cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21286227
title: Pangenomics of Candidatus Bipolaricaulota in hydrothermal aquifers of Biga Peninsula, Turkey

description: We surveyed the microbial diversity of eleven different deep geothermal aquifers and springs across the tectonically active Biga Peninsula (Turkey), a hydrothermal setting that is historically undersampled for environmental microbial community assessments. Across geothermal settings ranging in temperature from 35-80 oC, one the most highly represented groups was affiliated with the uncultivated group ‘<em>Candidatus</em> Bipolaricaulota’.
DOI: 10.6084/m9.figshare.21286227.v1
title: Pangenomics of Candidatus Bipolaricaulota in hydrothermal aquifers of Biga Peninsula, Turkey

description: We surveyed the microbial diversity of eleven different deep geothermal aquifers and springs across the tectonically active Biga Peninsula (Turkey), a hydrothermal setting that is historically undersampled for environmental microbial community assessments. Across geothermal settings ranging in temperature from 35-80 oC, one the most highly represented groups was affiliated with the uncultivated group ‘<em>Candidatus</em> Bipolaricaulota’.
DOI: 10.5281/zenodo.7152259
title: Laboratory risk factors for mortality in severe and critical COVID-19 patients admitted to the ICU

description: Data legends
DOI: 10.5281/zenodo.7152249
title: Combined effects of stream hydrology and land use on basin-scale hyporheic zone denitrification in the Columbia River Basin

description: <strong>This data includes inputs and outputs of a coupled carbon-nitrogen river corridor model (RCM) for the Columbia River Basin and sensitivity results with varying substrate concentrations, and random forest model results with key model inputs/watershed/stream variables. The detailed descriptions of the individual files are included in the readme.txt file. </strong>
description: This research was supported by the Department of Energy (DOE), Office of Science (SC) Biological and Environmental Research (BER) program, as part of BER's Environmental System Science (ESS) program. This contribution originates from the River Corridor Scientific Focus Area (SFA) at Pacific Northwest National Laboratory (PNNL). This research used resources from the National Energy Research Scientific Computing Center, a DOE-SC User Facility. PNNL is operated for DOE by Battelle Memorial Institute under contract DE-AC05-76RL01830.
DOI: 10.5281/zenodo.7152248
title: Combined effects of stream hydrology and land use on basin-scale hyporheic zone denitrification in the Columbia River Basin

description: <strong>This data includes inputs and outputs of a coupled carbon-nitrogen river corridor model (RCM) for the Columbia River Basin and sensitivity results with varying substrate concentrations, and random forest model results with key model inputs/watershed/stream variables. The detailed descriptions of the individual files are included in the readme.txt file. </strong>
description: This research was supported by the Department of Energy (DOE), Office of Science (SC) Biological and Environmental Research (BER) program, as part of BER's Environmental System Science (ESS) program. This contribution originates from the River Corridor Scientific Focus Area (SFA) at Pacific Northwest National Laboratory (PNNL). This research used resources from the National Energy Research Scientific Computing Center, a DOE-SC User Facility. PNNL is operated for DOE by Battelle Memorial Institute under contract DE-AC05-76RL01830.
DOI: 10.6084/m9.figshare.19524883
title: New molecular markers for distinguishing the main phylogenetic lineages within <i>Alternaria</i> section <i>Alternaria</i>

description: Several members of <i>Alternaria</i> section <i>Alternaria</i> are economically important plant-pathogenic fungi that cause disease on a wide range of host types and plant tissues. The production of <i>Alternaria</i>-derived mycotoxins can lead to significant post-harvest losses due to contamination of agricultural products. Multiple <i>Alternaria</i> species are listed as regulated organisms, which are monitored by international plant protection programmes. These taxa often share high levels of both morphological and phylogenetic similarity, and the establishment of molecular markers that are able to distinguish among them unambiguously has proven to be quite challenging. Previously, we examined fine-scale genome-wide phylogenetic patterns and proposed a list of candidate genes for development into informative markers that are diagnostic for the main section <i>Alternaria</i> lineages. Here, we design primer sets and sequence three new markers (<i>ASA-05, ASA-10, ASA-19</i>) in order to evaluate their diagnostic performance. Sequence data for 49 new independent test taxa were combined with existing data for 38 taxa, and phylogenetic analyses revealed that, in general, the new molecular markers consistently classified section <i>Alternaria</i> strains into one of the main lineages. A discrepancy among the three markers for lineage assignment was observed only for one strain. We also sequenced a commonly used marker in molecular phylogenetics of fungi (<i>rpb2</i>, RNA polymerase II second largest su bunit) and found it was outperformed by all three of the new markers. We suggest that an <i>ASA</i> marker presented here could form the basis of a convenient one-locus test for rapid and routine diagnostic screening of unknown section <i>Alternaria</i> strains.
DOI: 10.6084/m9.figshare.19524883.v2
title: New molecular markers for distinguishing the main phylogenetic lineages within <i>Alternaria</i> section <i>Alternaria</i>

description: Several members of <i>Alternaria</i> section <i>Alternaria</i> are economically important plant-pathogenic fungi that cause disease on a wide range of host types and plant tissues. The production of <i>Alternaria</i>-derived mycotoxins can lead to significant post-harvest losses due to contamination of agricultural products. Multiple <i>Alternaria</i> species are listed as regulated organisms, which are monitored by international plant protection programmes. These taxa often share high levels of both morphological and phylogenetic similarity, and the establishment of molecular markers that are able to distinguish among them unambiguously has proven to be quite challenging. Previously, we examined fine-scale genome-wide phylogenetic patterns and proposed a list of candidate genes for development into informative markers that are diagnostic for the main section <i>Alternaria</i> lineages. Here, we design primer sets and sequence three new markers (<i>ASA-05, ASA-10, ASA-19</i>) in order to evaluate their diagnostic performance. Sequence data for 49 new independent test taxa were combined with existing data for 38 taxa, and phylogenetic analyses revealed that, in general, the new molecular markers consistently classified section <i>Alternaria</i> strains into one of the main lineages. A discrepancy among the three markers for lineage assignment was observed only for one strain. We also sequenced a commonly used marker in molecular phylogenetics of fungi (<i>rpb2</i>, RNA polymerase II second largest su bunit) and found it was outperformed by all three of the new markers. We suggest that an <i>ASA</i> marker presented here could form the basis of a convenient one-locus test for rapid and routine diagnostic screening of unknown section <i>Alternaria</i> strains.
DOI: 10.6084/m9.figshare.19721874
title: Lifestyle, mating type and mitochondrial genome features of the plant pathogen <i>Calonectria hawksworthii</i> (Hypocreales, Nectriaceae) as revealed by genome analyses

description: In 2019, fungal necrotic spots were observed on the cotyledons of grafted avocado (<i>Persea americana</i>) seedlings from a nursery in Ventura County, California. Morphology and comparison of DNA sequences from eight loci identified the isolate as <i>Calonectria hawksworthii</i>, a species in the Nectriaceae not yet recorded in the United States. <i>Calonectria hawksworthii</i> is a necrotrophic fungal pathogen in the <i>C. cylindrospora</i> species complex. Most species in this group are associated with <i>Eucalyptus</i>, but the type host for <i>C. hawksworthii</i> is waterlilies (<i>Nelumbo nucifera</i>). In this study, the <i>C. hawksworthii</i> genome was sequenced using Illumina technologies. The draft assembly of 64.8 Mb contained 18 703 predicted gene models, of which 70% could be assigned to a GO functional category. The mating type loci indicated this species is heterothallic. Approximately, 3.79% of the draft genome consists of transposable elements (TE), and close to 36% of the predicted proteins were homologous to those known to be involved in pathogenicity in other fungal species. The <i>C. hawksworthii</i> genome displays elements typical of a necrotrophic lifestyle based on the composition of predicted genes encoding for carbohydrate-active enzymes, number of predicted secretory proteins including effectors, secondary metabolite biosynthesis clusters and cytochrome oxidase P450 (CYP) genes. The annotated mitochondrial genome was found to be 35.7 kb with very few intra or intergenic introns. This report constitutes the first draft genome of a <i>Calonectria</i> species belonging to the <i>C. cylindrospora</i> species complex, as well as the first report of <i>C. hawksworthii</i> species occurring in the United States on avocado.
DOI: 10.6084/m9.figshare.19721874.v1
title: Lifestyle, mating type and mitochondrial genome features of the plant pathogen <i>Calonectria hawksworthii</i> (Hypocreales, Nectriaceae) as revealed by genome analyses

description: In 2019, fungal necrotic spots were observed on the cotyledons of grafted avocado (<i>Persea americana</i>) seedlings from a nursery in Ventura County, California. Morphology and comparison of DNA sequences from eight loci identified the isolate as <i>Calonectria hawksworthii</i>, a species in the Nectriaceae not yet recorded in the United States. <i>Calonectria hawksworthii</i> is a necrotrophic fungal pathogen in the <i>C. cylindrospora</i> species complex. Most species in this group are associated with <i>Eucalyptus</i>, but the type host for <i>C. hawksworthii</i> is waterlilies (<i>Nelumbo nucifera</i>). In this study, the <i>C. hawksworthii</i> genome was sequenced using Illumina technologies. The draft assembly of 64.8 Mb contained 18 703 predicted gene models, of which 70% could be assigned to a GO functional category. The mating type loci indicated this species is heterothallic. Approximately, 3.79% of the draft genome consists of transposable elements (TE), and close to 36% of the predicted proteins were homologous to those known to be involved in pathogenicity in other fungal species. The <i>C. hawksworthii</i> genome displays elements typical of a necrotrophic lifestyle based on the composition of predicted genes encoding for carbohydrate-active enzymes, number of predicted secretory proteins including effectors, secondary metabolite biosynthesis clusters and cytochrome oxidase P450 (CYP) genes. The annotated mitochondrial genome was found to be 35.7 kb with very few intra or intergenic introns. This report constitutes the first draft genome of a <i>Calonectria</i> species belonging to the <i>C. cylindrospora</i> species complex, as well as the first report of <i>C. hawksworthii</i> species occurring in the United States on avocado.
DOI: 10.5281/zenodo.6785845
title: Transcribing audio data: overview and transcripts of several automatic transcription tools

description: Throughout institutions, audio recordings are being made regularly. To be able to further process these recordings, the audio often needs to be transcribed. In order to avoid having to transcribe the audio manually, there is a wealth of tools available for doing so automatically. In this record, we present an overview of several often-used tools to automatically transcribe pre-recorded audio data, including their features, costs, and security. To check the quality of the tool, we also recorded an audio fragment in Dutch that we ran through all tools in this overview in March of 2022. This original audio fragment (Test_interview_20220203.mp3), the cleaned-up transcription (Test_interview_cleaned_transcript.odt) and each tool’s raw transcript of the audio fragment (Test_interview_[name-tool]_raw_[date-run]) are included in this record as well. The raw transcripts were downloaded as .docx or .txt files and the .docx files saved as .odt. No edits to the transcripts were made before saving them, except an incidental removal of a personal email address or hyperlink. The overview contains information and transcripts of following transcription tools: Amberscript HappyScribe Kaldi NVIVO transcription Sonix SpokenOnline Transcribe Trint Microsoft Word 365 Online <strong>About</strong> This overview was created through a collaboration between Utrecht University’s Research Data Management (RDM) Support and the DataHub SSH programme situated at the faculty of Humanities. The details in the overview have last been updated April 19, 2022. Please note that at the time you are downloading these files, the quality of the (Dutch) speech-to-text conversion may have been improved by the respective supplier.
DOI: 10.5281/zenodo.6469895
title: Transcribing audio data: overview and transcripts of several automatic transcription tools

description: Throughout institutions, audio recordings are being made regularly. To be able to further process these recordings, the audio often needs to be transcribed. In order to avoid having to transcribe the audio manually, there is a wealth of tools available for doing so automatically. In this record, we present an overview of several often-used tools to automatically transcribe pre-recorded audio data, including their features, costs, and security. To check the quality of the tool, we also recorded an audio fragment in Dutch that we ran through all tools in this overview in March of 2022. This original audio fragment (Test_interview_20220203.mp3), the cleaned-up transcription (Test_interview_cleaned_transcript.odt) and each tool’s raw transcript of the audio fragment (Test_interview_[name-tool]_raw_[date-run]) are included in this record as well. The raw transcripts were downloaded as .docx or .txt files and the .docx files saved as .odt. No edits to the transcripts were made before saving them, except an incidental removal of a personal email address or hyperlink. The overview contains information and transcripts of following transcription tools: Amberscript HappyScribe Kaldi NVIVO transcription Sonix SpokenOnline Transcribe Trint Microsoft Word 365 Online <strong>About</strong> This overview was created through a collaboration between Utrecht University’s Research Data Management (RDM) Support and the DataHub SSH programme situated at the faculty of Humanities. The details in the overview have last been updated April 19, 2022. Please note that at the time you are downloading these files, the quality of the (Dutch) speech-to-text conversion may have been improved by the respective supplier.
DOI: 10.5281/zenodo.6597241
title: ArtTabGen Benchmarking Data Sets V1.0

description: These datasets can be used to benchmark information extraction systems. To see an exemplary benchmarking script, please<br> refer to our PLIX publication. For more information regarding the generation of this dataset, please check out our<br> ArtTabGen Generation Code repository and our paper.
DOI: 10.5281/zenodo.6597240
title: ArtTabGen Benchmarking Data Sets V1.0

description: These datasets can be used to benchmark information extraction systems. To see an exemplary benchmarking script, please<br> refer to our PLIX publication. For more information regarding the generation of this dataset, please check out our<br> ArtTabGen Generation Code repository and our paper.
DOI: 10.5281/zenodo.7152278
title: Dataset for "Imaging of Small-Scale Heterogeneity and Absorption Using Adjoint Envelope Tomography: Results from Laboratory Experiments"

description: The codes for Monte-Carlo simulation, scripts used to calculate the misfit kernels, and the processed data of the laboratory experiment.
DOI: 10.5281/zenodo.7152277
title: Dataset for "Imaging of Small-Scale Heterogeneity and Absorption Using Adjoint Envelope Tomography: Results from Laboratory Experiments"

description: The codes for Monte-Carlo simulation, scripts used to calculate the misfit kernels, and the processed data of the laboratory experiment.
DOI: 10.48510/fk2/d5ewhb
title: The diagnostic value of whole exome sequencing in male infertility patients - clinical data

description: The dataset consists of clinical data about infertility patients. The first block includes data about male patients from one infertility phenotype- azoospermia; The first block includes data about male patients with another infertility phenotype - olgioasthenozoospermia. In both blocks, similar information is available, including anthropometric data (weight, BMI, testis volume), medical history (infections, inherited diseases and other pathologies, missed abortion for a partner), lifestyle habits (smoking), hormone levels (testosterone, SHBG, MH, FSH, prolactin, estradiol, D vitamin), karyotyping and AZF testing outcomes, and spermograms (abstinence, sperm concentration, and volume, round cells, total numbers of cells, A, B, C, D motility, morphology).
DOI: 10.5281/zenodo.7151678
title: Legal Case Document Summarization: Extractive and Abstractive Methods and their Evaluation

description: This repository contains the following 3 datasets for legal document summarization : - IN-Abs : Indian Supreme Court case documents & their `abstractive' summaries, obtained from http://www.liiofindia.org/in/cases/cen/INSC/<br> - IN-Ext : Indian Supreme Court case documents & their `extractive' summaries, written by two law experts (A1, A2).<br> - UK-Abs : United Kingdom (U.K.) Supreme Court case documents & their `abstractive' summaries, obtained from https://www.supremecourt.uk/decided-cases/ Please refer to the paper and the README file for more details.
DOI: 10.5281/zenodo.7151679
title: Legal Case Document Summarization: Extractive and Abstractive Methods and their Evaluation

description: This repository contains the following 3 datasets for legal document summarization : - IN-Abs : Indian Supreme Court case documents & their `abstractive' summaries, obtained from http://www.liiofindia.org/in/cases/cen/INSC/<br> - IN-Ext : Indian Supreme Court case documents & their `extractive' summaries, written by two law experts (A1, A2).<br> - UK-Abs : United Kingdom (U.K.) Supreme Court case documents & their `abstractive' summaries, obtained from https://www.supremecourt.uk/decided-cases/ Please refer to the paper and the README file for more details.
DOI: 10.5281/zenodo.7152317
title: Legal Case Document Summarization: Extractive and Abstractive Methods and their Evaluation

description: This repository contains the following 3 datasets for legal document summarization : - IN-Abs : Indian Supreme Court case documents & their `abstractive' summaries, obtained from http://www.liiofindia.org/in/cases/cen/INSC/<br> - IN-Ext : Indian Supreme Court case documents & their `extractive' summaries, written by two law experts (A1, A2).<br> - UK-Abs : United Kingdom (U.K.) Supreme Court case documents & their `abstractive' summaries, obtained from https://www.supremecourt.uk/decided-cases/ Please refer to the paper and the README file for more details.
DOI: 10.34740/kaggle/dsv/4289877
title: Multi-domain Roman Urdu Sentiment Corpus (MRSC)
DOI: 10.6084/m9.figshare.21286254.v1
title: Supplementary Material for: Oral and Rectal Colonization by Antimicrobial-Resistant Gram-Negative Bacteria and Their Association with Death among Residents of Long-Term Care Facilities: A Prospective, Multicenter, Observational, Cohort Study

description: <b><i>Introduction:</i></b> The prevalence of antimicrobial-resistant bacteria (ARB) in long-term care facilities (LTCFs) remains unclear. Furthermore, the effect of ARB colonization on the clinical outcomes of LTCF residents has not been explored. <b><i>Methods:</i></b> We conducted a prospective multicenter cohort study and investigated the residents (<i>N</i> = 178) of six Japanese LTCFs (three Welfare Facilities for the Elderly Requiring Long-term Care and three Geriatric Health Service Facilities) for oral and rectal carriage of ARB. The clinical outcomes of the residents were evaluated based on isolating bacterial strains and subjecting them to whole-genome sequencing. <b><i>Results:</i></b> Of the 178 participants, 32 belonging to Geriatric Health Service Facilities with no information on their clinical outcome were excluded, and the remaining 146 were followed up for at most 21 months. Extended-spectrum β-lactamases (ESBL)-producing Enterobacterales and <i>Pseudomonas aeruginosa</i> were detected in 42.7% (<i>n</i> = 76) and 2.8% (<i>n</i> = 5) of the rectal swabs and 5.6% (<i>n</i> = 10) and 3.4% (<i>n</i> = 6) of the oral swabs, respectively. Detection of ARB in the oral and rectal cavities showed remarkable association with enteral nutrition. Further, <i>P. aeruginosa</i> was significantly associated with an increase in mortality of the residents, but there were not significant association between ESBL-producing Enterobacterales and mortality. Core-genome phylogeny of <i>P. aeruginosa</i> revealed a wide-spread distribution of the isolated strains across the phylogeny, which included a cluster of ST235 strains with substantially higher biofilm formation ability than the other isolated <i>P. aeruginosa</i> strains. <b><i>Discussion/Conclusion:</i></b> This study is the first to investigate the carriage of both oral and rectal ARB, genomic relatedness and determinants of antimicrobial resistance in isolated strains, and clinical outcomes of LTCF residents. Our study provides the first direct evidence for the burden of antimicrobial resistance in LTCFs.
DOI: 10.34740/kaggle/dsv/4289947
title: YouTube Daily
DOI: 10.6084/m9.figshare.21286503
title: SCB Dataset.xlsx

description: Clinical Data of multiple myeloma patients undergoing a stem cell boost
DOI: 10.5281/zenodo.7006686
title: Data supporting "Soil stratum tides"

description: This archive contains data that support the conclusions of the manuscript "Soil stratum tides". Detailed information is provided in the .xlsx file. <strong>Sheet No.</strong> <strong>Data type</strong> <strong>Unit</strong> <strong>Borehole</strong> <strong>Figure in manuscript</strong> 1 Soil tidal strain µε BO-1 2 2 Soil tidal strain µε BO-2 2 3 Soil tidal strain µε BO-3 2 4 Groundwater level m BO-1 2 5 Soil tidal strain µε BO-1 3 6 Groundwater level tidal fluctuation m BO-1 3 7 Soil tidal strain µε BO-1 4 8 Soil tidal strain µε BO-2 4 9 Soil tidal strain µε BO-3 4 10 Temperature °C BO-1 S4 11 Strain for interrogator stability testing µε N/A S5 11 Temperature for interrogator stability testing °C N/A S5 12 River water level m N/A S6
DOI: 10.5281/zenodo.7006685
title: Data supporting "Soil stratum tides"

description: This archive contains data that support the conclusions of the manuscript "Soil stratum tides". Detailed information is provided in the .xlsx file. <strong>Sheet No.</strong> <strong>Data type</strong> <strong>Unit</strong> <strong>Borehole</strong> <strong>Figure in manuscript</strong> 1 Soil tidal strain µε BO-1 2 2 Soil tidal strain µε BO-2 2 3 Soil tidal strain µε BO-3 2 4 Groundwater level m BO-1 2 5 Soil tidal strain µε BO-1 3 6 Groundwater level tidal fluctuation m BO-1 3 7 Soil tidal strain µε BO-1 4 8 Soil tidal strain µε BO-2 4 9 Soil tidal strain µε BO-3 4 10 Temperature °C BO-1 S4 11 Strain for interrogator stability testing µε N/A S5 11 Temperature for interrogator stability testing °C N/A S5 12 River water level m N/A S6