2. For details on the commands used, please refer to the thesis. The PoPoolation data is for Tajima's D and Pi. The PoPoolation2 data also contains Fishers Exact Test P values that correlated to the pairwise comparisons.