cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1378789.v3
title: Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function

description: A growing number of gene-centric studies have highlighted the emerging significance of lncRNAs in cancer. However, these studies primarily focus on a single cancer type. Therefore, we conducted a pan-cancer analysis of lncRNAs comparing tumor and matched normal expression levels using RNA-Seq data from ∼ 3,000 patients in 8 solid tumor types. While the majority of differentially expressed lncRNAs display tissue-specific expression we discovered 229 lncRNAs with outlier or differential expression across multiple cancers, which we refer to as 'onco-lncRNAs'. Due to their consistent altered expression, we hypothesize that these onco-lncRNAs may have conserved oncogenic and tumor suppressive functions across cancers. To address this, we associated the onco-lncRNAs in biological processes based on their co-expressed protein coding genes. To validate our predictions, we experimentally confirmed cell growth dependence of 2 novel oncogenic lncRNAs, <i>onco-lncRNA-3</i> and <i>onco-lncRNA-12</i>, and a previously identified lncRNA <i>CCAT1</i>. Overall, we discovered lncRNAs that may have broad oncogenic and tumor suppressor roles that could significantly advance our understanding of cancer lncRNA biology.
DOI: 10.6084/m9.figshare.1378786.v3
title: <i>Symbiodinium tridacnidorum</i> sp. nov., a dinoflagellate common to Indo-Pacific giant clams, and a revised morphological description of <i>Symbiodinium microadriaticum</i> Freudenthal, emended Trench & Blank

description: ABSTRACTThe dinoflagellate genus <i>Symbiodinium</i> contains numerous genetically distinct lineages that appear ‘morphologically cryptic’. However, detailed morphological assessments of plate formulae visible in the motile phase (mastigote) of two distantly related <i>Symbiodinium</i> spp., representing Clades ‘A’ and ‘E’, were recently shown to be different. While there are several formally described species in Clade A, genetic evidence indicates that many more remain uncharacterized. We focused on closely related phylogenetic lineages within this group to examine whether differences in morphology can be used together with genetic and ecological evidence to describe new species. We found fixed differences in nuclear (internal transcribed spacer (ITS) and large subunit rDNA), chloroplast (cp23S) and mitochondrial (cob) gene sequences from cultured and field-collected samples of <i>Symbiodinium microadriaticum</i> (<i>sensu</i> Trench & Blank, 1987) and <i>Symbiodinium</i> sp. associated predominantly with giant clams and Pacific <i>Cassiopea</i> jellyfish (comprising members of the ITS2 <i>A3</i> lineage, <i>sensu</i> LaJeunesse 2001). Amphiesmal plate tabulations were formulated for the strain of <i>S. microadriaticum</i> (CCMP2464) used by Trench & Blank (1987) in their emended description, and two strains of type <i>A3</i> (CCMP832 and rt-272) cultured from Indo-Pacific giant clams in the subfamily Tridacninae. The Kofoidian plate formula for type <i>A3</i> consists of the small plate (x), the elongated amphiesmal vesicle (EAV), 5′, 6a, 8′′, 9–11s, a 2-row cingulum, 7′′′ and 3′′′′ (and occasionally 2′′′′), and is different from <i>S. microadriaticum</i>, which has a plate formula of x, EAV, 4′, 5a, 8′′, 9–13s, a 2-row cingulum, 6′′′ and 2′′′′. Based on morphological and genetic comparisons, we recognized <i>Symbiodinium tridacnidorum</i> sp. nov., a new Indo-Pacific species. The plate arrangement exhibited by <i>S. microadriaticum</i> appears to be more similar to the distantly related <i>S. natans</i> (also in Clade A). When the tabulations for all three Clade A species are compared with <i>S. voratum</i> (Clade E), the amount of morphological differentiation between species does not correspond to their degree of genetic divergence.
DOI: 10.6084/m9.figshare.1378789.v2
title: Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function

description: A growing number of gene-centric studies have highlighted the emerging significance of lncRNAs in cancer. However, these studies primarily focus on a single cancer type. Therefore, we conducted a pan-cancer analysis of lncRNAs comparing tumor and matched normal expression levels using RNA-Seq data from ∼ 3,000 patients in 8 solid tumor types. While the majority of differentially expressed lncRNAs display tissue-specific expression we discovered 229 lncRNAs with outlier or differential expression across multiple cancers, which we refer to as 'onco-lncRNAs'. Due to their consistent altered expression, we hypothesize that these onco-lncRNAs may have conserved oncogenic and tumor suppressive functions across cancers. To address this, we associated the onco-lncRNAs in biological processes based on their co-expressed protein coding genes. To validate our predictions, we experimentally confirmed cell growth dependence of 2 novel oncogenic lncRNAs, <i>onco-lncRNA-3</i> and <i>onco-lncRNA-12</i>, and a previously identified lncRNA <i>CCAT1</i>. Overall, we discovered lncRNAs that may have broad oncogenic and tumor suppressor roles that could significantly advance our understanding of cancer lncRNA biology.
DOI: 10.6084/m9.figshare.1378781
title: Joint Bayesian Modeling of Binomial and Rank Data for Primate Cognition

description: In recent years, substantial effort has been devoted to methods for analyzing data containing mixed response types, but such techniques typically do not include rank data among the response types. Some unique challenges exist in analyzing rank data, particularly when ties are prevalent. We present techniques for jointly modeling binomial and rank data using Bayesian latent variable models. We apply these techniques to compare the cognitive abilities of nonhuman primates based on their performance on 17 cognitive tasks scored on either a rank or binomial scale. To jointly model the rank and binomial responses, we assume that responses are implicitly determined by latent cognitive abilities. We then model the latent variables using random effects models, with identifying restrictions chosen to promote parsimonious prior specification and model inferences. Results from the primate cognitive data are presented to illustrate the methodology. Our results suggest that the ordering of the cognitive abilities of species varies significantly across tasks, suggesting a partially independent evolution of cognitive abilities in primates. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1378786.v2
title: <i>Symbiodinium tridacnidorum</i> sp. nov., a dinoflagellate common to Indo-Pacific giant clams, and a revised morphological description of <i>Symbiodinium microadriaticum</i> Freudenthal, emended Trench & Blank

description: ABSTRACTThe dinoflagellate genus <i>Symbiodinium</i> contains numerous genetically distinct lineages that appear ‘morphologically cryptic’. However, detailed morphological assessments of plate formulae visible in the motile phase (mastigote) of two distantly related <i>Symbiodinium</i> spp., representing Clades ‘A’ and ‘E’, were recently shown to be different. While there are several formally described species in Clade A, genetic evidence indicates that many more remain uncharacterized. We focused on closely related phylogenetic lineages within this group to examine whether differences in morphology can be used together with genetic and ecological evidence to describe new species. We found fixed differences in nuclear (internal transcribed spacer (ITS) and large subunit rDNA), chloroplast (cp23S) and mitochondrial (cob) gene sequences from cultured and field-collected samples of <i>Symbiodinium microadriaticum</i> (<i>sensu</i> Trench & Blank, 1987) and <i>Symbiodinium</i> sp. associated predominantly with giant clams and Pacific <i>Cassiopea</i> jellyfish (comprising members of the ITS2 <i>A3</i> lineage, <i>sensu</i> LaJeunesse 2001). Amphiesmal plate tabulations were formulated for the strain of <i>S. microadriaticum</i> (CCMP2464) used by Trench & Blank (1987) in their emended description, and two strains of type <i>A3</i> (CCMP832 and rt-272) cultured from Indo-Pacific giant clams in the subfamily Tridacninae. The Kofoidian plate formula for type <i>A3</i> consists of the small plate (x), the elongated amphiesmal vesicle (EAV), 5′, 6a, 8′′, 9–11s, a 2-row cingulum, 7′′′ and 3′′′′ (and occasionally 2′′′′), and is different from <i>S. microadriaticum</i>, which has a plate formula of x, EAV, 4′, 5a, 8′′, 9–13s, a 2-row cingulum, 6′′′ and 2′′′′. Based on morphological and genetic comparisons, we recognized <i>Symbiodinium tridacnidorum</i> sp. nov., a new Indo-Pacific species. The plate arrangement exhibited by <i>S. microadriaticum</i> appears to be more similar to the distantly related <i>S. natans</i> (also in Clade A). When the tabulations for all three Clade A species are compared with <i>S. voratum</i> (Clade E), the amount of morphological differentiation between species does not correspond to their degree of genetic divergence.
DOI: 10.6084/m9.figshare.1378778
title: Ancient and modern introduction of <i>Broussonetia papyrifera</i> ([L.] Vent.; Moraceae) into the Pacific: genetic, geographical and historical evidence

description: <i>Broussonetia papyrifera</i> (L.) Vent. (Moraceae), or paper mulberry, is a species of cultural importance in South East Asia, East Asia and the Pacific. Originally from mainland South East Asia or East Asia, this plant was introduced into the Pacific range by prehistoric Austronesian voyagers. We used non-coding internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA and inter-simple sequence repeat (ISSR) on 79 samples of <i>B. papyrifera</i> from different islands of Remote Oceania, and South East Asia and East Asia. Our results show an absence of genetic diversity in the introduced range of Remote Oceania, with the sole exception of Hawaii. By contrast, Asian samples show genetic diversity. The data obtained suggest a prehistoric human-mediated introduction of this species from East Asia to Remote Oceania and a second, possibly historic, human-mediated introduction to Hawaii.
DOI: 10.6084/m9.figshare.1378778.v2
title: Ancient and modern introduction of <i>Broussonetia papyrifera</i> ([L.] Vent.; Moraceae) into the Pacific: genetic, geographical and historical evidence

description: <i>Broussonetia papyrifera</i> (L.) Vent. (Moraceae), or paper mulberry, is a species of cultural importance in South East Asia, East Asia and the Pacific. Originally from mainland South East Asia or East Asia, this plant was introduced into the Pacific range by prehistoric Austronesian voyagers. We used non-coding internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA and inter-simple sequence repeat (ISSR) on 79 samples of <i>B. papyrifera</i> from different islands of Remote Oceania, and South East Asia and East Asia. Our results show an absence of genetic diversity in the introduced range of Remote Oceania, with the sole exception of Hawaii. By contrast, Asian samples show genetic diversity. The data obtained suggest a prehistoric human-mediated introduction of this species from East Asia to Remote Oceania and a second, possibly historic, human-mediated introduction to Hawaii.
DOI: 10.6084/m9.figshare.1378781.v2
title: Joint Bayesian Modeling of Binomial and Rank Data for Primate Cognition

description: In recent years, substantial effort has been devoted to methods for analyzing data containing mixed response types, but such techniques typically do not include rank data among the response types. Some unique challenges exist in analyzing rank data, particularly when ties are prevalent. We present techniques for jointly modeling binomial and rank data using Bayesian latent variable models. We apply these techniques to compare the cognitive abilities of non-human primates based on their performance on 17 cognitive tasks scored on either a rank or binomial scale. In order to jointly model the rank and binomial responses, we assume that responses are implicitly determined by latent cognitive abilities. We then model the latent variables using random effects models, with identifying restrictions chosen to promote parsimonious prior specification and model inferences. Results from the primate cognitive data are presented to illustrate the methodology. Our results suggest that the ordering of the cognitive abilities of species varies significantly across tasks, suggesting a partially independent evolution of cognitive abilities in primates.
DOI: 10.6084/m9.figshare.1378778.v1
title: Ancient and modern introduction of <i>Broussonetia papyrifera</i> ([L.] Vent.; Moraceae) into the Pacific: genetic, geographical and historical evidence

description: <i>Broussonetia papyrifera</i> (L.) Vent. (Moraceae), or paper mulberry, is a species of cultural importance in South East Asia, East Asia and the Pacific. Originally from mainland South East Asia or East Asia, this plant was introduced into the Pacific range by prehistoric Austronesian voyagers. We used non-coding internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA and inter-simple sequence repeat (ISSR) on 79 samples of <i>B. papyrifera</i> from different islands of Remote Oceania, and South East Asia and East Asia. Our results show an absence of genetic diversity in the introduced range of Remote Oceania, with the sole exception of Hawaii. By contrast, Asian samples show genetic diversity. The data obtained suggest a prehistoric human-mediated introduction of this species from East Asia to Remote Oceania and a second, possibly historic, human-mediated introduction to Hawaii.
DOI: 10.6084/m9.figshare.1378781.v3
title: Joint Bayesian Modeling of Binomial and Rank Data for Primate Cognition

description: In recent years, substantial effort has been devoted to methods for analyzing data containing mixed response types, but such techniques typically do not include rank data among the response types. Some unique challenges exist in analyzing rank data, particularly when ties are prevalent. We present techniques for jointly modeling binomial and rank data using Bayesian latent variable models. We apply these techniques to compare the cognitive abilities of nonhuman primates based on their performance on 17 cognitive tasks scored on either a rank or binomial scale. To jointly model the rank and binomial responses, we assume that responses are implicitly determined by latent cognitive abilities. We then model the latent variables using random effects models, with identifying restrictions chosen to promote parsimonious prior specification and model inferences. Results from the primate cognitive data are presented to illustrate the methodology. Our results suggest that the ordering of the cognitive abilities of species varies significantly across tasks, suggesting a partially independent evolution of cognitive abilities in primates. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1378781.v5
title: Joint Bayesian Modeling of Binomial and Rank Data for Primate Cognition

description: In recent years, substantial effort has been devoted to methods for analyzing data containing mixed response types, but such techniques typically do not include rank data among the response types. Some unique challenges exist in analyzing rank data, particularly when ties are prevalent. We present techniques for jointly modeling binomial and rank data using Bayesian latent variable models. We apply these techniques to compare the cognitive abilities of nonhuman primates based on their performance on 17 cognitive tasks scored on either a rank or binomial scale. To jointly model the rank and binomial responses, we assume that responses are implicitly determined by latent cognitive abilities. We then model the latent variables using random effects models, with identifying restrictions chosen to promote parsimonious prior specification and model inferences. Results from the primate cognitive data are presented to illustrate the methodology. Our results suggest that the ordering of the cognitive abilities of species varies significantly across tasks, suggesting a partially independent evolution of cognitive abilities in primates. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1378781.v4
title: Joint Bayesian Modeling of Binomial and Rank Data for Primate Cognition

description: In recent years, substantial effort has been devoted to methods for analyzing data containing mixed response types, but such techniques typically do not include rank data among the response types. Some unique challenges exist in analyzing rank data, particularly when ties are prevalent. We present techniques for jointly modeling binomial and rank data using Bayesian latent variable models. We apply these techniques to compare the cognitive abilities of nonhuman primates based on their performance on 17 cognitive tasks scored on either a rank or binomial scale. To jointly model the rank and binomial responses, we assume that responses are implicitly determined by latent cognitive abilities. We then model the latent variables using random effects models, with identifying restrictions chosen to promote parsimonious prior specification and model inferences. Results from the primate cognitive data are presented to illustrate the methodology. Our results suggest that the ordering of the cognitive abilities of species varies significantly across tasks, suggesting a partially independent evolution of cognitive abilities in primates. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1378770
title: Metagenomic and Metatranscriptomic Analyses of Bacterial Communities Derived From a Calcifying Karst Water Creek Biofilm and Tufa

description: Calcification of freshwater streams and the involvement of microorganisms in this process are still not fully understood. Here, we report on the metagenomic and metatranscriptomic analyses of bacterial community structures derived from an actively calcifying karst water creek biofilm and underlying tufa by employing next-generation sequencing technologies.The persistent and metabolically active bacterial communities were assessed by DNA-based and RNA-based 16S rRNA gene sequence analysis, respectively. We identified filamentous <i>Cyanobacteria</i> belonging to the <i>Oscillatoriales</i> as the predominant bacterial microorganisms in the biofilm. <i>Cyanobacteria</i> were accompanied by a high diversity of mainly aerobic members affiliated to different bacterial phyla. The second most abundant phylum was <i>Proteobacteria,</i> represented by the classes <i>Alphaproteobacteria</i>, <i>Betaproteobacteria</i>, <i>Gammaproteobacteria</i>, and <i>Deltaproteobacteria</i>. In addition, <i>Chloroflexi</i>, <i>Planctomycetes</i>, <i>Actinobacteria</i>, <i>Acidobacteria</i>, <i>Bacteroidetes</i>, <i>Spirochaetes</i>, and <i>Verrucomicrobia</i> were present in higher abundances (&gt;0.5%). Several of these phyla included potentially novel subgroups. The tufa stromatolite carbonate one centimeter below the surface exhibited a similar prokaryotic community as the superficial biofilm but showed a lower abundance of <i>Cyanobacteria</i> and a more diverse microbial community. We obtained insights into the <i>in situ</i> microbial metabolism by employing directed sequencing of enriched mRNA (cDNA) and subsequent taxonomic and functional analysis of biofilm-derived reads. High activities in photosynthesis, carbon and protein metabolism were indicated.
DOI: 10.6084/m9.figshare.1378770.v2
title: Metagenomic and Metatranscriptomic Analyses of Bacterial Communities Derived From a Calcifying Karst Water Creek Biofilm and Tufa

description: Calcification of freshwater streams and the involvement of microorganisms in this process are still not fully understood. Here, we report on the metagenomic and metatranscriptomic analyses of bacterial community structures derived from an actively calcifying karst water creek biofilm and underlying tufa by employing next-generation sequencing technologies.The persistent and metabolically active bacterial communities were assessed by DNA-based and RNA-based 16S rRNA gene sequence analysis, respectively. We identified filamentous <i>Cyanobacteria</i> belonging to the <i>Oscillatoriales</i> as the predominant bacterial microorganisms in the biofilm. <i>Cyanobacteria</i> were accompanied by a high diversity of mainly aerobic members affiliated to different bacterial phyla. The second most abundant phylum was <i>Proteobacteria,</i> represented by the classes <i>Alphaproteobacteria</i>, <i>Betaproteobacteria</i>, <i>Gammaproteobacteria</i>, and <i>Deltaproteobacteria</i>. In addition, <i>Chloroflexi</i>, <i>Planctomycetes</i>, <i>Actinobacteria</i>, <i>Acidobacteria</i>, <i>Bacteroidetes</i>, <i>Spirochaetes</i>, and <i>Verrucomicrobia</i> were present in higher abundances (&gt;0.5%). Several of these phyla included potentially novel subgroups. The tufa stromatolite carbonate one centimeter below the surface exhibited a similar prokaryotic community as the superficial biofilm but showed a lower abundance of <i>Cyanobacteria</i> and a more diverse microbial community. We obtained insights into the <i>in situ</i> microbial metabolism by employing directed sequencing of enriched mRNA (cDNA) and subsequent taxonomic and functional analysis of biofilm-derived reads. High activities in photosynthesis, carbon and protein metabolism were indicated.
DOI: 10.6084/m9.figshare.1378768
title: Diversity of Microscopic Green Algae (Chlorophyta) in Calcifying Biofilms of Two Karstic Streams in Germany

description: For the first time the diversity of microscopic green algae (Chlorophyta) from calcified biofilms of karstic streams was analyzed using a combined approach based on pure cultures, i.e., 18S rRNA gene sequencing and microscopic analyses. Our study focused on two creeks in Germany. A considerable diversity of 34 species of green microalgae comprising three classes, the Trebouxiophyceae, Chlorophyceae and Ulvophyceae, was recovered. The biofilms of both streams were rather different in their species compositions which may reflect that they are exposed to differed hydrochemical conditions. The shallow Westerhöfer creek harbored predominantly Trebouxiophyceae and exhibited higher Mg<sup>2+</sup> and SO<sub>4</sub><sup>2−</sup> concentrations. In contrast, the deeper, longer and spatially more heterogeneous Deinschwanger creek harbored numerous species of Chlorophyceae. A lower number of species from the Ulvophyceae were spread on both studied streams. The closest relatives of the identified species were from other freshwater habitats, but mostly from phytoplankton. However, also several species we recovered from freshwater for the first time; so far they have been known from terrestrial habitats only. Less than half of the recovered species could be identified with names at the species level based on high sequence identities with available sequences from named reference strains. Most recovered species could not be identified with names to species level, i.e., they may represent species for which no 18S rRNA gene sequence have become available yet or which have been retrieved for the first time. The genus <i>Gongrosira</i> Kützing, often reported from freshwater tufa-stromatolites, was found to represent most likely a collective morphotype formed by several genera nested within the Ulvophyceae.