cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7887848
title: Nuclear phylogeny and hypothesized allopolyploidization events in the Subtribe Otachyriinae (Paspaleae, Poaceae)

description: Otachyriinae Butzin, one of the three subtribes within the Paspaleae tribe of grasses, includes seven genera and approximately 35 species. Interestingly, this subtribe comprises species with C<sub>3</sub>, C<sub>3</sub>-C<sub>4</sub> intermediate, and C<sub>4</sub> photosynthesis. The circumscription of Otachyriinae has changed through time, and still varies among treatments in current use. The monophyly of this subtribe has been recovered in previous studies based on plastid markers. A phylogenetic study taking into account polyploidy and a low-copy nuclear gene (LCNG) is still lacking in Paspaleae. A phylogeny including data from a LCNG is paramount to uncover reticulated evolution within the group. The purpose of the present study was to reconstruct the evolutionary history of Otachyriinae, based on both chloroplast and LCNG DNA with a focus on polyploidization. Several incongruences between gene trees allowed us to explore relationships between diploid and polyploid taxa. Our study identified several promising topics for future studies: genetic allopolyploidy and autopolyploidy was here documented using the characteristic pattern of double-labelled gene trees. The molecular evidence indicates that at least 40% of species of Otachyriinae show phylogenetic signature of polyploidy (16 taxa appear double-labelled in the nuclear gene trees); furthermore, the results support an allopolyploid origin of at least nine taxa in the subtribe: <i>Rugoloa polygonata</i>, a species with unknown photosynthetic pathway, the proto-kranz species <i>Steinchisma laxum</i> and <i>Rugoloa hylaeica</i>, and the C<sub>3</sub> species <i>Hymenachne felliana</i>, <i>H. grumosa</i>, <i>H. hemitomon</i>, <i>H. donacifolia</i>, <i>H. pernambucense</i>, and <i>P. grande</i>. Also, our results confirm that the C<sub>4</sub> genus <i>Anthaenantia</i> is unambiguously monophyletic and show that <i>Anthaenantia lanata</i> is an autopolyploid. We recognized six genera within subtribe Otachyriinae: <i>Anthaenantia</i>, <i>Hymenachne</i>, <i>Otachyrium</i>, <i>Plagiantha</i>, <i>Rugoloa</i>, and <i>Steinchisma</i>. Finally, <i>Panicum</i> species with historically ambiguous placements, i.e. <i>P. condensatum</i>, <i>P. grande</i>, <i>P. harleyi</i>, <i>P. leptachne</i>, <i>P. longum</i>, and <i>P. stagnatile</i> were transferred to the genus <i>Hymenachne</i>.
DOI: 10.6084/m9.figshare.7887848.v1
title: Nuclear phylogeny and hypothesized allopolyploidization events in the Subtribe Otachyriinae (Paspaleae, Poaceae)

description: Otachyriinae Butzin, one of the three subtribes within the Paspaleae tribe of grasses, includes seven genera and approximately 35 species. Interestingly, this subtribe comprises species with C<sub>3</sub>, C<sub>3</sub>-C<sub>4</sub> intermediate, and C<sub>4</sub> photosynthesis. The circumscription of Otachyriinae has changed through time, and still varies among treatments in current use. The monophyly of this subtribe has been recovered in previous studies based on plastid markers. A phylogenetic study taking into account polyploidy and a low-copy nuclear gene (LCNG) is still lacking in Paspaleae. A phylogeny including data from a LCNG is paramount to uncover reticulated evolution within the group. The purpose of the present study was to reconstruct the evolutionary history of Otachyriinae, based on both chloroplast and LCNG DNA with a focus on polyploidization. Several incongruences between gene trees allowed us to explore relationships between diploid and polyploid taxa. Our study identified several promising topics for future studies: genetic allopolyploidy and autopolyploidy was here documented using the characteristic pattern of double-labelled gene trees. The molecular evidence indicates that at least 40% of species of Otachyriinae show phylogenetic signature of polyploidy (16 taxa appear double-labelled in the nuclear gene trees); furthermore, the results support an allopolyploid origin of at least nine taxa in the subtribe: <i>Rugoloa polygonata</i>, a species with unknown photosynthetic pathway, the proto-kranz species <i>Steinchisma laxum</i> and <i>Rugoloa hylaeica</i>, and the C<sub>3</sub> species <i>Hymenachne felliana</i>, <i>H. grumosa</i>, <i>H. hemitomon</i>, <i>H. donacifolia</i>, <i>H. pernambucense</i>, and <i>P. grande</i>. Also, our results confirm that the C<sub>4</sub> genus <i>Anthaenantia</i> is unambiguously monophyletic and show that <i>Anthaenantia lanata</i> is an autopolyploid. We recognized six genera within subtribe Otachyriinae: <i>Anthaenantia</i>, <i>Hymenachne</i>, <i>Otachyrium</i>, <i>Plagiantha</i>, <i>Rugoloa</i>, and <i>Steinchisma</i>. Finally, <i>Panicum</i> species with historically ambiguous placements, i.e. <i>P. condensatum</i>, <i>P. grande</i>, <i>P. harleyi</i>, <i>P. leptachne</i>, <i>P. longum</i>, and <i>P. stagnatile</i> were transferred to the genus <i>Hymenachne</i>.
DOI: 10.6084/m9.figshare.7887845.v1
title: New species and records of bioluminescent <i>Mycena</i> from Mexico

description: Seven species of bioluminescent fungi are recorded from the cloud forests in Mexico. Six represent new species belonging to the genus <i>Mycena</i>, whereas <i>Mycena globulispora</i> is a new distribution record for the country. Descriptions, illustrations, photographs, and an identification key to bioluminescent fungi species from Mexico are provided. Sequences of nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) region were generated for barcoding purposes and comparisons with similar species.
DOI: 10.6084/m9.figshare.7887836
title: Diversity of Saint Helena Island and zoogeography of zoantharians in the Atlantic Ocean: Jigsaw falling into place

description: Diversity surveys in isolated sites, such as oceanic islands, provide biogeographic data that can improve our analyses and knowledge of evolutionary processes in the oceans. Zoantharians (Cnidaria: Anthozoa) are common and widespread components of shallow-water reefs, but distributional analyses are scarce for this group. In this study, we collected Zoantharia specimens from around Saint Helena Island (STH) in the mid-Atlantic and identified species using external morphology and molecular data. Moreover, we compiled and analysed the most comprehensive distributional data for zoantharian species in the subtropical and tropical Atlantic Ocean to date. Our results show eight zoantharian species in STH, which includes seven new records for STH waters. Furthermore, all families and genera of the suborder Brachycnemina recorded are widespread in the Atlantic Ocean, including at least four amphi-Atlantic species. The Caribbean is the richness centre in the Atlantic Ocean for zoantharian species, a pattern similar to that observed for many other subtropical/tropical marine taxa. However, Zoantharia may have a lower endemism rate in some areas than other common reef animals, for example zooxanthellate scleractinian corals and reef fishes. Moreover, zoantharian species have a more extensive distribution than close-related taxa such as zooxanthellate scleractinian corals and hydrocorals in the Atlantic Ocean.
DOI: 10.6084/m9.figshare.7887836.v2
title: Diversity of Saint Helena Island and zoogeography of zoantharians in the Atlantic Ocean: Jigsaw falling into place

description: Diversity surveys in isolated sites, such as oceanic islands, provide biogeographic data that can improve our analyses and knowledge of evolutionary processes in the oceans. Zoantharians (Cnidaria: Anthozoa) are common and widespread components of shallow-water reefs, but distributional analyses are scarce for this group. In this study, we collected Zoantharia specimens from around Saint Helena Island (STH) in the mid-Atlantic and identified species using external morphology and molecular data. Moreover, we compiled and analysed the most comprehensive distributional data for zoantharian species in the subtropical and tropical Atlantic Ocean to date. Our results show eight zoantharian species in STH, which includes seven new records for STH waters. Furthermore, all families and genera of the suborder Brachycnemina recorded are widespread in the Atlantic Ocean, including at least four amphi-Atlantic species. The Caribbean is the richness centre in the Atlantic Ocean for zoantharian species, a pattern similar to that observed for many other subtropical/tropical marine taxa. However, Zoantharia may have a lower endemism rate in some areas than other common reef animals, for example zooxanthellate scleractinian corals and reef fishes. Moreover, zoantharian species have a more extensive distribution than close-related taxa such as zooxanthellate scleractinian corals and hydrocorals in the Atlantic Ocean.
DOI: 10.6084/m9.figshare.7887746
title: Dataset

description: The dataset used in the article :"Navarro, L. Morin, H., Bergeron, Y., Montoro Girona, M (2018). Changes in spatiotemporal patterns of 20th century spruce budworm outbreaks in eastern Canadian boreal forests. Front. Plant Sci. doi : 10.3389/fpls.2018.01905"
DOI: 10.6084/m9.figshare.7887755
title: 3_Definição valores refe.xlsx

description: Metadata used to create reference values for areas undergoing restoration in the Brazilian Atlantic Forest.
DOI: 10.6084/m9.figshare.7887788
title: gVCF_HG01281

description: 1000 Genomes gVCF mapped to hs37d5 for HG01281. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7887788.v1
title: gVCF_HG01281

description: 1000 Genomes gVCF mapped to hs37d5 for HG01281. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7887836.v1
title: Diversity of Saint Helena Island and zoogeography of zoantharians in the Atlantic Ocean: Jigsaw falling into place

description: Diversity surveys in isolated sites, such as oceanic islands, provide biogeographic data that can improve our analyses and knowledge of evolutionary processes in the oceans. Zoantharians (Cnidaria: Anthozoa) are common and widespread components of shallow-water reefs, but distributional analyses are scarce for this group. In this study, we collected Zoantharia specimens from around Saint Helena Island (STH) in the mid-Atlantic and identified species using external morphology and molecular data. Moreover, we compiled and analysed the most comprehensive distributional data for zoantharian species in the subtropical and tropical Atlantic Ocean to date. Our results show eight zoantharian species in STH, which includes seven new records for STH waters. Furthermore, all families and genera of the suborder Brachycnemina recorded are widespread in the Atlantic Ocean, including at least four amphi-Atlantic species. The Caribbean is the richness centre in the Atlantic Ocean for zoantharian species, a pattern similar to that observed for many other subtropical/tropical marine taxa. However, Zoantharia may have a lower endemism rate in some areas than other common reef animals, for example zooxanthellate scleractinian corals and reef fishes. Moreover, zoantharian species have a more extensive distribution than close-related taxa such as zooxanthellate scleractinian corals and hydrocorals in the Atlantic Ocean.
DOI: 10.6084/m9.figshare.7887740
title: Pilot Study Data from Exogenous glucocorticoids amplify the costs of infection by reducing resistance and tolerance, but effects are mitigated by co-infection

description: Data from the study piloting corticosterone implants.
DOI: 10.6084/m9.figshare.7887755.v1
title: 3_Definição valores refe.xlsx

description: Metadata used to create reference values for areas undergoing restoration in the Brazilian Atlantic Forest.
DOI: 10.6084/m9.figshare.7887737
title: Main Study Data from Exogenous glucocorticoids amplify the costs of infection by reducing resistance and tolerance, but effects are mitigated by co-infection

description: Data collected during the primary experiment.
DOI: 10.6084/m9.figshare.7887740.v1
title: Pilot Study Data from Exogenous glucocorticoids amplify the costs of infection by reducing resistance and tolerance, but effects are mitigated by co-infection

description: Data from the study piloting corticosterone implants.
DOI: 10.6084/m9.figshare.7887725
title: Supplemental data

description: Supplemental file containing Figures, Figure legends and Tables<br>
DOI: 10.6084/m9.figshare.7887737.v1
title: Main Study Data from Exogenous glucocorticoids amplify the costs of infection by reducing resistance and tolerance, but effects are mitigated by co-infection

description: Data collected during the primary experiment.
DOI: 10.6084/m9.figshare.7887725.v1
title: Supplemental data

description: Supplemental file containing Figures, Figure legends and Tables<br>
DOI: 10.6084/m9.figshare.7887746.v1
title: Untitled Item

description: The dataset used in the article :"Navarro, L. Morin, H., Bergeron, Y., Montoro Girona, M (2018). Changes in spatiotemporal patterns of 20th century spruce budworm outbreaks in eastern Canadian boreal forests. Front. Plant Sci. doi : 10.3389/fpls.2018.01905"
DOI: 10.6084/m9.figshare.7887314
title: Complete Endnotes - Plundered Empire: Acquiring Antiquities from Ottoman Lands

description: Most accounts of the history of collecting and museums concentrate on the European end. <i>Plundered Empire</i> details how and where antiquities were sought, uncovered, bartered, paid for or stolen, and any tribulations in getting them home. The book provides evidence for the continuing debate about the ethics of museum collections, with 19th century international competition the spur to spectacular acquisitions.
DOI: 10.6084/m9.figshare.7887368
title: Figure legeneds_Tables_suppl.docx

description: Supplemental Figures Legends and Tables<br>
DOI: 10.6084/m9.figshare.7887314.v1
title: Complete Endnotes - Plundered Empire: Acquiring Antiquities from Ottoman Lands

description: Most accounts of the history of collecting and museums concentrate on the European end. <i>Plundered Empire</i> details how and where antiquities were sought, uncovered, bartered, paid for or stolen, and any tribulations in getting them home. The book provides evidence for the continuing debate about the ethics of museum collections, with 19th century international competition the spur to spectacular acquisitions.
DOI: 10.25376/hra.7887281
title: 1-s2.0-S2213231718310437-mmc2.docx

description: Supplemental data about sirtuin-1 actvity assay
DOI: 10.6084/m9.figshare.7887308
title: Bibliometrics analysis of publications of China University of Petroleum and Sinopec

description: <b>The aim of this research:</b><br>Scientometric investigation of publication activity of China University of Petroleum and Sinopec during 2016-2019 years. Topic Mining from bibliografic texts by network analysis and clustering.<br><b>Bibliographic Resources: </b> Web of Science Core Collection; <br>Dimensions - https://app.dimensions.ai/discover/publication<br><b>Main query:</b><br>Results: 11,226<br>(from Web of Science Core Collection)You searched for: ORGANIZATION-ENHANCED: (China University of Petroleum OR Sinopec)Timespan: 2016-2019. Indexes: SCI-EXPANDED, ESCIWoS Sort by Times Cited 23 files savedrecs([0-22]).txt<b>Files description:</b><br>list of resources Dimensions.txt<br>list-of-files-0-7-KW-634.txt<br>Workflow-some queries from WoS.txt<br>files-15-22-WoS.txt<br><b>Main tools:</b><br><b>VOSviewer - </b>a software tool for constructing and visualizing bibliometric networks - http://www.vosviewer.com/<br><b>KH Coder </b>- a free software for quantitative content analysis or text mining - http://khcoder.net/en/<br><b>Notepad++</b> - a free source code editor - https://notepad-plus-plus.org/<br><b>SmoothCSV -</b> a powerful CSV file editor - https://smoothcsv.com/2/ <b>The Next To-Do List:</b><br>define the files format for the table of contents and the list of captions for pictures<br>visual comparison of graphical resources hosted on Figshare<br>bibliometrics on define topic refers to funding agencies (based on WoS and Scopus; We have no subscription for the dimensions.ai)Suggestions are welcome<br>
DOI: 10.6084/m9.figshare.7887248
title: Supplementary Material for: Transcriptional Changes following Cellular Knockdown of the Schizophrenia Risk Gene <b><i>SETD1A</i></b> Are Enriched for Common Variant Association with the Disorder

description: Loss of function mutations in <i>SETD1A</i> are the first experiment-wide significant findings to emerge from exome sequencing studies of schizophrenia. Although <i>SETD1A</i> is known to encode a histone methyltransferase, the consequences of reduced S<i>ETD1A</i> activity on gene expression in neural cells have, to date, been unknown. To explore transcriptional changes through which genetic perturbation of <i>SETD1A</i> could confer risk for schizophrenia, we have performed genome-wide gene expression profiling of a commonly used human neuroblastoma cell line in which <i>SETD1A</i> expression has been experimentally reduced using RNA interference (RNAi). We identified 1,031 gene expression changes that were significant in two separate RNAi conditions compared with control, including effects on genes of known neurodevelopmental importance such as <i>DCX</i> and <i>DLX5</i>. Genes that were differentially expressed following<i> SETD1A</i> knockdown were enriched for annotation to metabolic pathways, peptidase regulator activity and integrin-mediated regulation of cell adhesion. Moreover, differentially expressed genes were enriched for common variant association with schizophrenia, suggesting a degree of molecular convergence between this rare schizophrenia risk factor and susceptibility variants for the disorder operating more generally.
DOI: 10.6084/m9.figshare.7887242
title: ERR552106_2.fastq.gz

description: MTBC sample input fastq second pair
DOI: 10.6084/m9.figshare.7887368.v2
title: Figure legeneds_Tables_suppl.docx

description: Supplemental Figures Legends and Tables<br>
DOI: 10.25376/hra.7887281.v1
title: 1-s2.0-S2213231718310437-mmc2.docx

description: Supplemental data about sirtuin-1 actvity assay
DOI: 10.6084/m9.figshare.7887236
title: ERR552106_1.fastq.gz

description: MTBC fastq file first pair
DOI: 10.6084/m9.figshare.7887248.v1
title: Supplementary Material for: Transcriptional Changes following Cellular Knockdown of the Schizophrenia Risk Gene <b><i>SETD1A</i></b> Are Enriched for Common Variant Association with the Disorder

description: Loss of function mutations in <i>SETD1A</i> are the first experiment-wide significant findings to emerge from exome sequencing studies of schizophrenia. Although <i>SETD1A</i> is known to encode a histone methyltransferase, the consequences of reduced S<i>ETD1A</i> activity on gene expression in neural cells have, to date, been unknown. To explore transcriptional changes through which genetic perturbation of <i>SETD1A</i> could confer risk for schizophrenia, we have performed genome-wide gene expression profiling of a commonly used human neuroblastoma cell line in which <i>SETD1A</i> expression has been experimentally reduced using RNA interference (RNAi). We identified 1,031 gene expression changes that were significant in two separate RNAi conditions compared with control, including effects on genes of known neurodevelopmental importance such as <i>DCX</i> and <i>DLX5</i>. Genes that were differentially expressed following<i> SETD1A</i> knockdown were enriched for annotation to metabolic pathways, peptidase regulator activity and integrin-mediated regulation of cell adhesion. Moreover, differentially expressed genes were enriched for common variant association with schizophrenia, suggesting a degree of molecular convergence between this rare schizophrenia risk factor and susceptibility variants for the disorder operating more generally.
DOI: 10.6084/m9.figshare.7887242.v1
title: ERR552106_2.fastq.gz

description: MTBC sample input fastq second pair
DOI: 10.6084/m9.figshare.7887230
title: snpEffectPredictor.bin

description: SnpEff binary reference for H37Rv NC_000962 genome.
DOI: 10.6084/m9.figshare.7887236.v1
title: ERR552106_1.fastq.gz

description: MTBC fastq file first pair
DOI: 10.6084/m9.figshare.7887128
title: Supplementary Material for: Diversity of Nontuberculous Mycobacteria in Kuwait: Rapid Identification and Differentiation of <b><i>Mycobacterium</i></b> Species by Multiplex PCR, INNO-LiPA Mycobacteria v2 Assay and PCR Sequencing of rDNA

description: <b><i>Objective:</i></b> Nontuberculous mycobacteria (NTM) often cause disease that is clinically indistinguishable from tuberculosis. Specific identification is important as treatment varies according to <i>Mycobacterium</i> species causing the infection. This study used multiplex PCR (mPCR) assay for rapid differentiation of mycobacterial growth indicator tube 960 system (MGIT) cultures as <i>Mycobacterium tuberculosis</i> (MTB) or NTM together with INNO LiPA Mycobacteria v2 assay (LiPA) and/or PCR sequencing of rDNA for species-specific identification of selected MTB and all NTM isolates in Kuwait. <b><i>Materials and Methods:</i></b> DNA was extracted from MGIT cultures (<i>n</i> = 1,033) grown from 664 pulmonary and 369 extrapulmonary specimens from 1,033 suspected tuberculosis patients. mPCR was performed to differentiate MTB from NTM. LiPA was performed and results were interpreted according to kit instructions. rDNA was amplified and sequenced by using panmycobacterial primers. <b><i>Results:</i></b> mPCR identified 979 isolates as MTB, 53 as NTM and 1 isolate as mixed culture. LiPA and/or PCR sequencing confirmed 112 of 979 selected isolates as MTB. Mixed culture contained <i>M. tuberculosis</i> and <i>M. fortuitum</i>. LiPA yielded 12 patterns and identified 10 species/species complexes among 47 NTM, <i>M. kansasii</i> +<i> M. scrofulaceum</i> in one culture and 5 isolates only at genus level. PCR sequencing yielded more specific identification for 22 isolates at the species/subspecies level. <b><i>Conclusions:</i></b> mPCR rapidly differentiated MTB from NTM. LiPA identified 44 of 52 NTM isolates at the species/species complex level and 2 mixed cultures. PCR sequencing yielded more specific identification at the species/subspecies level. Rapid differentiation as MTB or NTM by mPCR, followed by species-specific NTM identification by LiPA/PCR sequencing is suitable for the proper management of mycobacterial infections in Kuwait.