cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25934/pr00004988.1
title: Available IPD datapackage for study 'A trial to assess the effectiveness and tolerance of paroxetine by double-blind comparison with amitriptyline in the treatment of depressed patients in General Practice'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.25934/pr00004986.1
title: Available IPD datapackage for study 'Early Clinical Evaluation of a New Antidepressant: A Double-Blind Parallel Study Comparing Paroxetine 30mg Daily with Amitriptyline 150mg Daily'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.25934/pr00005000.1
title: Available IPD datapackage for study 'A Multicentre, Double-blind Randomised Dose Titration Study Comparing the Efficacy and Safety Profiles of an Increasing Dose Regimen of Oral Paroxetine and Oral Amitriptyline in Adult Patients with Major Depression'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.34740/kaggle/dsv/3918847
title: COVID Vaccination in World (updated daily)
DOI: 10.3886/e174721
title: 2022 T32 Program Evaluation

description: This repository includes data collection instruments and survey data for the paper: <b>Developing evidence-based resources for evaluating postgraduate trainees in the biomedical sciences. </b>Data collection instruments include a logic model template, interview guides, and survey template used to collect data from T32/R25 program directors. The survey data reflects responses from program directors. <br><br><br><br><br>
description: Response Rates: 81.81%<br>
description: Presence of Common Scales: Ratings (1-5) and rankings (1-6)<br>
description: Purposive sampling<br>
description: web-based survey;
DOI: 10.3886/e174721v1
title: 2022 T32 Program Evaluation

description: This repository includes data collection instruments and survey data for the paper: <b>Developing evidence-based resources for evaluating postgraduate trainees in the biomedical sciences. </b>Data collection instruments include a logic model template, interview guides, and survey template used to collect data from T32/R25 program directors. The survey data reflects responses from program directors. <br><br><br><br><br>
description: Response Rates: 81.81%<br>
description: Presence of Common Scales: Ratings (1-5) and rankings (1-6)<br>
description: Purposive sampling<br>
description: web-based survey;
DOI: 10.5281/zenodo.6811341
title: SORTIE MIVM Level 2

description: SORTIE IVM Level 2 data
DOI: 10.5281/zenodo.4611464
title: SORTIE MIVM Level 2

description: SORTIE IVM Level 2 data
DOI: 10.6084/m9.figshare.20272410
title: Codificação do autor dos textos selecionados para o trabalho

description: Tabela de codificação do autor relativa aos artigos selecionados
DOI: 10.6084/m9.figshare.20272410.v1
title: Codificação do autor dos textos selecionados para o trabalho

description: Tabela de codificação do autor relativa aos artigos selecionados
DOI: 10.6084/m9.figshare.19793758.v1
title: Supplementary Material

description: Supplementary Material for 'Pangenome evolution in Escherichia coli is sequence type, not phylogroup, specific'. <br> pangenome_data.zip contains the download list from Enterobase, gene presence/absence file, and linear reference genome for each sequence type.
DOI: 10.5281/zenodo.6811386
title: Zoanthus solanderi zanfona 1

description: .
DOI: 10.5281/zenodo.6811385
title: Zoanthus solanderi zanfona 1

description: .
DOI: 10.6084/m9.figshare.20060684
title: A phylogenetic overview of <i>Squamanita</i>, with descriptions of nine new species and four new combinations

description: Nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode) sequence data from eight type specimens of previously described <i>Squamanita</i> species were obtained. Phylogenetic analysis of ITS and partial nuc 28S rDNA data revealed <i>Squamanita</i> as paraphyletic splitting into two monophyletic groups, which we recognize as the genera <i>Squamanita</i> and <i>Dissoderma</i>. We accept 14 <i>Squamanita</i> and nine <i>Dissoderma</i> species, provide the first sequences of 13 of these, and describe six new species of <i>Squamanita</i> and three new species of <i>Dissoderma</i>. We transfer three species of <i>Squamanita</i> into <i>Dissoderma</i>, one into <i>Cystoderma</i>, and treat <i>S. basii</i> and <i>S. umbilicata</i> as synonyms of <i>D. paradoxum. Squamanita</i> can be distinguished from <i>Dissoderma</i> by the generally larger fleshier basidiomata with a tricholomatoid or amanitoid stature and yellowish to tawny brown pileus and often similarly colored stipe. Most species have cheilo- and pleurocystidia. Species of <i>Dissoderma</i> are small, collybioid or mycenoid, lack cystidia, and the pileus and often upper stipe are purplish gray. Both genera parasitize basidiomata of other agarics.
DOI: 10.6084/m9.figshare.20006729
title: In vitro thermal tolerance of a hypervirulent lineage of <i>Batrachochytrium dendrobatidis</i>: Growth arrestment by elevated temperature and recovery following thermal treatment

description: Chytridiomycosis, an emerging infectious disease caused by <i>Batrachochytrium dendrobatidis</i> (Bd), poses a serious threat to amphibians. The thermal optimum of Bd is lower than that of most amphibians, providing an opportunity to cure infected individuals with elevated temperature. However, this approach presupposes detailed knowledge about the thermal tolerance of the fungus. To determine the temperature that may effectively reduce infection burdens in vivo, detailed in vitro studies are needed to characterize thermal tolerance of the fungus without complexities introduced by the species-specific characteristics of hosts’ immune systems. The aim of our study was to evaluate the thermal tolerance of a hypervirulent isolate of Bd, considering the limits of its thermal tolerance and its capacity to rebound following heat treatment. We incubated Bd cell cultures at five different temperatures (21, 25.5, 27, 29, or 30.5 C) for one of six exposure durations (3, 4, 5, 6, 7, or 8 days) and subsequently counted the number of zoospores to assess the temperature dependence of Bd growth. We observed intensive Bd growth at 21 C. At 25.5 C, the number of zoospores also increased over time, but the curve plateaued at about half of the maximum values observed in the lower temperature treatment. At temperatures of 27 C and above, the fungus showed no measurable growth. However, when we moved the cultures back to 21 C after the elevated temperature treatments, we observed recovery of Bd growth in all cultures previously treated at 27 C. At 29 C, a treatment duration of 8 days was necessary to prevent recovery of Bd growth, and at 30.5 C a treatment duration of 5 days was needed to achieve the same result, revealing that these moderately elevated temperatures applied for only a few days have merely a fungistatic rather than a fungicidal effect under in vitro conditions.
DOI: 10.6084/m9.figshare.20039946
title: <i>Fusarium abutilonis</i> and <i>F. guadeloupense</i>, two novel species in the <i>Fusarium buharicum</i> clade supported by multilocus molecular phylogenetic analyses

description: This study was conducted to elucidate evolutionary relationships and species diversity within the <i>Fusarium buharicum</i> species complex (FBSC). We also evaluate the potential of these species to produce mycotoxins and other bioactive secondary metabolites. Maximum likelihood and maximum parsimony analyses of sequences from portions of four marker loci (ITS rDNA, <i>TEF1, RPB1</i>, and <i>RPB2</i>) and the combined 4495 bp data set support recognition of seven genealogically exclusive species within the FBSC. Two of the three newly discovered species are formally described as <i>F. abutilonis</i> and <i>F. guadeloupense</i> based on concordance of gene genealogies and morphological data. <i>Fusarium abutilonis</i> induces leaf, stem, and root lesions on several weedy Malvaceae (<i>Abution theophrasti, Anoda cristata, Sida spinosa</i>) and a fabaceous host (<i>Senna obtusifolia</i>) in North America and also was recovered from soil in New Caledonia. <i>Fusarium abutilonis</i>, together with its unnamed sister, <i>Fusarium</i> sp. ex common marsh mallow (<i>Hibiscus moscheutos</i>) from Washington state, and <i>F. buharicum</i> pathogenic to cotton and kenaf in Russia and Iran, respectively, were strongly supported as a clade of malvaceous pathogens. The four other species of the FBSC are not known to be phytopathogenic; however, <i>F. guadeloupense</i> was isolated from human blood in Texas and soil in Guadeloupe. The former isolate is unique because it represents the only known case of a fusarial infection disseminated hematogenously by a species lacking microconidia and the only documented fusariosis caused by a member of the FBSC. Whole genome sequence data and extracts of cracked maize kernel cultures were analyzed to assess the potential of FBSC isolates to produce mycotoxins, pigments, and phytohormones.
DOI: 10.6084/m9.figshare.20051848.v1
title: <i>Cordyceps mexicana</i> sp. nov., parasitizing <i>Paradirphia</i> sp. moths: A new sister species of the <i>Cordyceps militaris</i> complex, distributed in central Mexican <i>Quercus-Pinus</i> mixed forests

description: <i>Cordyceps</i> s.l. is a paraphyletic group of ascomycete fungi that exhibit multifunctional lifestyles, that is, as saprotrophs, endophytes, and pathogens of insects, spiders, fungi, and grasses. The family Cordycipitaceae includes macroscopically similar species that have been erroneously considered to be conspecific with <i>Cordyceps militaris</i>. In this study, we describe a new species within the <i>C. militaris</i> complex that is distributed in the <i>Quercus-Pinus</i> forests of central Mexico on the basis of its morphology, phylogenetic relationships, and life cycle. Phylogenetically, <i>Cordyceps mexicana</i> is a well-supported new sister species of the <i>C. militaris</i> complex. It is distinguished by the morphology of its conidiophore, host association, and geographic distribution. This species parasitizes pupae of <i>Paradirphia</i> sp. (Lepidoptera: Saturniidae: Hemileucinae) and might be macroscopically confused with <i>C. militaris</i>. Its stromata are large, can measure up to 10 cm in length, and the fertile part is always bright yellow. This species develops whitish mycelial cords that emerge from the stromata and grow toward the host. Microscopically, it develops asci with filiform ascospores disarticulating in part-spores. Its life cycle and geographic distribution are also discussed.
DOI: 10.6084/m9.figshare.20020515
title: Transcriptome analysis of <i>Epichloë</i> strains in tall fescue in response to drought stress

description: <i>Epichloë coenophiala</i>, a systemic fungal symbiont (endophyte) of tall fescue (<i>Lolium arundinaceum</i>), has been documented to confer to this grass better persistence than plants lacking the endophyte, especially under stress conditions such as drought. The response, if any, of the endophyte to imposition of stress on the host plant has not been characterized previously. Therefore, we investigated effects on gene expression by <i>E. coenophiala</i> and a related endophyte when plant-endophyte symbiota were subjected to acute water-deficit stress. Plants harboring different endophyte strains were grown in sand in the greenhouse, then half were deprived of water for 48 h and the other half were watered controls. RNA was isolated from different plant tissues, and mRNA sequencing (RNA-seq) was conducted to identify genes that were differentially expressed comparing stress treatment with control. We compared two different plants harboring the common toxic <i>E. coenophiala</i> strain (CTE) and two non–ergot-alkaloid-producing <i>Epichloë</i> strains in tall fescue pseudostems, and in a second experiment we compared responses of <i>E. coenophiala</i> CTE in plant pseudostem and crown tissues. The endophytes responded to the stress with increased expression of genes involved in oxidative stress response, oxygen radical detoxification, C-compound carbohydrate metabolism, heat shock, and cellular transport pathways. The magnitude of fungal gene responses during stress varied among plant-endophyte symbiota. Responses in pseudostems and crowns involved some common pathways as well as some tissue-specific pathways. The fungal response to water-deficit stress involved gene expression changes in similar pathways that have been documented for plant stress responses, indicating that <i>Epichloë</i> spp. and their host plants either coordinate stress responses or separately activate similar stress response mechanisms that work together for mutual protection.
DOI: 10.6084/m9.figshare.20020515.v1
title: Transcriptome analysis of <i>Epichloë</i> strains in tall fescue in response to drought stress

description: <i>Epichloë coenophiala</i>, a systemic fungal symbiont (endophyte) of tall fescue (<i>Lolium arundinaceum</i>), has been documented to confer to this grass better persistence than plants lacking the endophyte, especially under stress conditions such as drought. The response, if any, of the endophyte to imposition of stress on the host plant has not been characterized previously. Therefore, we investigated effects on gene expression by <i>E. coenophiala</i> and a related endophyte when plant-endophyte symbiota were subjected to acute water-deficit stress. Plants harboring different endophyte strains were grown in sand in the greenhouse, then half were deprived of water for 48 h and the other half were watered controls. RNA was isolated from different plant tissues, and mRNA sequencing (RNA-seq) was conducted to identify genes that were differentially expressed comparing stress treatment with control. We compared two different plants harboring the common toxic <i>E. coenophiala</i> strain (CTE) and two non–ergot-alkaloid-producing <i>Epichloë</i> strains in tall fescue pseudostems, and in a second experiment we compared responses of <i>E. coenophiala</i> CTE in plant pseudostem and crown tissues. The endophytes responded to the stress with increased expression of genes involved in oxidative stress response, oxygen radical detoxification, C-compound carbohydrate metabolism, heat shock, and cellular transport pathways. The magnitude of fungal gene responses during stress varied among plant-endophyte symbiota. Responses in pseudostems and crowns involved some common pathways as well as some tissue-specific pathways. The fungal response to water-deficit stress involved gene expression changes in similar pathways that have been documented for plant stress responses, indicating that <i>Epichloë</i> spp. and their host plants either coordinate stress responses or separately activate similar stress response mechanisms that work together for mutual protection.
DOI: 10.6084/m9.figshare.20006729.v1
title: In vitro thermal tolerance of a hypervirulent lineage of <i>Batrachochytrium dendrobatidis</i>: Growth arrestment by elevated temperature and recovery following thermal treatment

description: Chytridiomycosis, an emerging infectious disease caused by <i>Batrachochytrium dendrobatidis</i> (Bd), poses a serious threat to amphibians. The thermal optimum of Bd is lower than that of most amphibians, providing an opportunity to cure infected individuals with elevated temperature. However, this approach presupposes detailed knowledge about the thermal tolerance of the fungus. To determine the temperature that may effectively reduce infection burdens in vivo, detailed in vitro studies are needed to characterize thermal tolerance of the fungus without complexities introduced by the species-specific characteristics of hosts’ immune systems. The aim of our study was to evaluate the thermal tolerance of a hypervirulent isolate of Bd, considering the limits of its thermal tolerance and its capacity to rebound following heat treatment. We incubated Bd cell cultures at five different temperatures (21, 25.5, 27, 29, or 30.5 C) for one of six exposure durations (3, 4, 5, 6, 7, or 8 days) and subsequently counted the number of zoospores to assess the temperature dependence of Bd growth. We observed intensive Bd growth at 21 C. At 25.5 C, the number of zoospores also increased over time, but the curve plateaued at about half of the maximum values observed in the lower temperature treatment. At temperatures of 27 C and above, the fungus showed no measurable growth. However, when we moved the cultures back to 21 C after the elevated temperature treatments, we observed recovery of Bd growth in all cultures previously treated at 27 C. At 29 C, a treatment duration of 8 days was necessary to prevent recovery of Bd growth, and at 30.5 C a treatment duration of 5 days was needed to achieve the same result, revealing that these moderately elevated temperatures applied for only a few days have merely a fungistatic rather than a fungicidal effect under in vitro conditions.
DOI: 10.6084/m9.figshare.20060645
title: <i>Diachea mitchellii</i>: A new myxomycete species from high elevation forests in the tropical Andes of Peru

description: A new species of the genus <i>Diachea</i> (order Physarales, Myxomycetes, Amoebozoa) is described from Peru. Relevant details on spore germination, as well as morphological and phylogenetic data, are provided. At first glance, the new species shares some morphological similarities with both <i>D. leucopodia</i>, type of the genus, and <i>D. koazei</i>, but it strikingly differs from all other species of its genus by combining a short dark stalk, with a reticulate columella, and clustered spores. Moreover, it seems to be the only species of <i>Diachea</i> exclusively associated with <i>Polylepis</i> tropical forests at elevations above 3500 m. Apart from a comprehensive morphological study of 31 specimens, we here provide phylogenetic evidence to confirm the inclusion of this species in the genus <i>Diachea</i>. Specifically, our phylogenetic analyses of the nuclear 18S rDNA (18S), mitochondrial 17S rDNA (17S), and elongation factor-1 alpha (<i>EF-1α</i>) genes show that the new species is related to <i>D. leucopodia</i> and <i>D. bulbillosa</i>. The remarkably different morphological characters distinguishing the new <i>Diachea</i> from all other species of its genus, along with its particular ecological preferences and geographic distribution, indicate that it is a distinct entity deserving recognition as an independent species.
DOI: 10.6084/m9.figshare.20060645.v1
title: <i>Diachea mitchellii</i>: A new myxomycete species from high elevation forests in the tropical Andes of Peru

description: A new species of the genus <i>Diachea</i> (order Physarales, Myxomycetes, Amoebozoa) is described from Peru. Relevant details on spore germination, as well as morphological and phylogenetic data, are provided. At first glance, the new species shares some morphological similarities with both <i>D. leucopodia</i>, type of the genus, and <i>D. koazei</i>, but it strikingly differs from all other species of its genus by combining a short dark stalk, with a reticulate columella, and clustered spores. Moreover, it seems to be the only species of <i>Diachea</i> exclusively associated with <i>Polylepis</i> tropical forests at elevations above 3500 m. Apart from a comprehensive morphological study of 31 specimens, we here provide phylogenetic evidence to confirm the inclusion of this species in the genus <i>Diachea</i>. Specifically, our phylogenetic analyses of the nuclear 18S rDNA (18S), mitochondrial 17S rDNA (17S), and elongation factor-1 alpha (<i>EF-1α</i>) genes show that the new species is related to <i>D. leucopodia</i> and <i>D. bulbillosa</i>. The remarkably different morphological characters distinguishing the new <i>Diachea</i> from all other species of its genus, along with its particular ecological preferences and geographic distribution, indicate that it is a distinct entity deserving recognition as an independent species.
DOI: 10.6084/m9.figshare.20051848
title: <i>Cordyceps mexicana</i> sp. nov., parasitizing <i>Paradirphia</i> sp. moths: A new sister species of the <i>Cordyceps militaris</i> complex, distributed in central Mexican <i>Quercus-Pinus</i> mixed forests

description: <i>Cordyceps</i> s.l. is a paraphyletic group of ascomycete fungi that exhibit multifunctional lifestyles, that is, as saprotrophs, endophytes, and pathogens of insects, spiders, fungi, and grasses. The family Cordycipitaceae includes macroscopically similar species that have been erroneously considered to be conspecific with <i>Cordyceps militaris</i>. In this study, we describe a new species within the <i>C. militaris</i> complex that is distributed in the <i>Quercus-Pinus</i> forests of central Mexico on the basis of its morphology, phylogenetic relationships, and life cycle. Phylogenetically, <i>Cordyceps mexicana</i> is a well-supported new sister species of the <i>C. militaris</i> complex. It is distinguished by the morphology of its conidiophore, host association, and geographic distribution. This species parasitizes pupae of <i>Paradirphia</i> sp. (Lepidoptera: Saturniidae: Hemileucinae) and might be macroscopically confused with <i>C. militaris</i>. Its stromata are large, can measure up to 10 cm in length, and the fertile part is always bright yellow. This species develops whitish mycelial cords that emerge from the stromata and grow toward the host. Microscopically, it develops asci with filiform ascospores disarticulating in part-spores. Its life cycle and geographic distribution are also discussed.
DOI: 10.5281/zenodo.6811400
title: Supplement to: Enhanced surveillance of monkeypox in Bas-Uélé, Democratic Republic of Congo: the limitations of symptom-based case definitions

description: This repository contains data and R code which are supplements to: <em>Enhanced surveillance of monkeypox in Bas-Uélé, Democratic Republic of Congo: the limitations of symptom-based case definitions</em><br> Gaspard Mande, Innocent Akonda, Anja De Weggheleire, Isabel Brosius, Laurens Liesenborghs, Emmanuel Bottieau, Noam Ross, Guy Crispin Gembue, Robert Colebunders, Erik Verheyen Ngonda Daulya, Herwig Leirsh, and Anne Laudisoit (2022). A data dictionary and instructions for reproducing the analysis are provided. Details can be found in the README.md file.