cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1427411.v2
title: Complete description of the skull and mandible of the giant mustelid <i>Eomellivora piveteaui</i> Ozansoy, 1965 (Mammalia, Carnivora, Mustelidae), from Batallones (MN10), late Miocene (Madrid, Spain)

description: ABSTRACTWe describe cranial, mandibular, and dental remains of five individuals of the giant mustelid <i>Eomellivora piveteaui</i> Ozansoy, 1965, from the late Miocene (MN10) site of Cerro de los Batallones (Madrid, Spain)—the first complete cranial remains recorded for this species and the most complete remains of the genus. This new sample enables a review of the systematic status of <i>Eomellivora</i>, leading us to accept as valid the species <i>E. piveteaui</i> Ozansoy, 1965, <i>E. wimani</i> Zdansky, 1924, <i>E. ursogulo</i> (Orlov, 1948), and <i>E. hungarica</i> Kretzoi, 1942. Our phylogenetic hypothesis indicates that <i>Eomellivora</i> is the sister taxon of the extant <i>Mellivora capensis</i> and <i>E. piveteaui</i> had a common ancestor within the crown group <i>E. wimani</i>–<i>E. ursogulo. Eomellivora piveteaui</i> was specialized for a more hypercarnivorous diet than the largest extant terrestrial mustelids, although it also had some derived bone-crushing adaptations. <i>Eomellivora piveteaui</i> had an active predatory role in the late Miocene carnivore faunas, exploiting both small and relatively large prey.SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1427403
title: The use of high-throughput sequencing methods for plant microRNA research

description: MicroRNA (miRNA) acts as a critical regulator of gene expression at post-transcriptional and occasionally transcriptional levels in plants. Identification of reliable miRNA genes, monitoring the procedures of transcription, processing and maturation of the miRNAs, quantification of the accumulation levels of the miRNAs in specific biological samples, and validation of miRNA–target interactions become the basis for thoroughly understanding of the miRNA-mediated regulatory networks and the underlying mechanisms. Great progresses have been achieved for sequencing technology. Based on the high degree of sequencing depth and coverage, the high-throughput sequencing (HTS, also called next-generation sequencing) technology provides unprecedentedly efficient way for genome-wide or transcriptome-wide studies. In this review, we will introduce several HTS platform-based methods useful for plant miRNA research, including RNA-seq (RNA sequencing), RNA-PET-seq (paired end tag sequencing of RNAs), sRNA-seq (small RNA sequencing), dsRNA-seq (double-stranded RNA sequencing), ssRNA-seq (single-stranded RNA sequencing) and degradome-seq (degradome sequencing). In particular, we will provide some special cases to illustrate the novel use of HTS methods for investigation of the processing modes of the miRNA precursors, identification of the RNA editing sites on miRNA precursors, mature miRNAs and target transcripts, re-examination of the current miRNA registries, and discovery of novel miRNA species and novel miRNA–target interactions. Summarily, we opinioned that integrative use of the above mentioned HTS methods could make the studies on miRNAs more efficient.
DOI: 10.6084/m9.figshare.1427397
title: Demultiplexed reads from Aquarium Project

description: These are the demultiplexed and merged 16S reads for the aquarium project from the Eisen Lab at UC Davis. Publication information forthcoming.
DOI: 10.6084/m9.figshare.1427394
title: Regular Tessellation Link Complements

description: By a regular tessellation, we mean a hyperbolic 3-manifold tessellated by ideal Platonic solids such that the symmetry group acts transitively on oriented flags. A regular tessellation has an invariant that we call the cusp modulus. For small cusp modulus, we classify all regular tessellations. For large cusp modulus, we prove that a regular tessellation has to be of infinite volume if its fundamental group is generated by peripheral curves only. This shows that there are at least 19 and at most 21 link complements that are regular tessellations (computer experiments suggest that at least one of the two remaining cases fails to be a link complement, but so far, we have no proof). In particular, we complete the classification of all principal congruence link complements given by Baker and Reid for the cases of discriminant <i>D</i> = −3 and <i>D</i> = −4. We describe only the manifolds arising as complements of links here, with a future publication “Regular Tessellation Links” giving explicit pictures of these links.
DOI: 10.6084/m9.figshare.1427403.v1
title: The use of high-throughput sequencing methods for plant microRNA research

description: MicroRNA (miRNA) acts as a critical regulator of gene expression at post-transcriptional and occasionally transcriptional levels in plants. Identification of reliable miRNA genes, monitoring the procedures of transcription, processing and maturation of the miRNAs, quantification of the accumulation levels of the miRNAs in specific biological samples, and validation of miRNA–target interactions become the basis for thoroughly understanding of the miRNA-mediated regulatory networks and the underlying mechanisms. Great progresses have been achieved for sequencing technology. Based on the high degree of sequencing depth and coverage, the high-throughput sequencing (HTS, also called next-generation sequencing) technology provides unprecedentedly efficient way for genome-wide or transcriptome-wide studies. In this review, we will introduce several HTS platform-based methods useful for plant miRNA research, including RNA-seq (RNA sequencing), RNA-PET-seq (paired end tag sequencing of RNAs), sRNA-seq (small RNA sequencing), dsRNA-seq (double-stranded RNA sequencing), ssRNA-seq (single-stranded RNA sequencing) and degradome-seq (degradome sequencing). In particular, we will provide some special cases to illustrate the novel use of HTS methods for investigation of the processing modes of the miRNA precursors, identification of the RNA editing sites on miRNA precursors, mature miRNAs and target transcripts, re-examination of the current miRNA registries, and discovery of novel miRNA species and novel miRNA–target interactions. Summarily, we opinioned that integrative use of the above mentioned HTS methods could make the studies on miRNAs more efficient.
DOI: 10.6084/m9.figshare.1427394.v1
title: Regular Tessellation Link Complements

description: By a regular tessellation, we mean a hyperbolic 3-manifold tessellated by ideal Platonic solids such that the symmetry group acts transitively on oriented flags. A regular tessellation has an invariant that we call the cusp modulus. For small cusp modulus, we classify all regular tessellations. For large cusp modulus, we prove that a regular tessellation has to be of infinite volume if its fundamental group is generated by peripheral curves only. This shows that there are at least 19 and at most 21 link complements that are regular tessellations (computer experiments suggest that at least one of the two remaining cases fails to be a link complement, but so far, we have no proof). In particular, we complete the classification of all principal congruence link complements given by Baker and Reid for the cases of discriminant <i>D</i> = −3 and <i>D</i> = −4. We describe only the manifolds arising as complements of links here, with a future publication “Regular Tessellation Links” giving explicit pictures of these links.
DOI: 10.6084/m9.figshare.1427403.v3
title: The use of high-throughput sequencing methods for plant microRNA research

description: MicroRNA (miRNA) acts as a critical regulator of gene expression at post-transcriptional and occasionally transcriptional levels in plants. Identification of reliable miRNA genes, monitoring the procedures of transcription, processing and maturation of the miRNAs, quantification of the accumulation levels of the miRNAs in specific biological samples, and validation of miRNA–target interactions become the basis for thoroughly understanding of the miRNA-mediated regulatory networks and the underlying mechanisms. Great progresses have been achieved for sequencing technology. Based on the high degree of sequencing depth and coverage, the high-throughput sequencing (HTS, also called next-generation sequencing) technology provides unprecedentedly efficient way for genome-wide or transcriptome-wide studies. In this review, we will introduce several HTS platform-based methods useful for plant miRNA research, including RNA-seq (RNA sequencing), RNA-PET-seq (paired end tag sequencing of RNAs), sRNA-seq (small RNA sequencing), dsRNA-seq (double-stranded RNA sequencing), ssRNA-seq (single-stranded RNA sequencing) and degradome-seq (degradome sequencing). In particular, we will provide some special cases to illustrate the novel use of HTS methods for investigation of the processing modes of the miRNA precursors, identification of the RNA editing sites on miRNA precursors, mature miRNAs and target transcripts, re-examination of the current miRNA registries, and discovery of novel miRNA species and novel miRNA–target interactions. Summarily, we opinioned that integrative use of the above mentioned HTS methods could make the studies on miRNAs more efficient.
DOI: 10.6084/m9.figshare.1427403.v2
title: The use of high-throughput sequencing methods for plant microRNA research

description: MicroRNA (miRNA) acts as a critical regulator of gene expression at post-transcriptional and occasionally transcriptional levels in plants. Identification of reliable miRNA genes, monitoring the procedures of transcription, processing and maturation of the miRNAs, quantification of the accumulation levels of the miRNAs in specific biological samples, and validation of miRNA–target interactions become the basis for thoroughly understanding of the miRNA-mediated regulatory networks and the underlying mechanisms. Great progresses have been achieved for sequencing technology. Based on the high degree of sequencing depth and coverage, the high-throughput sequencing (HTS, also called next-generation sequencing) technology provides unprecedentedly efficient way for genome-wide or transcriptome-wide studies. In this review, we will introduce several HTS platform-based methods useful for plant miRNA research, including RNA-seq (RNA sequencing), RNA-PET-seq (paired end tag sequencing of RNAs), sRNA-seq (small RNA sequencing), dsRNA-seq (double-stranded RNA sequencing), ssRNA-seq (single-stranded RNA sequencing) and degradome-seq (degradome sequencing). In particular, we will provide some special cases to illustrate the novel use of HTS methods for investigation of the processing modes of the miRNA precursors, identification of the RNA editing sites on miRNA precursors, mature miRNAs and target transcripts, re-examination of the current miRNA registries, and discovery of novel miRNA species and novel miRNA–target interactions. Summarily, we opinioned that integrative use of the above mentioned HTS methods could make the studies on miRNAs more efficient.
DOI: 10.6084/m9.figshare.1425528
title: NRP-1 data

description: Design of the expeirments that produced data for Figs 1 and 4
DOI: 10.6084/m9.figshare.1425528.v1
title: NRP-1 data

description: Design of the expeirments that produced data for Figs 1 and 4
DOI: 10.6084/m9.figshare.1425519.v2
title: The systematic approach to describing conformational rearrangements in G-quadruplexes

description: Conformational changes in DNA G-quadruplex (GQ)-forming regions affect genome function and, thus, compose an interesting research topic. Computer modelling may yield insight into quadruplex folding and rearrangement, particularly molecular dynamics simulations. Here, we show that specific parameters, which are distinct from those commonly used in DNA conformational analyses, must be introduced for adequate interpretation and, most importantly, convenient visual representation of the quadruplex modelling results. We report a set of parameters that comprehensively and systematically describe GQ geometry in dynamics. The parameters include those related to quartet planarity, quadruplex twist, and quartet stacking; they are used to quantitatively characterise various types of quadruplexes and rearrangements, such as quartet distortion/disruption or deviation/bulging of a single nucleotide from the quartet plane. Our approach to describing conformational changes in quadruplexes using the new parameters is exemplified by telomeric quadruplex rearrangement, and the benefits of applying this approach to analyse other structures are discussed.
DOI: 10.6084/m9.figshare.1425519.v1
title: The Systematic Approach to Describing Conformational Rearrangements in G-quadruplexes

description: Conformational changes in DNA G-quadruplex-forming regions affect genome function and, thus, compose an interesting research topic. Computer modelling may yield insight into quadruplex folding and rearrangement, particularly molecular dynamics simulations. Here, we show that specific parameters, which are distinct from those commonly used in DNA conformational analyses, must be introduced for adequate interpretation and, most importantly, convenient visual representation of the quadruplex modelling results. We report a set of parameters that comprehensively and systematically describe G-quadruplex geometry in dynamics. The parameters include those related to quartet planarity, quadruplex twist, and quartet stacking; they are used to quantitatively characterise various types of quadruplexes and rearrangements, such as quartet distortion/disruption or deviation/bulging of a single nucleotide from the quartet plane. Our approach to describing conformational changes in quadruplexes using the new parameters is exemplified by telomeric quadruplex rearrangement, and the benefits of applying this approach to analyse other structures are discussed.
DOI: 10.6084/m9.figshare.1425503
title: Wild-type yeast gene read counts from 48 replicate experiment

description: These data are RNA-seq read counts for 48 biological replicates of wild-type yeast. The reads were aligned to the Saccharomyces cerevisiae genome with Tophat and gene counts determined with htseq-count. Reference genome and gene annotations were taken from Ensembl. See the linked papers for more details and the source for the raw data.
DOI: 10.6084/m9.figshare.1425504
title: Kernel Probability Estimation

description: Demonstrations of a method for obtaining smoothed estimates of probability in binomial and multinomial time series.
DOI: 10.6084/m9.figshare.1425502
title: SNF2 knock-out yeast gene read counts from a 48 replicate experiment

description: These data are RNA-seq read counts for 48 biological replicates of SNF2 yeast knock-out. The reads were aligned to the Saccharomyces cerevisiae genome with Tophat and gene counts determined with htseq-count. Reference genome and gene annotations were taken from Ensembl. See the linked papers for more details and the source of the raw data.
DOI: 10.6084/m9.figshare.1425502.v1
title: SNF2 knock-out yeast gene read counts from a 48 replicate experiment

description: These data are RNA-seq read counts for 48 biological replicates of SNF2 yeast knock-out. The reads were aligned to the Saccharomyces cerevisiae genome with Tophat and gene counts determined with htseq-count. Reference genome and gene annotations were taken from Ensembl. See the linked papers for more details and the source of the raw data.
DOI: 10.6084/m9.figshare.1425504.v2
title: Kernel Probability Estimation

description: Demonstrations of a method for obtaining smoothed estimates of probability in binomial and multinomial time series.
DOI: 10.6084/m9.figshare.1425504.v1
title: Kernel Probability Estimation

description: Demonstrations of a method for obtaining smoothed estimates of probability in binomial and multinomial time series.
DOI: 10.6084/m9.figshare.1425492
title: Following the footsteps of chlamydial gene regulation

description: Regulation of gene expression ensures an organism responds to stimuli and undergoes proper development. While the regulatory networks in bacteria have been investigated in model microorganisms, nearly nothing is known about the evolution and plasticity of these networks in obligate, intracellular bacteria. The phylum Chlamydiae contains a vast array of host-associated microbes, including several human pathogens. The Chlamydiae are unique among obligate, intracellular bacteria as they undergo a complex bi-phasic developmental cycle in which large swaths of genes are temporally regulated. Coupled with the low number of transcription factors, these organisms offer a model to study the evolution of regulatory networks in intracellular organisms. We provide the first comprehensive analysis exploring the diversity and evolution of regulatory networks across the phylum. We utilized a comparative genomics approach to construct predicted co-regulatory networks, which unveiled genus and family specific regulatory motifs and architectures, most notably those of virulence-associated genes. Surprisingly, our analysis suggests that few regulatory components are conserved across the phylum, and those that are conserved are involved in the exploitation of the intracellular niche. Our study thus lends insight into a component of chlamydial evolution that has otherwise remained largely unexplored.
DOI: 10.6084/m9.figshare.1425492.v1
title: Following the footsteps of chlamydial gene regulation

description: Regulation of gene expression ensures an organism responds to stimuli and undergoes proper development. While the regulatory networks in bacteria have been investigated in model microorganisms, nearly nothing is known about the evolution and plasticity of these networks in obligate, intracellular bacteria. The phylum Chlamydiae contains a vast array of host-associated microbes, including several human pathogens. The Chlamydiae are unique among obligate, intracellular bacteria as they undergo a complex bi-phasic developmental cycle in which large swaths of genes are temporally regulated. Coupled with the low number of transcription factors, these organisms offer a model to study the evolution of regulatory networks in intracellular organisms. We provide the first comprehensive analysis exploring the diversity and evolution of regulatory networks across the phylum. We utilized a comparative genomics approach to construct predicted co-regulatory networks, which unveiled genus and family specific regulatory motifs and architectures, most notably those of virulence-associated genes. Surprisingly, our analysis suggests that few regulatory components are conserved across the phylum, and those that are conserved are involved in the exploitation of the intracellular niche. Our study thus lends insight into a component of chlamydial evolution that has otherwise remained largely unexplored.
DOI: 10.6084/m9.figshare.1425436
title: Maximum clade credibility tree from host association analysis

description: Phylogenetic tree from BEAST analysis to recontruct host associations. Phylogeny is best viewed in FigTree, where host associations can be viewed (should appear automatically, edit by /Appearance/Colour by: HostAssociation. Posterior supports for host association analysis can be viewed by setting Node or Branch Labels to HostAssociation.prob.
DOI: 10.6084/m9.figshare.1425431
title: BEAST alignment

description: Trimmed Gblocks alignment used for BEAST analysis.
DOI: 10.6084/m9.figshare.1425432
title: Supplementary data 1: sample ID, location and infection status.

description: Sample identification (by COI sequencing), collection location and date, and virus infection status of individual insects used for RNAseq.
DOI: 10.6084/m9.figshare.1425420
title: Dataset Hopstaken et al. 2015 PLOSONE

description: Data belonging to paper published in PLOSONE
DOI: 10.6084/m9.figshare.1425419
title: Supplementary data 2: taxa, accessions and host information

description: Table with ID number (used for constructing phylogenies), virus name, genbank accession, assigned host association for Bayesian state reconstruction analysis and host information.
DOI: 10.6084/m9.figshare.1425420.v1
title: Dataset Hopstaken et al. 2015 PLOSONE

description: Data belonging to paper published in PLOSONE
DOI: 10.6084/m9.figshare.1425431.v1
title: BEAST alignment

description: Trimmed Gblocks alignment used for BEAST analysis.
DOI: 10.6084/m9.figshare.1425406
title: Incidence of Category II and III Dog Bites among 5-14 year old children in El Nido estimated from passive and active surveillance, 2011 to 2012

description: Active surveillance At enrollment, a questionnaire was completed in order to collect the history of potential rabies exposures (animal bites and scratches) over the past 6 months in the cohort children. Information about a child’s possible rabies exposures was collected retrospectively through home visits, mobile phone contact, and through consultations with midwives and village health workers, teachers and neighbors. During the 18 months of follow-up beginning July 2011, active detection of rabies exposures was conducted every three months until December 2012 and included the interview of the exposed patient’s parent regarding incidents of contact with a suspected rabid animal. Parents were contacted and asked whether their child had experienced contact with a suspect rabid animal since the previous interview and follow-up forms were completed. All patients that had experienced a potential exposure during the previous three months were visited at home and standardized rabies exposure forms (REF) were completed. All follow-up questionnaires administered during the study were similar except the questionnaire provided in March 2012, in which questions regarding the PrEP were added. Also in 2012, a small survey was carried out of the parents of 328 randomly chosen children who were not vaccinated, to determine the reasons for this. During the follow-up period, the ABTC data were collected on all children with a reported contact with a suspect rabid animal. Every three months thereafter, an ABTC data retrieval form was completed for every rabies exposure consultation for a child included in the study cohort. Passive surveillance Data on animal bite consultations of children in the same age group as the study cohort at the ABTC were collected retrospectively for the period from January 2011 to December 2012 in order to establish a temporal trend of exposures. Bite incidence was calculated from the number of bites amongst children divided by the total number of children aged 5-14 years old based on the 2007 Population Census.
DOI: 10.6084/m9.figshare.1425407
title: Visual cue data multi-sensory control condition

description: Visual cue data of dot arrays constructed with an adaptation of the script of Gebuis and Reynvoet (2011) in which only the selected numerosities were adapted
DOI: 10.6084/m9.figshare.1425436.v3
title: Maximum clade credibility tree from host association analysis

description: Phylogenetic tree from BEAST analysis to recontruct host associations. Phylogeny is best viewed in FigTree, where host associations can be viewed by /Appearance/Colour by: HostAssociation. Posterior supports for host association analysis can be viewed by setting Node or Branch Labels to HostAssociation.prob.
DOI: 10.6084/m9.figshare.1425407.v1
title: Visual cue data multi-sensory control condition

description: Visual cue data of dot arrays constructed with an adaptation of the script of Gebuis and Reynvoet (2011) in which only the selected numerosities were adapted
DOI: 10.6084/m9.figshare.1425436.v5
title: Maximum clade credibility tree from host association analysis

description: Phylogenetic tree from BEAST analysis to recontruct host associations. Phylogeny is best viewed in FigTree, where host associations can be viewed (should appear automatically, edit by /Appearance/Colour by: HostAssociation. Posterior supports for host association analysis can be viewed by setting Node or Branch Labels to HostAssociation.prob.