cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9083348
title: Extended data on the study titled 'Acute and sub-acute toxicity study of the root extracts of Fagaropsis hildebrandtii in mice and evaluation of their antimicrobial effects'

description: The extended data contains the following sections;<br>1. The ethical approval document from the biosafety animal use and ethics committee of the University of Nairobi<br>2. A summary of the animals used in the experiment<br>3. Data on the mean body weight of mice in the acute toxicity protocol<br>4. Data on the feed and water consumption of mice in the acute toxicity protocol (both aqueous and hexane extracts)<br>5. Data on the relative mean organ weight of mice in the acute toxicity protocol<br>6. Data on the mean body weight of mice in the sub-acute toxicity protocol (Aqueous extract)<br>7. Data on the feed and water consumption of mice in the sub-acute toxicity protocol (both aqueous and hexane extracts)<br>8. Data on the mean body weight of mice treated with the aqueous extract of F. hildebrandtii in mice in the sub-acute toxicity protocol<br><br>9. Data on the mean body weight of mice treated with the hexane extract of F. hildebrandtii in the sub-acute toxicity protocol<br>10. Data on the relative mean organ weight of mice treated with the aqueous extract of F. hildebrandtii in the sub-acute toxicity protocol<br>11. Data on the relative mean organ weight of mice treated with the hexane extracr of F. hildebrandtii in the sub-acute toxicity protocol<br>
DOI: 10.6084/m9.figshare.9083936.v1
title: TestData.tar

description: This test data archive contains OMICS datasets (DNAseq, RNAseq, microarrays) for the manual testing of the TIMS (Translational Informatics Management System) software.<br>
DOI: 10.6084/m9.figshare.9076868
title: Silica catalyzed one pot synthesis of hybrid thiazolidin-4-one derivatives as anti-tubercular and anti-inflammatory agent by attenuating COX-2 pathway

description: A novel series of a hybrid class of hybrid thiazolidin-4-one derivatives were designed and synthesized through one-pot catalytic synthesis. The reaction was catalyzed in the presence of silica-H<sub>2</sub>SO4<sup>(+6)</sup>. The derivatives computational ADMET profile was calculated. The study shows that most active derivatives have optimal logP, higher anti-inflammatory activity score, and poor metabolism at the sight of P450-3A4 and 2D6. The entire series of derivatives were further evaluated for anti-tubercular (against <i>Mycobacterium tuberculosis</i> H37Rv (Resistant strain)) and anti-inflammatory activity (in-vivo assay using Wistar rat). The result showed that derivatives <b>4c</b>, <b>4h</b>, and <b>4m</b> have significant potency against tested <i>M. tuberculosis</i>. However, derivatives <b>4i</b> and <b>4j</b> found significantly active against inflammation. <i>In vitro</i> COX inhibition assay also supported the result in favor of selectivity and efficacy of derivatives.
DOI: 10.6084/m9.figshare.9076868.v1
title: Silica catalyzed one pot synthesis of hybrid thiazolidin-4-one derivatives as anti-tubercular and anti-inflammatory agent by attenuating COX-2 pathway

description: A novel series of a hybrid class of hybrid thiazolidin-4-one derivatives were designed and synthesized through one-pot catalytic synthesis. The reaction was catalyzed in the presence of silica-H<sub>2</sub>SO4<sup>(+6)</sup>. The derivatives computational ADMET profile was calculated. The study shows that most active derivatives have optimal logP, higher anti-inflammatory activity score, and poor metabolism at the sight of P450-3A4 and 2D6. The entire series of derivatives were further evaluated for anti-tubercular (against <i>Mycobacterium tuberculosis</i> H37Rv (Resistant strain)) and anti-inflammatory activity (in-vivo assay using Wistar rat). The result showed that derivatives <b>4c</b>, <b>4h</b>, and <b>4m</b> have significant potency against tested <i>M. tuberculosis</i>. However, derivatives <b>4i</b> and <b>4j</b> found significantly active against inflammation. <i>In vitro</i> COX inhibition assay also supported the result in favor of selectivity and efficacy of derivatives.
DOI: 10.6084/m9.figshare.9070598
title: Pertussis in Latin America and the Hispanic Caribbean: a systematic review

description: <b>Introduction:</b> Pertussis in Latin America continues to cause periodic epidemics with substantial morbidity particularly among young children. The disease has persisted despite long-standing vaccination programs in the region. <b>Areas covered:</b> We conducted a systematic review to characterize the recent epidemiology of pertussis in Latin America and Hispanic Caribbean. We undertook a holistic approach and attempted to include all available data concerning pertussis that may explain the changing dynamics of the disease. <b>Expert opinion:</b> There are wide disparities in the reported annual incidence rates of pertussis both within and between countries in the region. General trends in pertussis incidence are difficult to ascertain due to the heterogeneity in the epidemiological data. Available data suggests that the disease burden has changed over the years such that now it predominantly affects those &lt;1 year. Coverage with three doses of the pertussis vaccine has been highly variable, and very few countries have consistently achieved ≥90% coverage annually since 2000. There remain inequalities in vaccination coverage in some regions/localities and specific groups, which sustains the risk of pertussis dissemination. The WHO considers that maternal pertussis immunization provides protection to infants too young to be vaccinated; &gt;10 Latin American countries currently recommend vaccination of pregnant women.
DOI: 10.6084/m9.figshare.9070598.v1
title: Pertussis in Latin America and the Hispanic Caribbean: a systematic review

description: <b>Introduction:</b> Pertussis in Latin America continues to cause periodic epidemics with substantial morbidity particularly among young children. The disease has persisted despite long-standing vaccination programs in the region. <b>Areas covered:</b> We conducted a systematic review to characterize the recent epidemiology of pertussis in Latin America and Hispanic Caribbean. We undertook a holistic approach and attempted to include all available data concerning pertussis that may explain the changing dynamics of the disease. <b>Expert opinion:</b> There are wide disparities in the reported annual incidence rates of pertussis both within and between countries in the region. General trends in pertussis incidence are difficult to ascertain due to the heterogeneity in the epidemiological data. Available data suggests that the disease burden has changed over the years such that now it predominantly affects those &lt;1 year. Coverage with three doses of the pertussis vaccine has been highly variable, and very few countries have consistently achieved ≥90% coverage annually since 2000. There remain inequalities in vaccination coverage in some regions/localities and specific groups, which sustains the risk of pertussis dissemination. The WHO considers that maternal pertussis immunization provides protection to infants too young to be vaccinated; &gt;10 Latin American countries currently recommend vaccination of pregnant women.
DOI: 10.6084/m9.figshare.9047915
title: Russian river precipitation data

description: Data to generate precipitation values in manuscript
DOI: 10.6084/m9.figshare.9048359
title: Sonoma county weather data

description: Weather data for Sonoma county
DOI: 10.6084/m9.figshare.9043862
title: Additional file 4: of Quantitative assessment of LASSO probe assembly and long-read multiplexed cloning

description: Table S3. Single Target Capture ImageJ Pixel Density Plot. Single target LASSO captures were visualized on PAGE gels and imaged. Major and minor bands were highlighted using ImageJ to obtain pixel density plots. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.9043853
title: Additional file 2 of A plea for taking all available clinical information into account when assessing the predictive value of omics data

description: This.zip file contains all the codes necessary to reproduce the analysis presented in this study. (ZIP 21 kb)
DOI: 10.6084/m9.figshare.9043862.v1
title: Additional file 4: of Quantitative assessment of LASSO probe assembly and long-read multiplexed cloning

description: Table S3. Single Target Capture ImageJ Pixel Density Plot. Single target LASSO captures were visualized on PAGE gels and imaged. Major and minor bands were highlighted using ImageJ to obtain pixel density plots. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.9047915.v1
title: Russian river precipitation data

description: Data to generate precipitation values in manuscript
DOI: 10.6084/m9.figshare.9043853.v1
title: Additional file 2 of A plea for taking all available clinical information into account when assessing the predictive value of omics data

description: This.zip file contains all the codes necessary to reproduce the analysis presented in this study. (ZIP 21 kb)
DOI: 10.6084/m9.figshare.9043850
title: Additional file 3: of Quantitative assessment of LASSO probe assembly and long-read multiplexed cloning

description: Table S2. NGS Read Accounting of Sequenced LASSO E. coli ORF-eome Captures. The table shows raw sequencing output (HiSeq 1 × 50 bp platform) of PCR amplified multiplexed ORF-eome capture. Reads were first aligned to both E. coli genome and LASSO probe backbone sequence, then read mapped exclusively to genomic DNA was cleaned, filtered, and separated according to targets or non-targets (untargeted ORFs and intergenic regions). Also included are the median read depths of gDNA sequencing enrichment. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9043841
title: Additional file 2: of Quantitative assessment of LASSO probe assembly and long-read multiplexed cloning

description: Table S1. NGS Read Accounting of Sequenced Assembled LASSO Probes The table shows raw sequencing output (MiSeq 2 × 75 bp platform) of inversion PCR products before and after read pairing, sequencing duplicate removal, and alignment using our NGS pipeline. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.9043841.v1
title: Additional file 2: of Quantitative assessment of LASSO probe assembly and long-read multiplexed cloning

description: Table S1. NGS Read Accounting of Sequenced Assembled LASSO Probes The table shows raw sequencing output (MiSeq 2 × 75 bp platform) of inversion PCR products before and after read pairing, sequencing duplicate removal, and alignment using our NGS pipeline. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.9043850.v1
title: Additional file 3: of Quantitative assessment of LASSO probe assembly and long-read multiplexed cloning

description: Table S2. NGS Read Accounting of Sequenced LASSO E. coli ORF-eome Captures. The table shows raw sequencing output (HiSeq 1 × 50 bp platform) of PCR amplified multiplexed ORF-eome capture. Reads were first aligned to both E. coli genome and LASSO probe backbone sequence, then read mapped exclusively to genomic DNA was cleaned, filtered, and separated according to targets or non-targets (untargeted ORFs and intergenic regions). Also included are the median read depths of gDNA sequencing enrichment. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9043715
title: Additional file 2: of First-in-human phase 1 study of IT1208, a defucosylated humanized anti-CD4 depleting antibody, in patients with advanced solid tumors

description: Appendix Materials and Methods. (ZIP 358 kb)
DOI: 10.6084/m9.figshare.9043715.v1
title: Additional file 2: of First-in-human phase 1 study of IT1208, a defucosylated humanized anti-CD4 depleting antibody, in patients with advanced solid tumors

description: Appendix Materials and Methods. (ZIP 358 kb)
DOI: 10.6084/m9.figshare.9043691
title: Additional file 2: of Glucocorticoid receptor modulation decreases ER-positive breast cancer cell proliferation and suppresses wild-type and mutant ER chromatin association

description: Supplemental data. MCF-7 cells were treated with Vehicle (Veh, ETOH), 10 nM estradiol (E2), 100 nM Dexamethasone (Dex), or Dex/E2 for 4 h, RNA was isolated and examined by microarray. Microarray fold-changes were calculated relative to Veh and a 1.3 fold-change cut-off was used. (XLSX 255 kb)
DOI: 10.6084/m9.figshare.9043691.v1
title: Additional file 2: of Glucocorticoid receptor modulation decreases ER-positive breast cancer cell proliferation and suppresses wild-type and mutant ER chromatin association

description: Supplemental data. MCF-7 cells were treated with Vehicle (Veh, ETOH), 10 nM estradiol (E2), 100 nM Dexamethasone (Dex), or Dex/E2 for 4 h, RNA was isolated and examined by microarray. Microarray fold-changes were calculated relative to Veh and a 1.3 fold-change cut-off was used. (XLSX 255 kb)
DOI: 10.6084/m9.figshare.9043574
title: Additional file 4 of Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae)

description: : Metrics associated with the 1856 SCOTags. Excel file containing all metrics that served to assess the phylogenetic utility of the 1856 SCOTags. Metrics such as sequence variability, phylogenetic informativeness, node-by-node topological conflict and structural annotation are detailed for each of the 1856 SCOTags. (XLSX 722 kb)
DOI: 10.6084/m9.figshare.9043562
title: Additional file 3 of Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae)

description: : Sequences of the 1856 SCOTags across seven Rosaceae outgroups and 12 Rosa species. Raw fasta sequences associated with the 1856 SCOTags per species. These sequences correspond to either target-assembled SCOTags from whole genome shotgun Illumina paired-end reads or SCOTags that were found in already assembled datasets. (TXT 11170 kb)
DOI: 10.6084/m9.figshare.9043574.v1
title: Additional file 4 of Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae)

description: : Metrics associated with the 1856 SCOTags. Excel file containing all metrics that served to assess the phylogenetic utility of the 1856 SCOTags. Metrics such as sequence variability, phylogenetic informativeness, node-by-node topological conflict and structural annotation are detailed for each of the 1856 SCOTags. (XLSX 722 kb)
DOI: 10.6084/m9.figshare.9043550
title: Additional file 2 of Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae)

description: : List of the 1856 SCOTags primer pairs for Rosa phylogenomics. Excel file listing sequences of primer pairs associated with the 1856 SCOTags, as well as information about melting temperature and corresponding SCOTag amplicons in the haploid reference genome of Rosa ‘Old Blush’ (genome coordinates and fragment length). (XLSX 178 kb)
DOI: 10.6084/m9.figshare.9043562.v1
title: Additional file 3 of Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae)

description: : Sequences of the 1856 SCOTags across seven Rosaceae outgroups and 12 Rosa species. Raw fasta sequences associated with the 1856 SCOTags per species. These sequences correspond to either target-assembled SCOTags from whole genome shotgun Illumina paired-end reads or SCOTags that were found in already assembled datasets. (TXT 11170 kb)
DOI: 10.6084/m9.figshare.9043550.v1
title: Additional file 2 of Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae)

description: : List of the 1856 SCOTags primer pairs for Rosa phylogenomics. Excel file listing sequences of primer pairs associated with the 1856 SCOTags, as well as information about melting temperature and corresponding SCOTag amplicons in the haploid reference genome of Rosa ‘Old Blush’ (genome coordinates and fragment length). (XLSX 178 kb)
DOI: 10.6084/m9.figshare.9043508
title: Additional file 2: of Divergence in larval jaw gene expression reflects differential trophic adaptation in haplochromine cichlids prior to foraging

description: Statistical results and raw gene expression data. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.9043487
title: Additional file 3: of Comparative transcriptomics suggest unique molecular adaptations within tardigrade lineages

description: Rc_seqannot.zip containing sequencing (fasta) files of the analyzed genes from Richtersius cf. coronifer. (7Z 177 kb)
DOI: 10.6084/m9.figshare.9043505
title: Additional file 1: of Divergence in larval jaw gene expression reflects differential trophic adaptation in haplochromine cichlids prior to foraging

description: Information about qPCR primers used in this study. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.9043508.v1
title: Additional file 2: of Divergence in larval jaw gene expression reflects differential trophic adaptation in haplochromine cichlids prior to foraging

description: Statistical results and raw gene expression data. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.9043481
title: Additional file 2: of Comparative transcriptomics suggest unique molecular adaptations within tardigrade lineages

description: Es_seqannot.zip containing sequencing (fasta) files of the analyzed genes from Echiniscoides cf. sigismundi. (7Z 133 kb)
DOI: 10.6084/m9.figshare.9043487.v1
title: Additional file 3: of Comparative transcriptomics suggest unique molecular adaptations within tardigrade lineages

description: Rc_seqannot.zip containing sequencing (fasta) files of the analyzed genes from Richtersius cf. coronifer. (7Z 177 kb)
DOI: 10.6084/m9.figshare.9043505.v1
title: Additional file 1: of Divergence in larval jaw gene expression reflects differential trophic adaptation in haplochromine cichlids prior to foraging

description: Information about qPCR primers used in this study. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.9043475
title: Additional file 1: of Comparative transcriptomics suggest unique molecular adaptations within tardigrade lineages

description: Comparative analysis of stress related genes among 10 species. Es = Echiniscoides cf. sigismundi, Rc = Richtersius cf. coronifer, Rv = Ramazzottius cf. varieornatus, He = Hypsibius exemplaris, Ce = Caenorhabditis elegans, Dm = Drosophila melanogaster, Xt = Xenopus tropicalis, Dr. = Danio rerio, Hs = Homo sapiens and Sc = Saccharomyces cerevisiae. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.9043481.v1
title: Additional file 2: of Comparative transcriptomics suggest unique molecular adaptations within tardigrade lineages

description: Es_seqannot.zip containing sequencing (fasta) files of the analyzed genes from Echiniscoides cf. sigismundi. (7Z 133 kb)
DOI: 10.6084/m9.figshare.9043475.v1
title: Additional file 1: of Comparative transcriptomics suggest unique molecular adaptations within tardigrade lineages

description: Comparative analysis of stress related genes among 10 species. Es = Echiniscoides cf. sigismundi, Rc = Richtersius cf. coronifer, Rv = Ramazzottius cf. varieornatus, He = Hypsibius exemplaris, Ce = Caenorhabditis elegans, Dm = Drosophila melanogaster, Xt = Xenopus tropicalis, Dr. = Danio rerio, Hs = Homo sapiens and Sc = Saccharomyces cerevisiae. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.9043340
title: Additional file 1: of Experimental study on the effects of isoflurane with and without remifentanil or dexmedetomidine on heart rate variability before and after nociceptive stimulation at different MAC multiples in cats

description: Table S1. HRV parameter values before and after nociceptive stimulation. Values of selected HRV parameters and their differencesdetermined at 1-minute intervals before and after nociceptive stimulation in 7 European domestic short-haircats (6 in group ID) during anaesthesia with isoflurane alone (I), with isoflurane and remifentanil (IR, 18 Îźg/kg/h IV) or with dexmedetomidine (ID, 3 Îźg/kg/h IV) at different MAC-defined anaesthetic depths. Data are reported as the median (minimum; maximum). (XLSM 14 kb)
DOI: 10.6084/m9.figshare.9043340.v1
title: Additional file 1: of Experimental study on the effects of isoflurane with and without remifentanil or dexmedetomidine on heart rate variability before and after nociceptive stimulation at different MAC multiples in cats

description: Table S1. HRV parameter values before and after nociceptive stimulation. Values of selected HRV parameters and their differencesdetermined at 1-minute intervals before and after nociceptive stimulation in 7 European domestic short-haircats (6 in group ID) during anaesthesia with isoflurane alone (I), with isoflurane and remifentanil (IR, 18 Îźg/kg/h IV) or with dexmedetomidine (ID, 3 Îźg/kg/h IV) at different MAC-defined anaesthetic depths. Data are reported as the median (minimum; maximum). (XLSM 14 kb)
DOI: 10.6084/m9.figshare.9043037
title: Additional file 3: of Identification of intermediate-sized deletions and inference of their impact on gene expression in a human population

description: Table S1. List of eQTL causal intermediate-sized deletions chosen for PCR validation, and the results of the PCR validation using 30 1000 Genomes JPT samples. Table S2. Annotation of regulatory features and predicted chromatin states for identified intermediate-sized deletions. Table S3. List of highconfidence intermediate-sized deletions after detection and filtering. Table S4. Results of enrichment analysis for annotated overall regulatory features. Table S5. Results of enrichment analysis for annotated GM12878 cell line-specific regulatory features. Table S6. Results of enrichment analysis of annotated regulatory features comparing causal intermediate-sized deletions that increased gene expression levels against those with decreased gene expression levels. Table S7. Results of enrichment analysis for deletion candidates overlapping Alu transposons. Table S8. Results of enrichment analysis for phylogenetic status of causal and non-causal deletions, as well as for deletions the overlap Alu transposons. (XLSX 5262 kb)
DOI: 10.6084/m9.figshare.9043037.v1
title: Additional file 3: of Identification of intermediate-sized deletions and inference of their impact on gene expression in a human population

description: Table S1. List of eQTL causal intermediate-sized deletions chosen for PCR validation, and the results of the PCR validation using 30 1000 Genomes JPT samples. Table S2. Annotation of regulatory features and predicted chromatin states for identified intermediate-sized deletions. Table S3. List of highconfidence intermediate-sized deletions after detection and filtering. Table S4. Results of enrichment analysis for annotated overall regulatory features. Table S5. Results of enrichment analysis for annotated GM12878 cell line-specific regulatory features. Table S6. Results of enrichment analysis of annotated regulatory features comparing causal intermediate-sized deletions that increased gene expression levels against those with decreased gene expression levels. Table S7. Results of enrichment analysis for deletion candidates overlapping Alu transposons. Table S8. Results of enrichment analysis for phylogenetic status of causal and non-causal deletions, as well as for deletions the overlap Alu transposons. (XLSX 5262 kb)
DOI: 10.6084/m9.figshare.9042938
title: MOESM6 of Comparison of ultraconserved elements (UCEs) to microsatellite markers for the study of avian hybrid zones: a test in Aphelocoma jays

description: Additional file 6. VCF file of SNPs from UCE loci.
DOI: 10.6084/m9.figshare.9042929
title: MOESM1 of Detection of Wolbachia in field-collected Aedes aegypti mosquitoes in metropolitan Manila, Philippines

description: Additional file 1: Table S1. Demographic profile (sex, sampling site code, location), detection status (wsp and 16S rDNA) of all individual adult Aedes aegypti mosquitoes used in the study and their supergroup classification.