cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6938921
title: MOESM4 of Reduced-representation sequencing identifies small effective population sizes of Anopheles gambiae in the north-western Lake Victoria basin, Uganda

description: Additional file 4: Table S4. Chromosome 2L inversion molecular karyotype results.
DOI: 10.6084/m9.figshare.6938921.v1
title: MOESM4 of Reduced-representation sequencing identifies small effective population sizes of Anopheles gambiae in the north-western Lake Victoria basin, Uganda

description: Additional file 4: Table S4. Chromosome 2L inversion molecular karyotype results.
DOI: 10.6084/m9.figshare.6938912
title: Additional file 6 of Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

description: Table S3. Blast result with only hits related to miRNA features. (XLSX 246 kb)
DOI: 10.6084/m9.figshare.6938912.v1
title: Additional file 6 of Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

description: Table S3. Blast result with only hits related to miRNA features. (XLSX 246 kb)
DOI: 10.6084/m9.figshare.6938903
title: MOESM3 of Reduced-representation sequencing identifies small effective population sizes of Anopheles gambiae in the north-western Lake Victoria basin, Uganda

description: Additional file 3: Table S3. Kinship coefficient estimates and percentage missing data values per individual.
DOI: 10.6084/m9.figshare.6938900
title: Additional file 4: of Modeling of the GC content of the substituted bases in bacterial core genomes

description: An Excel file containing data used for bulk sbGC/cgGC analyses (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6938903.v1
title: MOESM3 of Reduced-representation sequencing identifies small effective population sizes of Anopheles gambiae in the north-western Lake Victoria basin, Uganda

description: Additional file 3: Table S3. Kinship coefficient estimates and percentage missing data values per individual.
DOI: 10.6084/m9.figshare.6938900.v1
title: Additional file 4: of Modeling of the GC content of the substituted bases in bacterial core genomes

description: An Excel file containing data used for bulk sbGC/cgGC analyses (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6938891
title: Additional file 2: of RNA-seq analysis of lignocellulose-related genes in hybrid Eucalyptus with contrasting wood basic density

description: Table S2. Gene-specific primers used in qRT-PCR. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.6938891.v1
title: Additional file 2: of RNA-seq analysis of lignocellulose-related genes in hybrid Eucalyptus with contrasting wood basic density

description: Table S2. Gene-specific primers used in qRT-PCR. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.6938885
title: Additional file 3: of Modeling of the GC content of the substituted bases in bacterial core genomes

description: An Excel file containing data used for strain-wise sbGC/cgGC analyses (XLSX 44Â kb)
DOI: 10.6084/m9.figshare.6938885.v1
title: Additional file 3: of Modeling of the GC content of the substituted bases in bacterial core genomes

description: An Excel file containing data used for strain-wise sbGC/cgGC analyses (XLSX 44Â kb)
DOI: 10.6084/m9.figshare.6938879
title: Additional file 1: of RNA-seq analysis of lignocellulose-related genes in hybrid Eucalyptus with contrasting wood basic density

description: Table S1. The total RNA-seq dataset (RPKM &gt;â 10). (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6938882
title: Additional file 4 of Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

description: Table S2. Blast result with all hits to database files found (E-MTAB-6201). (XLSX 2127 kb)
DOI: 10.6084/m9.figshare.6938882.v1
title: Additional file 4 of Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

description: Table S2. Blast result with all hits to database files found (E-MTAB-6201). (XLSX 2127 kb)
DOI: 10.6084/m9.figshare.6938879.v1
title: Additional file 1: of RNA-seq analysis of lignocellulose-related genes in hybrid Eucalyptus with contrasting wood basic density

description: Table S1. The total RNA-seq dataset (RPKM &gt;â 10). (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6938873
title: Additional file 2: of TRH site-specific methylation in oral and oropharyngeal squamous cell carcinoma

description: Demographic data and TRH methylation percentage in screening experiments. (XLS 29 kb)
DOI: 10.6084/m9.figshare.6938870
title: MOESM1 of Reduced-representation sequencing identifies small effective population sizes of Anopheles gambiae in the north-western Lake Victoria basin, Uganda

description: Additional file 1: Table S1. GPS co-ordinates and distances between entomological sampling sites.
DOI: 10.6084/m9.figshare.6938873.v1
title: Additional file 2: of TRH site-specific methylation in oral and oropharyngeal squamous cell carcinoma

description: Demographic data and TRH methylation percentage in screening experiments. (XLS 29 kb)
DOI: 10.6084/m9.figshare.6938870.v1
title: MOESM1 of Reduced-representation sequencing identifies small effective population sizes of Anopheles gambiae in the north-western Lake Victoria basin, Uganda

description: Additional file 1: Table S1. GPS co-ordinates and distances between entomological sampling sites.
DOI: 10.6084/m9.figshare.6938864
title: Additional file 3 of Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

description: Table S1. Filtering details for potential miRNAs. (XLSX 73 kb)
DOI: 10.6084/m9.figshare.6938864.v1
title: Additional file 3 of Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

description: Table S1. Filtering details for potential miRNAs. (XLSX 73 kb)
DOI: 10.6084/m9.figshare.6938855
title: Additional file 1: of TRH site-specific methylation in oral and oropharyngeal squamous cell carcinoma

description: Microsoft Office Excel displayed average methylation percentage of each methylated CpG sites of each sample from the seven GSEs. (XLS 8189 kb)
DOI: 10.6084/m9.figshare.6938855.v1
title: Additional file 1: of TRH site-specific methylation in oral and oropharyngeal squamous cell carcinoma

description: Microsoft Office Excel displayed average methylation percentage of each methylated CpG sites of each sample from the seven GSEs. (XLS 8189 kb)
DOI: 10.6084/m9.figshare.6938837
title: Additional file 15 of Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

description: Table S9. IsomiR count table. (XLSX 594 kb)
DOI: 10.6084/m9.figshare.6938837.v1
title: Additional file 15 of Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

description: Table S9. IsomiR count table. (XLSX 594 kb)
DOI: 10.6084/m9.figshare.6938828
title: Additional file 14 of Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

description: Table S8. IsomiR analysis. (XLSX 202 kb)
DOI: 10.6084/m9.figshare.6938828.v1
title: Additional file 14 of Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

description: Table S8. IsomiR analysis. (XLSX 202 kb)
DOI: 10.6084/m9.figshare.6938822
title: Additional file 7: of The genetic diversity of Borrelia afzelii is not maintained by the diversity of the rodent hosts

description: Table S7. Distribution of haplotypes over the ticks sampled from the three rodent species. (CSV 1 kb)
DOI: 10.6084/m9.figshare.6938822.v1
title: Additional file 7: of The genetic diversity of Borrelia afzelii is not maintained by the diversity of the rodent hosts

description: Table S7. Distribution of haplotypes over the ticks sampled from the three rodent species. (CSV 1 kb)
DOI: 10.6084/m9.figshare.6938810
title: Additional file 13 of Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

description: Table S7. Expression level embryo Day 10 in percentage. (XLSX 7 kb)
DOI: 10.6084/m9.figshare.6938807
title: Additional file 6: of The genetic diversity of Borrelia afzelii is not maintained by the diversity of the rodent hosts

description: Table S6. Haplotype sequences of IGS, dbpA, and ospC found in the ticks sampled from the three rodent species. (CSV 201 kb)
DOI: 10.6084/m9.figshare.6938807.v1
title: Additional file 6: of The genetic diversity of Borrelia afzelii is not maintained by the diversity of the rodent hosts

description: Table S6. Haplotype sequences of IGS, dbpA, and ospC found in the ticks sampled from the three rodent species. (CSV 201 kb)
DOI: 10.6084/m9.figshare.6938810.v1
title: Additional file 13 of Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

description: Table S7. Expression level embryo Day 10 in percentage. (XLSX 7 kb)
DOI: 10.6084/m9.figshare.6938792
title: Additional file 5: of The genetic diversity of Borrelia afzelii is not maintained by the diversity of the rodent hosts

description: Table S5. Primers for conventional PCR and sequencing. (CSV 677 bytes)
DOI: 10.6084/m9.figshare.6938792.v1
title: Additional file 5: of The genetic diversity of Borrelia afzelii is not maintained by the diversity of the rodent hosts

description: Table S5. Primers for conventional PCR and sequencing. (CSV 677 bytes)
DOI: 10.6084/m9.figshare.6938789
title: Additional file 12 of Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

description: Table S6. MiRmine result of potential embryo- and endometrium-specific miRNAs. (XLSX 67 kb)
DOI: 10.6084/m9.figshare.6938789.v1
title: Additional file 12 of Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

description: Table S6. MiRmine result of potential embryo- and endometrium-specific miRNAs. (XLSX 67 kb)
DOI: 10.6084/m9.figshare.6938783
title: Additional file 11 of Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

description: Table S5. Embryo Day 10 miRNAs expression versus endometrium Day 10 and Day 12. (XLSX 70 kb)
DOI: 10.6084/m9.figshare.6938783.v1
title: Additional file 11 of Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

description: Table S5. Embryo Day 10 miRNAs expression versus endometrium Day 10 and Day 12. (XLSX 70 kb)
DOI: 10.6084/m9.figshare.6938777
title: Additional file 4: of The genetic diversity of Borrelia afzelii is not maintained by the diversity of the rodent hosts

description: Table S4. Primers and probes used in the qPCR analyses. (CSV 824 bytes)
DOI: 10.6084/m9.figshare.6938777.v1
title: Additional file 4: of The genetic diversity of Borrelia afzelii is not maintained by the diversity of the rodent hosts

description: Table S4. Primers and probes used in the qPCR analyses. (CSV 824 bytes)
DOI: 10.6084/m9.figshare.6938762
title: Additional file 3: of The genetic diversity of Borrelia afzelii is not maintained by the diversity of the rodent hosts

description: Table S3. Infestation level of small mammals with I. ricinus ticks: centrality and dispersion descriptors. (CSV 757 bytes)
DOI: 10.6084/m9.figshare.6938762.v1
title: Additional file 3: of The genetic diversity of Borrelia afzelii is not maintained by the diversity of the rodent hosts

description: Table S3. Infestation level of small mammals with I. ricinus ticks: centrality and dispersion descriptors. (CSV 757 bytes)
DOI: 10.6084/m9.figshare.6938756
title: Additional file 3: of Behavioural and demographic correlates of undiagnosed HIV infection in a MSM sample recruited in 13 European cities

description: Stata do-file of the analysis. (TXT 10 kb)
DOI: 10.6084/m9.figshare.6938756.v1
title: Additional file 3: of Behavioural and demographic correlates of undiagnosed HIV infection in a MSM sample recruited in 13 European cities

description: Stata do-file of the analysis. (TXT 10 kb)
DOI: 10.6084/m9.figshare.6938759
title: Additional file 10 of Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

description: Table S4. EdgeR result of all comparisons on isomiR level. (XLSX 32902 kb)
DOI: 10.6084/m9.figshare.6938759.v1
title: Additional file 10 of Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

description: Table S4. EdgeR result of all comparisons on isomiR level. (XLSX 32902 kb)
DOI: 10.6084/m9.figshare.6938750
title: Additional file 2: of The genetic diversity of Borrelia afzelii is not maintained by the diversity of the rodent hosts

description: Table S2. Tick burdens of rodents and B. burgdorferi (s.l.) prevalence of infection in tested ticks. (CSV 9 kb)
DOI: 10.6084/m9.figshare.6938750.v1
title: Additional file 2: of The genetic diversity of Borrelia afzelii is not maintained by the diversity of the rodent hosts

description: Table S2. Tick burdens of rodents and B. burgdorferi (s.l.) prevalence of infection in tested ticks. (CSV 9 kb)
DOI: 10.6084/m9.figshare.6938744
title: Additional file 2: of Behavioural and demographic correlates of undiagnosed HIV infection in a MSM sample recruited in 13 European cities

description: Sialon II dataset used for the analysis presented in this manuscript. (CSV 11362 kb)
DOI: 10.6084/m9.figshare.6938747
title: MOESM3 of Weighted single-step GWAS and gene network analysis reveal new candidate genes for semen traits in pigs

description: Additional file 3: Table S3. Three SNP windows that explained the highest proportion of genetic variance of each semen trait in L2. The data provided represent the chromosome, average window position (in basepairs) and the percentage of variance explained by the three SNP windows that explained the highest proportion of genetic variance for each semen trait in L2.
DOI: 10.6084/m9.figshare.6938744.v1
title: Additional file 2: of Behavioural and demographic correlates of undiagnosed HIV infection in a MSM sample recruited in 13 European cities

description: Sialon II dataset used for the analysis presented in this manuscript. (CSV 11362 kb)
DOI: 10.6084/m9.figshare.6938747.v1
title: MOESM3 of Weighted single-step GWAS and gene network analysis reveal new candidate genes for semen traits in pigs

description: Additional file 3: Table S3. Three SNP windows that explained the highest proportion of genetic variance of each semen trait in L2. The data provided represent the chromosome, average window position (in basepairs) and the percentage of variance explained by the three SNP windows that explained the highest proportion of genetic variance for each semen trait in L2.
DOI: 10.6084/m9.figshare.6938738
title: MOESM2 of Weighted single-step GWAS and gene network analysis reveal new candidate genes for semen traits in pigs

description: Additional file 2: Table S2. The three SNP windows that explained the highest proportion of genetic variance of each semen trait in L1. The data provided represent the chromosome, average window position (in basepairs) and the percentage of variance explained by the three SNP windows that explained the highest proportion of genetic variance for each semen trait in L1.
DOI: 10.6084/m9.figshare.6938741
title: Additional file 1: of The genetic diversity of Borrelia afzelii is not maintained by the diversity of the rodent hosts

description: Table S1. Location of sampling sites. (CSV 688 bytes)
DOI: 10.6084/m9.figshare.6938738.v1
title: MOESM2 of Weighted single-step GWAS and gene network analysis reveal new candidate genes for semen traits in pigs

description: Additional file 2: Table S2. The three SNP windows that explained the highest proportion of genetic variance of each semen trait in L1. The data provided represent the chromosome, average window position (in basepairs) and the percentage of variance explained by the three SNP windows that explained the highest proportion of genetic variance for each semen trait in L1.
DOI: 10.6084/m9.figshare.6938741.v1
title: Additional file 1: of The genetic diversity of Borrelia afzelii is not maintained by the diversity of the rodent hosts

description: Table S1. Location of sampling sites. (CSV 688 bytes)
DOI: 10.6084/m9.figshare.6938732
title: MOESM1 of Weighted single-step GWAS and gene network analysis reveal new candidate genes for semen traits in pigs

description: Additional file 1: Table S1. Variance components and standard errors (in parenthesis) for semen traits. The data provided represent the values of variance components (additive genetic, environmental and residual) and the respective standard errors for each semen trait and pig line.
DOI: 10.6084/m9.figshare.6938732.v1
title: MOESM1 of Weighted single-step GWAS and gene network analysis reveal new candidate genes for semen traits in pigs

description: Additional file 1: Table S1. Variance components and standard errors (in parenthesis) for semen traits. The data provided represent the values of variance components (additive genetic, environmental and residual) and the respective standard errors for each semen trait and pig line.
DOI: 10.6084/m9.figshare.6938567
title: RNA melting and RNA chaperone activities of plant cold shock domain proteins are not correlated

description: Cold shock domain proteins (CSDPs) participate in plant development and resistance, but the underlying molecular mechanisms are poorly understood. In this study, we demonstrated that the CSDPs, including EsCSDP1, EsCSDP2, and EsCSDP3, from the extremophyte <i>Eutrema salsugineum</i> possess all basic properties of RNA chaperones. EsCSDP1–3 melt secondary structures in RNAs with various nucleotide sequences and exhibit RNA chaperone activity <i>in vitro</i>. EsCSDP1 and EsCSDP3 were shown to have higher RNA melting activity, whereasile EsCSDP2 had higher RNA chaperone activity. We demonstrated that higher RNA melting activity correlates with the longer C-terminal fragment in many zinc finger motifs, whereas increased RNA chaperone activity was most likely due to the higher glycine content and RGG repeat number in the C-terminal fragment.
DOI: 10.6084/m9.figshare.6938567.v1
title: RNA melting and RNA chaperone activities of plant cold shock domain proteins are not correlated

description: Cold shock domain proteins (CSDPs) participate in plant development and resistance, but the underlying molecular mechanisms are poorly understood. In this study, we demonstrated that the CSDPs, including EsCSDP1, EsCSDP2, and EsCSDP3, from the extremophyte <i>Eutrema salsugineum</i> possess all basic properties of RNA chaperones. EsCSDP1–3 melt secondary structures in RNAs with various nucleotide sequences and exhibit RNA chaperone activity <i>in vitro</i>. EsCSDP1 and EsCSDP3 were shown to have higher RNA melting activity, whereasile EsCSDP2 had higher RNA chaperone activity. We demonstrated that higher RNA melting activity correlates with the longer C-terminal fragment in many zinc finger motifs, whereas increased RNA chaperone activity was most likely due to the higher glycine content and RGG repeat number in the C-terminal fragment.
DOI: 10.6084/m9.figshare.6938540
title: Noisy Hamiltonian Monte Carlo for Doubly Intractable Distributions

description: Hamiltonian Monte Carlo (HMC) has been progressively incorporated within the statistician’s toolbox as an alternative sampling method in settings when standard Metropolis–Hastings is inefficient. HMC generates a Markov chain on an augmented state space with transitions based on a deterministic differential flow derived from Hamiltonian mechanics. In practice, the evolution of Hamiltonian systems cannot be solved analytically, requiring numerical integration schemes. Under numerical integration, the resulting approximate solution no longer preserves the measure of the target distribution, therefore an accept–reject step is used to correct the bias. For doubly intractable distributions—such as posterior distributions based on Gibbs random fields—HMC suffers from some computational difficulties: computation of gradients in the differential flow and computation of the accept–reject proposals poses difficulty. In this article, we study the behavior of HMC when these quantities are replaced by Monte Carlo estimates. Supplemental codes for implementing methods used in the article are available online.
DOI: 10.6084/m9.figshare.6938540.v2
title: Noisy Hamiltonian Monte Carlo for Doubly Intractable Distributions

description: Hamiltonian Monte Carlo (HMC) has been progressively incorporated within the statistician’s toolbox as an alternative sampling method in settings when standard Metropolis–Hastings is inefficient. HMC generates a Markov chain on an augmented state space with transitions based on a deterministic differential flow derived from Hamiltonian mechanics. In practice, the evolution of Hamiltonian systems cannot be solved analytically, requiring numerical integration schemes. Under numerical integration, the resulting approximate solution no longer preserves the measure of the target distribution, therefore an accept–reject step is used to correct the bias. For doubly intractable distributions—such as posterior distributions based on Gibbs random fields—HMC suffers from some computational difficulties: computation of gradients in the differential flow and computation of the accept–reject proposals poses difficulty. In this article, we study the behavior of HMC when these quantities are replaced by Monte Carlo estimates. Supplemental codes for implementing methods used in the article are available online.
DOI: 10.6084/m9.figshare.6938540.v1
title: Noisy Hamiltonian Monte Carlo for doubly-intractable distributions

description: Hamiltonian Monte Carlo (HMC) has been progressively incorporated within the statistician’s toolbox as an alternative sampling method in settings when standard Metropolis-Hastings is inefficient. HMC generates a Markov chain on an augmented state space with transitions based on a deterministic differential flow derived from Hamiltonian mechanics. In practice, the evolution of Hamiltonian systems cannot be solved analytically, requiring numerical integration schemes. Under numerical integration, the resulting approximate solution no longer preserves the measure of the target distribution, therefore an accept-reject step is used to correct the bias. For doubly-intractable distributions - - such as posterior distributions based on Gibbs random fields – HMC suffers from some computational difficulties: computation of gradients in the differential flow and computation of the accept-reject proposals poses difficulty. In this paper, we study the behaviour of HMC when these quantities are replaced by Monte Carlo estimates. Supplemental codes for implementing methods used in the paper are available online.