cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5981266
title: Additional file 8 of CNVs are associated with genomic architecture in a songbird

description: Syntenic regions in the great tit genome. (CSV 693 kb)
DOI: 10.6084/m9.figshare.5981266.v1
title: Additional file 8 of CNVs are associated with genomic architecture in a songbird

description: Syntenic regions in the great tit genome. (CSV 693 kb)
DOI: 10.6084/m9.figshare.5981260
title: Additional file 7 of CNVs are associated with genomic architecture in a songbird

description: Enrichment analysis of genes in CNV breakpoints (frequency â Ľâ 4). (TXT 3 kb)
DOI: 10.6084/m9.figshare.5981260.v1
title: Additional file 7 of CNVs are associated with genomic architecture in a songbird

description: Enrichment analysis of genes in CNV breakpoints (frequency â Ľâ 4). (TXT 3 kb)
DOI: 10.6084/m9.figshare.5981254
title: Additional file 6 of CNVs are associated with genomic architecture in a songbird

description: Enrichment analysis of genes in CNVRs. (TXT 65 kb)
DOI: 10.6084/m9.figshare.5981254.v1
title: Additional file 6 of CNVs are associated with genomic architecture in a songbird

description: Enrichment analysis of genes in CNVRs. (TXT 65 kb)
DOI: 10.6084/m9.figshare.5981251
title: Additional file 6: of Formation of chimeric genes with essential functions at the origin of eukaryotes

description: Annotation of the 573 S-gene families detected in our study. Columns B, C, and D correspond to the EggNog automatic annotation. Column K corresponds to the manual annotation. Columns H, I, and J correspond to additional annotations for S-gene families present in the well-annotated model organism Saccharomyces cerevisiae (gene symbol, gene essentiality, and protein complexes). Columns L and M show the most abundant common protein architecture according CDD and Pfam (numbers between brackets correspond to the percentage of proteins in the given family having the given protein architecture). Column N corresponds to the cluster assignment found in Fig. 4, while columns O, P, Q, and R correspond to the ratios used to determine these clusters. Column S corresponds to the consistency between BLASTP and phylogeny strategies for taxonomic assignment. Column T corresponds to the domains removed for the ‘conservative’ component origin assignment and columns U, V, W, X, and Y correspond to the cluster and the ratios computed for the conservative assignment. The column Z indicates families for which the detection of components is restricted (restricted) to a portion of the S-gene (i.e., BAC-X/ARC-X/PROK-X). Column Z also indicates the families carrying BAC/ARC/PROK components detected by HMM (HMM-detected-component). Columns AA, AB, AC, AD, and AE correspond to the subcellular localization performed using TargetP. Columns AA, AB, AC, and AD correspond to the ratio of protein members having a mitochondrion transit peptide, chloroplast transit peptide, a signal peptide, and any other location, respectively. Column AE is the general annotation regarding whether the family is targeted or not (if more than 50% of the members of a family were predicted to contain a signal or a transit peptide, the family was considered as targeted). Columns AF and AG correspond to information about intron conservation within and between components, respectively. (XLSX 208 kb)
DOI: 10.6084/m9.figshare.5981251.v1
title: Additional file 6: of Formation of chimeric genes with essential functions at the origin of eukaryotes

description: Annotation of the 573 S-gene families detected in our study. Columns B, C, and D correspond to the EggNog automatic annotation. Column K corresponds to the manual annotation. Columns H, I, and J correspond to additional annotations for S-gene families present in the well-annotated model organism Saccharomyces cerevisiae (gene symbol, gene essentiality, and protein complexes). Columns L and M show the most abundant common protein architecture according CDD and Pfam (numbers between brackets correspond to the percentage of proteins in the given family having the given protein architecture). Column N corresponds to the cluster assignment found in Fig. 4, while columns O, P, Q, and R correspond to the ratios used to determine these clusters. Column S corresponds to the consistency between BLASTP and phylogeny strategies for taxonomic assignment. Column T corresponds to the domains removed for the ‘conservative’ component origin assignment and columns U, V, W, X, and Y correspond to the cluster and the ratios computed for the conservative assignment. The column Z indicates families for which the detection of components is restricted (restricted) to a portion of the S-gene (i.e., BAC-X/ARC-X/PROK-X). Column Z also indicates the families carrying BAC/ARC/PROK components detected by HMM (HMM-detected-component). Columns AA, AB, AC, AD, and AE correspond to the subcellular localization performed using TargetP. Columns AA, AB, AC, and AD correspond to the ratio of protein members having a mitochondrion transit peptide, chloroplast transit peptide, a signal peptide, and any other location, respectively. Column AE is the general annotation regarding whether the family is targeted or not (if more than 50% of the members of a family were predicted to contain a signal or a transit peptide, the family was considered as targeted). Columns AF and AG correspond to information about intron conservation within and between components, respectively. (XLSX 208 kb)
DOI: 10.6084/m9.figshare.5981245
title: Additional file 5: of Formation of chimeric genes with essential functions at the origin of eukaryotes

description: Results of phylogenetic analysis of S-gene families and of components of S-genes. (XLSX 78 kb)
DOI: 10.6084/m9.figshare.5981245.v1
title: Additional file 5: of Formation of chimeric genes with essential functions at the origin of eukaryotes

description: Results of phylogenetic analysis of S-gene families and of components of S-genes. (XLSX 78 kb)
DOI: 10.6084/m9.figshare.5981242
title: Additional file 4 of CNVs are associated with genomic architecture in a songbird

description: Interspersed repeats and low complexity (regions masked by RepeatMasker [45]) and their family classification. (TXT 18544 kb)
DOI: 10.6084/m9.figshare.5981242.v1
title: Additional file 4 of CNVs are associated with genomic architecture in a songbird

description: Interspersed repeats and low complexity (regions masked by RepeatMasker [45]) and their family classification. (TXT 18544 kb)
DOI: 10.6084/m9.figshare.5981236
title: Additional file 3 of CNVs are associated with genomic architecture in a songbird

description: qPCR validation of CNVs. Genomic regions validated, qPCR-PennCNV state correspondence and applied primers. (CSV 192 kb)
DOI: 10.6084/m9.figshare.5981236.v1
title: Additional file 3 of CNVs are associated with genomic architecture in a songbird

description: qPCR validation of CNVs. Genomic regions validated, qPCR-PennCNV state correspondence and applied primers. (CSV 192 kb)
DOI: 10.6084/m9.figshare.5981230
title: Additional file 2 of CNVs are associated with genomic architecture in a songbird

description: CNV breakpoints and their correspondent frequency. (TXT 1102 kb)
DOI: 10.6084/m9.figshare.5981230.v1
title: Additional file 2 of CNVs are associated with genomic architecture in a songbird

description: CNV breakpoints and their correspondent frequency. (TXT 1102 kb)
DOI: 10.6084/m9.figshare.5981224
title: Additional file 1 of CNVs are associated with genomic architecture in a songbird

description: CNV regions (CNVRs) in the great tit (Parus major) genome. (CSV 333 kb)
DOI: 10.6084/m9.figshare.5981224.v1
title: Additional file 1 of CNVs are associated with genomic architecture in a songbird

description: CNV regions (CNVRs) in the great tit (Parus major) genome. (CSV 333 kb)
DOI: 10.6084/m9.figshare.5981221
title: Additional file 21: of Formation of chimeric genes with essential functions at the origin of eukaryotes

description: Supporting data for this study, consisting of fasta sequences of S-genes, intron position alignments, components information, and phylogenetic trees. (ZIP 11370 kb)
DOI: 10.6084/m9.figshare.5981218
title: Additional file 10 of CNVs are associated with genomic architecture in a songbird

description: (i) Genes overlapping CNV breakpoints (frequency â Ľâ 4), homologous regions and SNPs under selection concomitantly; (ii) Genes overlapping evolutionary breakpoints at CNV regions in chicken and (iii) genes overlapping evolutionary breakpoints at CNV regions in zebra finch. (CVS 696 kb)
DOI: 10.6084/m9.figshare.5981221.v1
title: Additional file 21: of Formation of chimeric genes with essential functions at the origin of eukaryotes

description: Supporting data for this study, consisting of fasta sequences of S-genes, intron position alignments, components information, and phylogenetic trees. (ZIP 11370 kb)
DOI: 10.6084/m9.figshare.5981218.v1
title: Additional file 10 of CNVs are associated with genomic architecture in a songbird

description: (i) Genes overlapping CNV breakpoints (frequency â Ľâ 4), homologous regions and SNPs under selection concomitantly; (ii) Genes overlapping evolutionary breakpoints at CNV regions in chicken and (iii) genes overlapping evolutionary breakpoints at CNV regions in zebra finch. (CVS 696 kb)
DOI: 10.6084/m9.figshare.5981215
title: Additional file 20: of Formation of chimeric genes with essential functions at the origin of eukaryotes

description: List of 38 eukaryote genomes and the 382 prokaryotic genomes used in our comparative analysis. (XLSX 277 kb)
DOI: 10.6084/m9.figshare.5981215.v1
title: Additional file 20: of Formation of chimeric genes with essential functions at the origin of eukaryotes

description: List of 38 eukaryote genomes and the 382 prokaryotic genomes used in our comparative analysis. (XLSX 277 kb)
DOI: 10.6084/m9.figshare.5981131
title: Additional file 12: of Formation of chimeric genes with essential functions at the origin of eukaryotes

description: Detailed origin of prokaryotic S-gene components. Fam: S-gene family, Cpt: component, Cluster: cluster number according to Fig. 4, Bacteria: number of hits from Bacteria, Archaea: number of hits from Archaea. For each S-gene component, the rank in the BLAST search and the taxonomic assignation of the 25 sequences with the best hits to that component were reported (Aci: Acidobacteria, Act: Actinobacteria, Aqu: Aquificae, Arm: Armatimonadetes, Bac: Bacteroidetes, Chl: Chloroflexi, Cre: Crenarchaeota, Cya: Cyanobacteria, Def: Deferribacteres, Dei: Deinococcus-Thermus, Eur: Euryarchaeota, Fir: Firmicutes, Fus: Fusobacteria, Gem: Gemmatimonadetes, Ign: Ignavibacteriae, Nit: Nitrospirae, Pla: Planctomycetes, Pro: Proteobacteria, Spi: Spirochaetes, Syn: Synergistetes, Ten: Tenericutes, Tha: Thaumarchaeota, The: Thermotogae, Ver: Verrucomicrobia, roo: Unknown). Red cells correspond to bacterial phyla while blue cells correspond to archaeal phyla. When only one S-gene component is described, the unrepresented S-gene components from the S-gene family are either exclusively found in photosynthetic eukaryotes, or have diverged too much to be confidently assigned to a prokaryotic group. (XLSX 1743 kb)
DOI: 10.6084/m9.figshare.5981131.v1
title: Additional file 12: of Formation of chimeric genes with essential functions at the origin of eukaryotes

description: Detailed origin of prokaryotic S-gene components. Fam: S-gene family, Cpt: component, Cluster: cluster number according to Fig. 4, Bacteria: number of hits from Bacteria, Archaea: number of hits from Archaea. For each S-gene component, the rank in the BLAST search and the taxonomic assignation of the 25 sequences with the best hits to that component were reported (Aci: Acidobacteria, Act: Actinobacteria, Aqu: Aquificae, Arm: Armatimonadetes, Bac: Bacteroidetes, Chl: Chloroflexi, Cre: Crenarchaeota, Cya: Cyanobacteria, Def: Deferribacteres, Dei: Deinococcus-Thermus, Eur: Euryarchaeota, Fir: Firmicutes, Fus: Fusobacteria, Gem: Gemmatimonadetes, Ign: Ignavibacteriae, Nit: Nitrospirae, Pla: Planctomycetes, Pro: Proteobacteria, Spi: Spirochaetes, Syn: Synergistetes, Ten: Tenericutes, Tha: Thaumarchaeota, The: Thermotogae, Ver: Verrucomicrobia, roo: Unknown). Red cells correspond to bacterial phyla while blue cells correspond to archaeal phyla. When only one S-gene component is described, the unrepresented S-gene components from the S-gene family are either exclusively found in photosynthetic eukaryotes, or have diverged too much to be confidently assigned to a prokaryotic group. (XLSX 1743 kb)
DOI: 10.6084/m9.figshare.5981104
title: MOESM2 of The Penicillium chrysogenum transporter PcAraT enables high-affinity, glucose-insensitive l-arabinose transport in Saccharomyces cerevisiae

description: Additional file 2. Differentially expressed genes in P. chrysogenum chemostat cultures over three different conditions (d-glucose-, l-arabinose, and ethanol-limited). The table includes 540 genes that were differentially expressed amongst d-glucose-, l-arabinose, and ethanol-limited chemostat cultures of P. chrysogenum (7.5 g L−1, 7.5 g L−1, 5.8 g L−1, respectively, D = 0.03 h−1, T = 30 °C). 137 transcripts exhibited a fold-change higher than three on l-arabinose and lower than three on ethanol relative to the d-glucose condition (the top 137 genes presented in the table). Shown are averages from triplicate (d-glucose) or duplicate chemostat cultures (l-arabinose, ethanol), the respective standard deviation and the ratio of gene expression levels in the presence of l-arabinose over d-glucose (Ara vs. Glc), as well as ethanol over d-glucose (EtOH vs. Glc).
DOI: 10.6084/m9.figshare.5981104.v1
title: MOESM2 of The Penicillium chrysogenum transporter PcAraT enables high-affinity, glucose-insensitive l-arabinose transport in Saccharomyces cerevisiae

description: Additional file 2. Differentially expressed genes in P. chrysogenum chemostat cultures over three different conditions (d-glucose-, l-arabinose, and ethanol-limited). The table includes 540 genes that were differentially expressed amongst d-glucose-, l-arabinose, and ethanol-limited chemostat cultures of P. chrysogenum (7.5 g L−1, 7.5 g L−1, 5.8 g L−1, respectively, D = 0.03 h−1, T = 30 °C). 137 transcripts exhibited a fold-change higher than three on l-arabinose and lower than three on ethanol relative to the d-glucose condition (the top 137 genes presented in the table). Shown are averages from triplicate (d-glucose) or duplicate chemostat cultures (l-arabinose, ethanol), the respective standard deviation and the ratio of gene expression levels in the presence of l-arabinose over d-glucose (Ara vs. Glc), as well as ethanol over d-glucose (EtOH vs. Glc).
DOI: 10.6084/m9.figshare.5980882
title: MOESM5 of Efficacy and safety of artemisinin-based combination therapy for uncomplicated Plasmodium falciparum malaria in Sudan: a systematic review and meta-analysis

description: Additional file 5. Adverse drug reactions of anti-malarial treatment.
DOI: 10.6084/m9.figshare.5980882.v1
title: MOESM5 of Efficacy and safety of artemisinin-based combination therapy for uncomplicated Plasmodium falciparum malaria in Sudan: a systematic review and meta-analysis

description: Additional file 5. Adverse drug reactions of anti-malarial treatment.
DOI: 10.6084/m9.figshare.5980873
title: MOESM4 of Efficacy and safety of artemisinin-based combination therapy for uncomplicated Plasmodium falciparum malaria in Sudan: a systematic review and meta-analysis

description: Additional file 4. Comparisons of success rate based on different treatment regimens.
DOI: 10.6084/m9.figshare.5980873.v1
title: MOESM4 of Efficacy and safety of artemisinin-based combination therapy for uncomplicated Plasmodium falciparum malaria in Sudan: a systematic review and meta-analysis

description: Additional file 4. Comparisons of success rate based on different treatment regimens.
DOI: 10.6084/m9.figshare.5980855
title: MOESM3 of Efficacy and safety of artemisinin-based combination therapy for uncomplicated Plasmodium falciparum malaria in Sudan: a systematic review and meta-analysis

description: Additional file 3. Characteristics of the included studies with 100% success rates.
DOI: 10.6084/m9.figshare.5980855.v1
title: MOESM3 of Efficacy and safety of artemisinin-based combination therapy for uncomplicated Plasmodium falciparum malaria in Sudan: a systematic review and meta-analysis

description: Additional file 3. Characteristics of the included studies with 100% success rates.
DOI: 10.6084/m9.figshare.5980840
title: Additional file 1: of Validation of the adapted Leeds sleep evaluation questionnaire in Ethiopian university students

description: (SAV 30Â kb)
DOI: 10.6084/m9.figshare.5980840.v1
title: Additional file 1: of Validation of the adapted Leeds sleep evaluation questionnaire in Ethiopian university students

description: (SAV 30Â kb)
DOI: 10.6084/m9.figshare.5980828
title: MOESM2 of Efficacy and safety of artemisinin-based combination therapy for uncomplicated Plasmodium falciparum malaria in Sudan: a systematic review and meta-analysis

description: Additional file 2. Assessment of publication bias.
DOI: 10.6084/m9.figshare.5980828.v1
title: MOESM2 of Efficacy and safety of artemisinin-based combination therapy for uncomplicated Plasmodium falciparum malaria in Sudan: a systematic review and meta-analysis

description: Additional file 2. Assessment of publication bias.
DOI: 10.6084/m9.figshare.5980813
title: MOESM1 of Efficacy and safety of artemisinin-based combination therapy for uncomplicated Plasmodium falciparum malaria in Sudan: a systematic review and meta-analysis

description: Additional file 1. Characteristics of all studies of this systematic review and meta-analysis (included, excluded and unpublished studies).
DOI: 10.6084/m9.figshare.5980813.v1
title: MOESM1 of Efficacy and safety of artemisinin-based combination therapy for uncomplicated Plasmodium falciparum malaria in Sudan: a systematic review and meta-analysis

description: Additional file 1. Characteristics of all studies of this systematic review and meta-analysis (included, excluded and unpublished studies).
DOI: 10.6084/m9.figshare.5980786
title: Dataset for: Spatial Regression with an Informatively-Missing Covariate

description: The US EPA has established a large network of stations to monitor fine particulate matter (PM2.5) that is known to be harmful to human health. Unfortunately, the network has limited spatial coverage and stations often only measure \PM every few days. Satellite-measured aerosol optical depth (AOD) is a low-cost surrogate with greater spatiotemporal coverage, and spatial regression models have established that including AOD as a covariate improves spatial interpolation of PM2.5. However, AOD is often missing, and our analysis reveals that the conditions that lead to missing AOD are also conducive to high AOD. Therefore, naive interpolation that ignores informative missingness may lead to bias. We propose a joint hierarchical model for PM and AOD that accounts for informatively missing AOD. We conduct a simulation study of the effects of ignoring informative missingness in the covariate, and evaluate the performance of the proposed model. We apply the method to map daily PM in the Southeastern United States. Our analysis reveals statistically-significant informative missingness and relationships between PM and AOD in many seasons after accounting for meteorological and land-use variables.
DOI: 10.6084/m9.figshare.5980786.v1
title: Dataset for: Spatial Regression with an Informatively-Missing Covariate

description: The US EPA has established a large network of stations to monitor fine particulate matter (PM2.5) that is known to be harmful to human health. Unfortunately, the network has limited spatial coverage and stations often only measure \PM every few days. Satellite-measured aerosol optical depth (AOD) is a low-cost surrogate with greater spatiotemporal coverage, and spatial regression models have established that including AOD as a covariate improves spatial interpolation of PM2.5. However, AOD is often missing, and our analysis reveals that the conditions that lead to missing AOD are also conducive to high AOD. Therefore, naive interpolation that ignores informative missingness may lead to bias. We propose a joint hierarchical model for PM and AOD that accounts for informatively missing AOD. We conduct a simulation study of the effects of ignoring informative missingness in the covariate, and evaluate the performance of the proposed model. We apply the method to map daily PM in the Southeastern United States. Our analysis reveals statistically-significant informative missingness and relationships between PM and AOD in many seasons after accounting for meteorological and land-use variables.
DOI: 10.6084/m9.figshare.5980555
title: Figure 3&S5

description: ddPCR dataset<br>
DOI: 10.6084/m9.figshare.5980555.v1
title: Figure 3&S5

description: ddPCR dataset<br>
DOI: 10.6084/m9.figshare.5980552
title: Figure S4

description: ddPCR dataset<br>
DOI: 10.6084/m9.figshare.5980552.v1
title: Figure S4

description: ddPCR dataset<br>
DOI: 10.6084/m9.figshare.5980528
title: Figure 5C

description: ddPCR dataset<br>
DOI: 10.6084/m9.figshare.5980528.v1
title: Figure 5C

description: ddPCR dataset<br>
DOI: 10.6084/m9.figshare.5980489
title: Figure 4

description: ddPCR dataset<br>
DOI: 10.6084/m9.figshare.5980489.v1
title: Figure 4

description: ddPCR dataset<br>
DOI: 10.6084/m9.figshare.5980480.v3
title: Drosophila Ubiquitin C-Terminal Hydrolase Knockdown Model of Parkinson’s Disease

description: Parkinson’s disease (PD) is the second most common neurodegenerative disorder worldwide. Many factors have been shown to contribute to its pathogenesis including genetic and environmental factors. Ubiquitin C-terminal hydrolase L1 (UCHL1) is also known to be involved in the pathogenesis of PD. We herein modeled the study of UCHL1 in Drosophila melanogaster and investigated its functions in PD. The specific knockdown of the Drosophila ortholog of UCHL1 (dUCH) in dopaminergic neurons (DA neurons) led to the underdevelopment and/or degeneration of these neurons, specifically in DL1 DA neuron cluster in the larval brain lobe and PPM2, PPM3, PPL2ab, and VUM DA neuron clusters in the adult brain. These defects were followed by a shortage of dopamine in the brain, which subsequently resulted in locomotor dysfunction. The degeneration of DA neurons in dUCH knockdown adult brain, which occurred progressively and severely during the course of aging, mimics the epidemiology of PD. DA neuron and locomotor defects were rescued when dUCH knockdown flies were treated with vitamin C, a well-known antioxidant. These results suggest that dUCH knockdown fly is a promising model for studying the pathogenesis and epidemiology of PD as well as the screening of potential antioxidants for PD therapeutics.<br>
DOI: 10.6084/m9.figshare.5980480.v4
title: Drosophila Ubiquitin C-Terminal Hydrolase Knockdown Model of Parkinson’s Disease

description: Parkinson’s disease (PD) is the second most common neurodegenerative disorder worldwide. Many factors have been shown to contribute to its pathogenesis including genetic and environmental factors. Ubiquitin C-terminal hydrolase L1 (UCHL1) is also known to be involved in the pathogenesis of PD. We herein modeled the study of UCHL1 in Drosophila melanogaster and investigated its functions in PD. The specific knockdown of the Drosophila ortholog of UCHL1 (dUCH) in dopaminergic neurons (DA neurons) led to the underdevelopment and/or degeneration of these neurons, specifically in DL1 DA neuron cluster in the larval brain lobe and PPM2, PPM3, PPL2ab, and VUM DA neuron clusters in the adult brain. These defects were followed by a shortage of dopamine in the brain, which subsequently resulted in locomotor dysfunction. The degeneration of DA neurons in dUCH knockdown adult brain, which occurred progressively and severely during the course of aging, mimics the epidemiology of PD. DA neuron and locomotor defects were rescued when dUCH knockdown flies were treated with vitamin C, a well-known antioxidant. These results suggest that dUCH knockdown fly is a promising model for studying the pathogenesis and epidemiology of PD as well as the screening of potential antioxidants for PD therapeutics.<br>