cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7823741.v2
title: Burden of drug-resistant pulmonary tuberculosis in Pakistani children.sav

description: Burden of drug-resistant pulmonary tuberculosis in Pakistani children
DOI: 10.6084/m9.figshare.7823741.v4
title: Burden of drug-resistant pulmonary tuberculosis in Pakistani children

description: "Burden of drug-resistant pulmonary tuberculosis in Pakistani children" questionnaire and data<br>
DOI: 10.6084/m9.figshare.7823741.v3
title: Burden of drug-resistant pulmonary tuberculosis in Pakistani children

description: "Burden of drug-resistant pulmonary tuberculosis in Pakistani children" questionnaire and data<br>
DOI: 10.6084/m9.figshare.7823696
title: The Design and Effects of STR Regulation

description: STR regulation data for 17 American cities
DOI: 10.6084/m9.figshare.7823693
title: W22 rDNA and tDNA gff

description: A gff file of rDNA and tDNA loci in the W22 reference. See manuscript for a description of methods to determine loci.
DOI: 10.6084/m9.figshare.7823696.v1
title: The Design and Effects of STR Regulation

description: STR regulation data for 17 American cities
DOI: 10.6084/m9.figshare.7823684
title: B73 rDNA and tDNA GFF

description: A gff file for rDNA and tDNA repeats in the reference B73 v4 genome. See the manuscript for the details of how the annotations were determined.
DOI: 10.6084/m9.figshare.7823687
title: W22 Knob Repeats gff

description: A gff file of knob repeats from the maize W22 genome. See manuscript for a description of how annotations were determined.
DOI: 10.6084/m9.figshare.7823690
title: The annotated transcriptome of a 59 dpo (Stage 42) embryo (ID: BJP18) associated with, “Griffing et al. 2019. Embryonic development of a parthenogenetic vertebrate, the mourning gecko (Lepidodactylus lugubris). Dev Dyn.”

description: See README.txt file.
DOI: 10.6084/m9.figshare.7823684.v1
title: B73 rDNA and tDNA GFF

description: A gff file for rDNA and tDNA repeats in the reference B73 v4 genome. See the manuscript for the details of how the annotations were determined.
DOI: 10.6084/m9.figshare.7823681
title: B73.knobs.gff

description: A gff file for the knob and cent repeats identified in reference B73 v4 genome. See the manuscript for how these annotations were determined.
DOI: 10.6084/m9.figshare.7823687.v1
title: W22 Knob Repeats gff

description: A gff file of knob repeats from the maize W22 genome. See manuscript for a description of how annotations were determined.
DOI: 10.6084/m9.figshare.7823690.v1
title: The annotated transcriptome of a 59 dpo (Stage 42) embryo (ID: BJP18) associated with, “Griffing et al. 2019. Embryonic development of a parthenogenetic vertebrate, the mourning gecko (Lepidodactylus lugubris).”

description: See README.txt file.
DOI: 10.6084/m9.figshare.7823681.v2
title: B73.knobs.gff

description: A gff file for the knob and cent repeats identified in reference B73 v4 genome. See the manuscript for how these annotations were determined.
DOI: 10.6084/m9.figshare.7823681.v1
title: B73.knobs.gff

description: A gff file for the knob and cent repeats identified in reference B73 v4 genome. See the manuscript for how these annotations were determined.
DOI: 10.6084/m9.figshare.7823651
title: Study Documents Agir03

description: These are the study documents used in "Evaluation de l’adoption et de la diffusion de l’intégration de la planificationfamiliale dans la prise en charge des soins après avortement et postnataux/postpartum au Togo, Afrique de l’ouest (AGIR03)."
DOI: 10.6084/m9.figshare.7823651.v1
title: Study Documents Agir03

description: These are the study documents used in "Evaluation de l’adoption et de la diffusion de l’intégration de la planificationfamiliale dans la prise en charge des soins après avortement et postnataux/postpartum au Togo, Afrique de l’ouest (AGIR03)."
DOI: 10.6084/m9.figshare.7823585
title: A Hierarchical Model of Nonhomogeneous Poisson Processes for Twitter Retweets

description: We present a hierarchical model of nonhomogeneous Poisson processes (NHPP) for information diffusion on online social media, in particular Twitter retweets. The retweets of each original tweet are modelled by a NHPP, for which the intensity function is a product of time-decaying components and another component that depends on the follower count of the original tweet author. The latter allows us to explain or predict the ultimate retweet count by a network centrality-related covariate. The inference algorithm enables the Bayes factor to be computed, to facilitate model selection. Finally, the model is applied to the retweet datasets of two hashtags. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement
DOI: 10.6084/m9.figshare.7823582
title: Automatic Response Category Combination in Multinomial Logistic Regression

description: We propose a penalized likelihood method that simultaneously fits the multinomial logistic regression model and combines subsets of the response categories. The penalty is nondifferentiable when pairs of columns in the optimization variable are equal. This encourages pairwise equality of these columns in the estimator, which corresponds to response category combination. We use an alternating direction method of multipliers algorithm to compute the estimator and we discuss the algorithm’s convergence. Prediction and model selection are also addressed. Supplemental materials for this article are available online.
DOI: 10.6084/m9.figshare.7823582.v1
title: Automatic Response Category Combination in Multinomial Logistic Regression

description: We propose a penalized likelihood method that simultaneously fits the multinomial logistic regression model and combines subsets of the response categories. The penalty is nondifferentiable when pairs of columns in the optimization variable are equal. This encourages pairwise equality of these columns in the estimator, which corresponds to response category combination. We use an alternating direction method of multipliers algorithm to compute the estimator and we discuss the algorithm’s convergence. Prediction and model selection are also addressed. Supplemental materials for this article are available online.
DOI: 10.6084/m9.figshare.7823585.v1
title: A hierarchical model of non-homogeneous Poisson processes for Twitter retweets

description: We present a hierarchical model of non-homogeneous Poisson processes (NHPP) for information diffusion on online social media, in particular Twitter retweets. The retweets of each original tweet are modelled by a NHPP, for which the intensity function is a product of time-decaying components and another component that depends on the follower count of the original tweet author. The latter allows us to explain or predict the ultimate retweet count by a network centrality-related covariate. The inference algorithm enables the Bayes factor to be computed, in order to facilitate model selection. Finally, the model is applied to the retweet data sets of two hashtags.
DOI: 10.6084/m9.figshare.7823585.v3
title: A Hierarchical Model of Nonhomogeneous Poisson Processes for Twitter Retweets

description: We present a hierarchical model of nonhomogeneous Poisson processes (NHPP) for information diffusion on online social media, in particular Twitter retweets. The retweets of each original tweet are modelled by a NHPP, for which the intensity function is a product of time-decaying components and another component that depends on the follower count of the original tweet author. The latter allows us to explain or predict the ultimate retweet count by a network centrality-related covariate. The inference algorithm enables the Bayes factor to be computed, to facilitate model selection. Finally, the model is applied to the retweet datasets of two hashtags. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement
DOI: 10.6084/m9.figshare.7823585.v2
title: A Hierarchical Model of Nonhomogeneous Poisson Processes for Twitter Retweets

description: We present a hierarchical model of nonhomogeneous Poisson processes (NHPP) for information diffusion on online social media, in particular Twitter retweets. The retweets of each original tweet are modelled by a NHPP, for which the intensity function is a product of time-decaying components and another component that depends on the follower count of the original tweet author. The latter allows us to explain or predict the ultimate retweet count by a network centrality-related covariate. The inference algorithm enables the Bayes factor to be computed, to facilitate model selection. Finally, the model is applied to the retweet datasets of two hashtags. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement
DOI: 10.6084/m9.figshare.7823429
title: Journal of nanomaterials

description: Journal of nanomaterials
DOI: 10.6084/m9.figshare.7823465.v1
title: A Hierarchical Framework for Correcting Under-Reporting in Count Data

description: Tuberculosis poses a global health risk and Brazil is among the top twenty countries by absolute mortality. However, this epidemiological burden is masked by under-reporting, which impairs planning for effective intervention. We present a comprehensive investigation and application of a Bayesian hierarchical approach to modelling and correcting under-reporting in tuberculosis counts, a general problem arising in observational count data. The framework is applicable to fully under-reported data, relying only on an informative prior distribution for the mean reporting rate to supplement the partial information in the data. Covariates are used to inform both the true count generating process and the under-reporting mechanism, while also allowing for complex spatio-temporal structures. We present several sensitivity analyses based on simulation experiments to aid the elicitation of the prior distribution for the mean reporting rate and decisions relating to the inclusion of covariates. Both prior and posterior predictive model checking are presented, as well as a critical evaluation of the approach.
DOI: 10.6084/m9.figshare.7823420.v2
title: Full-length transcriptome Dataset of yellowhorn (Xanthoceras sorbifolium Bunge) under natural drought

description: <i>Xanthoceras sorbifolium </i>is an important woody oil seed tree in North China and has strong drought resistance. However few global gene expression profiling datasets have been published for studies addressing the drought-resistant mechanism of yellowhorn. Therefore, we generated a comprehensive gene expression dataset using RNA sequencing based on Illumina and Pacbio sequencing technology in this study. As a result, 10 Illumina RNA-seq sequencing datasets (over 52 million raw reads per sample) and 1 full length transcriptome dataset (5,964,241 reads of insert) were obtained and resulted in 110,584 unigenes. These transcriptomic data provide a foundation to elucidate the mechanisms of the drought-resistant of yellowhorn.
DOI: 10.6084/m9.figshare.7823420.v1
title: Full length transcriptome analysis of yellowhorn under natural drought.

description: <i>Xanthoceras sorbifolium </i>is an important woody oil seed tree in North China and has strong drought resistance. However few global gene expression profiling datasets have been published for studies addressing the drought-resistant mechanism of yellowhorn. Therefore, we generated a comprehensive gene expression dataset using RNA sequencing based on Illumina and Pacbio sequencing technology in this study. As a result, 10 Illumina RNA-seq sequencing datasets (over 52 million raw reads per sample) and 1 full length transcriptome dataset (5,964,241 reads of insert) were obtained and resulted in 110,584 unigenes. These transcriptomic data provide a foundation to elucidate the mechanisms of the drought-resistant of yellowhorn.
DOI: 10.6084/m9.figshare.7823066
title: MOESM1 of Design, implementation, and operation of a rapid, robust named entity recognition web service

description: Additional file 1. Supplementary tables with detailed performance evaluation data.
DOI: 10.6084/m9.figshare.7823066.v1
title: MOESM1 of Design, implementation, and operation of a rapid, robust named entity recognition web service

description: Additional file 1. Supplementary tables with detailed performance evaluation data.
DOI: 10.6084/m9.figshare.7822934
title: Additional file 2: of Diabetic and cardiovascular patients’ willingness to pay for upcoming national health insurance scheme in Côte d’Ivoire

description: Questionnaire_DAP.qes (QES 3 kb)
DOI: 10.6084/m9.figshare.7822934.v1
title: Additional file 2: of Diabetic and cardiovascular patients’ willingness to pay for upcoming national health insurance scheme in Côte d’Ivoire

description: Questionnaire_DAP.qes (QES 3 kb)
DOI: 10.6084/m9.figshare.7822916
title: Additional file 7: of Genome-wide methylation is modified by caloric restriction in Daphnia magna

description: R code used in methylKit, pvclust, bsseq, and comb-p sections of this study. (TXT 8 kb)
DOI: 10.6084/m9.figshare.7822910
title: Additional file 6: of Genome-wide methylation is modified by caloric restriction in Daphnia magna

description: Raw read files used in this study deposited in the European Nucleotide Archive under accession PRJEB24784. Treatment, H: normal food and L: caloric restricted. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.7822916.v1
title: Additional file 7: of Genome-wide methylation is modified by caloric restriction in Daphnia magna

description: R code used in methylKit, pvclust, bsseq, and comb-p sections of this study. (TXT 8 kb)
DOI: 10.6084/m9.figshare.7822904
title: Additional file 5: of Genome-wide methylation is modified by caloric restriction in Daphnia magna

description: GO term hierarchies for the two enriched GO terms: A) Biological Process and B) Molecular Function. Ovals and rectangles contain GO identification, GO name, p-value and number of genes tested and over total number of genes from that category. Red rectangles represent significant terms under the topGO criteria applied. (PS 91 kb)
DOI: 10.6084/m9.figshare.7822910.v1
title: Additional file 6: of Genome-wide methylation is modified by caloric restriction in Daphnia magna

description: Raw read files used in this study deposited in the European Nucleotide Archive under accession PRJEB24784. Treatment, H: normal food and L: caloric restricted. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.7822898
title: Additional file 4: of Genome-wide methylation is modified by caloric restriction in Daphnia magna

description: Gene annotations for genes with overlapping significantly hypermethylated regions under caloric restriction. Genes overlapped by a DMR of greater than 20% mean difference in methylation level are indicated in column 3. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7822904.v1
title: Additional file 5: of Genome-wide methylation is modified by caloric restriction in Daphnia magna

description: GO term hierarchies for the two enriched GO terms: A) Biological Process and B) Molecular Function. Ovals and rectangles contain GO identification, GO name, p-value and number of genes tested and over total number of genes from that category. Red rectangles represent significant terms under the topGO criteria applied. (PS 91 kb)
DOI: 10.6084/m9.figshare.7822892
title: Additional file 3: of Genome-wide methylation is modified by caloric restriction in Daphnia magna

description: Gene annotations for genes with overlapping significantly hypomethylated regions under caloric restriction. Genes overlapped by a DMR of greater than 20% mean difference in methylation level are indicated in column 3. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7822892.v1
title: Additional file 3: of Genome-wide methylation is modified by caloric restriction in Daphnia magna

description: Gene annotations for genes with overlapping significantly hypomethylated regions under caloric restriction. Genes overlapped by a DMR of greater than 20% mean difference in methylation level are indicated in column 3. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7822898.v1
title: Additional file 4: of Genome-wide methylation is modified by caloric restriction in Daphnia magna

description: Gene annotations for genes with overlapping significantly hypermethylated regions under caloric restriction. Genes overlapped by a DMR of greater than 20% mean difference in methylation level are indicated in column 3. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7822880
title: Additional file 1: of Genome-wide methylation is modified by caloric restriction in Daphnia magna

description: Reads sequenced per replicate for both converted and unconverted libraries. Alignments analysed is number of read-pairs per bisulphite converted library aligned by Bismark; deduplicated is number of read pairs after removal of PCR duplicates; non CpG filtered is read-pairs remaining after removal of CHH and CHG containing reads; bases remaining are number of bases left for CpG methylation prediction in Bismark; average coverage is for filtered bases at a D. magna genome size of 240 megabases; CpG sites remaining before and after filtering of polymorphic sites, polymorphic sites were identified from unconverted libraries against a reference genome converted to Clone 32; Non CpG % methylated are CHH and CHG sites methylated (100 minus this figure is equivalent to bisulphite conversion efficiency), CpG % methylated is the genome-wide percentage of CpG methylation, and CpG % methylated filtered is the percentage remaining after reads containing CHH or CHG methylation are removed from the analysis. Diet, H: normal food, L: caloric restriction, code: combination of diet and mother. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.7822886
title: Additional file 2: of Genome-wide methylation is modified by caloric restriction in Daphnia magna

description: MultiQC report in html format reporting general statistics from the Bismark alignment process for all replicates. Including alignment rates, deduplication effect, overall cytosine methylation and m-bias plot. This plot shows average methylation level per position across reads, demonstrating minimal bias at 5â ˛ and 3â ˛ reads after trimming of first and last nine base pairs of each read. (HTML 1089 kb)
DOI: 10.6084/m9.figshare.7822880.v1
title: Additional file 1: of Genome-wide methylation is modified by caloric restriction in Daphnia magna

description: Reads sequenced per replicate for both converted and unconverted libraries. Alignments analysed is number of read-pairs per bisulphite converted library aligned by Bismark; deduplicated is number of read pairs after removal of PCR duplicates; non CpG filtered is read-pairs remaining after removal of CHH and CHG containing reads; bases remaining are number of bases left for CpG methylation prediction in Bismark; average coverage is for filtered bases at a D. magna genome size of 240 megabases; CpG sites remaining before and after filtering of polymorphic sites, polymorphic sites were identified from unconverted libraries against a reference genome converted to Clone 32; Non CpG % methylated are CHH and CHG sites methylated (100 minus this figure is equivalent to bisulphite conversion efficiency), CpG % methylated is the genome-wide percentage of CpG methylation, and CpG % methylated filtered is the percentage remaining after reads containing CHH or CHG methylation are removed from the analysis. Diet, H: normal food, L: caloric restriction, code: combination of diet and mother. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.7822886.v1
title: Additional file 2: of Genome-wide methylation is modified by caloric restriction in Daphnia magna

description: MultiQC report in html format reporting general statistics from the Bismark alignment process for all replicates. Including alignment rates, deduplication effect, overall cytosine methylation and m-bias plot. This plot shows average methylation level per position across reads, demonstrating minimal bias at 5â ˛ and 3â ˛ reads after trimming of first and last nine base pairs of each read. (HTML 1089 kb)
DOI: 10.6084/m9.figshare.7822865
title: Additional file 1: of Hydra vulgaris exhibits day-night variation in behavior and gene expression levels

description: List of HyDCGs lists 380 diel cycle genes in Hydra vulgaris. “Gene ID” refers to the gene number registered in the Hydra 2.0 Genome Portal ( https://research.nhgri.nih.gov/hydra/ ). The homologue descriptions and gene ontology terms are based on information in the Hydra 2.0 Genome Portal. “Cluster” represents a group of IDs determined by K-means clustering (see Fig. 4). The subsequent columns refer to the significance levels obtained from the three algorithms for rhythmicity detection (ARSER, JTK_CYCLE and empirical JTK_CYCLE) and the normalized expression levels at six time points (two biological replicates). The expression level of each gene was normalized so that the mean intensity and the standard deviation were 0.0 and 1.0, respectively. (XLS 316 kb)
DOI: 10.6084/m9.figshare.7822865.v1
title: Additional file 1: of Hydra vulgaris exhibits day-night variation in behavior and gene expression levels

description: List of HyDCGs lists 380 diel cycle genes in Hydra vulgaris. “Gene ID” refers to the gene number registered in the Hydra 2.0 Genome Portal ( https://research.nhgri.nih.gov/hydra/ ). The homologue descriptions and gene ontology terms are based on information in the Hydra 2.0 Genome Portal. “Cluster” represents a group of IDs determined by K-means clustering (see Fig. 4). The subsequent columns refer to the significance levels obtained from the three algorithms for rhythmicity detection (ARSER, JTK_CYCLE and empirical JTK_CYCLE) and the normalized expression levels at six time points (two biological replicates). The expression level of each gene was normalized so that the mean intensity and the standard deviation were 0.0 and 1.0, respectively. (XLS 316 kb)
DOI: 10.6084/m9.figshare.7822835
title: Additional file 1: of Akkermansia muciniphila ameliorates the age-related decline in colonic mucus thickness and attenuates immune activation in accelerated aging Ercc1−/Δ7 mice

description: Gene expression profiles (Microarray analysis) of colon and ileum. Only genes that were statistically significantly different (p 1.2 between groups are included. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.7822841
title: Additional file 2: of Akkermansia muciniphila ameliorates the age-related decline in colonic mucus thickness and attenuates immune activation in accelerated aging Ercc1â /Î 7 mice

description: Gene set enrichment analysis (GSEA) results of ileum and colon. Only significantly enriched pathways (FDRâ
DOI: 10.6084/m9.figshare.7822835.v1
title: Additional file 1: of Akkermansia muciniphila ameliorates the age-related decline in colonic mucus thickness and attenuates immune activation in accelerated aging Ercc1−/Δ7 mice

description: Gene expression profiles (Microarray analysis) of colon and ileum. Only genes that were statistically significantly different (p 1.2 between groups are included. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.7822841.v1
title: Additional file 2: of Akkermansia muciniphila ameliorates the age-related decline in colonic mucus thickness and attenuates immune activation in accelerated aging Ercc1â /Î 7 mice

description: Gene set enrichment analysis (GSEA) results of ileum and colon. Only significantly enriched pathways (FDRâ
DOI: 10.6084/m9.figshare.7822805
title: Additional file 1 of JOA: Joint Overlap Analysis of multiple genomic interval sets

description: Supplementary Table S1 contains all jointly overlapping intervals for 141 interval sets of Dnase hypersensitive sites. (XLSX 75 kb)
DOI: 10.6084/m9.figshare.7822805.v1
title: Additional file 1 of JOA: Joint Overlap Analysis of multiple genomic interval sets

description: Supplementary Table S1 contains all jointly overlapping intervals for 141 interval sets of Dnase hypersensitive sites. (XLSX 75 kb)