cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16397879
title: Supplementary Table Appendix: from Characteristics of the 100 largest modern zoonotic disease outbreaks

description: contains Tables S13-S47. Detailed analyses of drivers, pathogen type and transmission modes both excluding and including covariates accounting for variation in reporting effort, detection capabilities, and disease diversity among years and countries where outbreaks occurred.
DOI: 10.6084/m9.figshare.16397879.v1
title: Supplementary Table Appendix: from Characteristics of the 100 largest modern zoonotic disease outbreaks

description: contains Tables S13-S47. Detailed analyses of drivers, pathogen type and transmission modes both excluding and including covariates accounting for variation in reporting effort, detection capabilities, and disease diversity among years and countries where outbreaks occurred.
DOI: 10.6084/m9.figshare.16397876.v1
title: Dataset S4: from Characteristics of the 100 largest modern zoonotic disease outbreaks

description: Data on sample bias covariates for the outbreaks listed in Dataset S2 (typical background outbreaks).
DOI: 10.6084/m9.figshare.16397873
title: Dataset S2: from Characteristics of the 100 largest modern zoonotic disease outbreaks

description: Data for the 100 largest and typical background outbreaks.
DOI: 10.6084/m9.figshare.12543587.v2
title: UI logs

description: This is the collection of UI logs used in the evaluation in the research paper: "Candidate routines identification from unsegmented UI logs". The real-life logs are in CSV format and recorded via Action Logger. The synthetic logs are in XES format and generated from colored Petri net models. The models are attached.
DOI: 10.5281/zenodo.5519411
title: Neuronal HSF-1 activity coordinates fat desaturation across tissues in C. elegans via TGF-β/BMP signalling

description: To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell-autonomous. We have discovered that, in <em>Caenorhabditis elegans,</em> neuronal Heat shock Factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR)- causes extensive fat remodelling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine, and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodelling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least six TAX-2/TAX-4 cGMP gated channel expressing sensory neurons and TGF-β/BMP are required for signalling across tissues to modulate fat desaturation. We also find neuronal <em>hsf-1</em> is not only sufficient but also partially necessary to control the fat remodelling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell non-autonomously coordinate membrane saturation and composition across tissues in a multicellular animal.
DOI: 10.6084/m9.figshare.12543587
title: UI logs

description: This is the collection of UI logs used in the evaluation in the research paper: "Candidate routines identification from unsegmented UI logs". The real-life logs are in CSV format and recorded via Action Logger. The synthetic logs are in XES format and generated from colored Petri net models. The models are attached.
DOI: 10.5281/zenodo.5012729
title: Research data supporting "Considerations for Implementing Electronic Laboratory Notebooks in an Academic Research Environment"

description: <em>Research data supporting the publication:</em> <em>Higgins SG, Nogiwa-Valdez AA, Stevens MM, Considerations for Implementing Electronic Laboratory Notebooks in an Academic Research Environment, Nature Protocols, 2021.</em> This repository contains the raw survey data of 172 current and historic electronic laboratory notebook (ELN) software packages. Main files: "ELN_Review_Higgins_2021_Survey.csv" = raw survey data in 'tidy' data format "ELN_Review_Higgins_2021.Rmd" = an R Markdown File (R Notebook) that takes the survey data as input and produces summary statistics and plots. This file was written using R Studio as the IDE. Derived files, generated from those above: "ELN_Review_Higgins_2021.nb.html" = a self-contained HTML file that is automatically generated by R Studio, based on the markdown file. This can be opened in any web browser to allow manual inspection of the code and comments without the need for specialist software. Embedded within this file is also the original markdown script (i.e. a copy of the code in "ELN_Review_Higgins_2021.Rmd") "ELN_Review_Higgins_2021_Lifetimes_Interactive_Figure1.html" = an HTML file generated by the script above via the plotly package. It contains an interactive version of the ELN survey data, allowing the user to hover over the timeline and explore the data. "ELN_Review_Higgins_2021_Timeline.pdf" = static version of ELN timeline, used to generate figure in main manuscript. "ELN_Review_Higgins_2021_Releases-Per-Year.pdf" = static version of number of new ELNs per year, used to generate figure in main manuscript. This survey was generated from a mixture of primary and secondary sources (see references for secondary sources).
description: {"references": ["Douglas, S. \"ELN vendor.\" LIMSWiki, (2021) https://www.limswiki.org/index.php/ELN_vendor", "Rubacha, M., Rattan, A. K. & Hosselet, S. C. A Review of Electronic Laboratory Notebooks Available in the Market Today. JALA J. Assoc. Lab. Autom. 16, 90\u201398 (2011).", "Kanza, S. et al. Electronic lab notebooks: can they replace paper? J. Cheminformatics 9, 31 (2017)."]}
DOI: 10.5281/zenodo.5012728
title: Research data supporting "Considerations for Implementing Electronic Laboratory Notebooks in an Academic Research Environment"

description: <em>Research data supporting the publication:</em> <em>Higgins SG, Nogiwa-Valdez AA, Stevens MM, Considerations for Implementing Electronic Laboratory Notebooks in an Academic Research Environment, Nature Protocols, 2021.</em> This repository contains the raw survey data of 172 current and historic electronic laboratory notebook (ELN) software packages. Main files: "ELN_Review_Higgins_2021_Survey.csv" = raw survey data in 'tidy' data format "ELN_Review_Higgins_2021.Rmd" = an R Markdown File (R Notebook) that takes the survey data as input and produces summary statistics and plots. This file was written using R Studio as the IDE. Derived files, generated from those above: "ELN_Review_Higgins_2021.nb.html" = a self-contained HTML file that is automatically generated by R Studio, based on the markdown file. This can be opened in any web browser to allow manual inspection of the code and comments without the need for specialist software. Embedded within this file is also the original markdown script (i.e. a copy of the code in "ELN_Review_Higgins_2021.Rmd") "ELN_Review_Higgins_2021_Lifetimes_Interactive_Figure1.html" = an HTML file generated by the script above via the plotly package. It contains an interactive version of the ELN survey data, allowing the user to hover over the timeline and explore the data. "ELN_Review_Higgins_2021_Timeline.pdf" = static version of ELN timeline, used to generate figure in main manuscript. "ELN_Review_Higgins_2021_Releases-Per-Year.pdf" = static version of number of new ELNs per year, used to generate figure in main manuscript. This survey was generated from a mixture of primary and secondary sources (see references for secondary sources).
description: {"references": ["Douglas, S. \"ELN vendor.\" LIMSWiki, (2021) https://www.limswiki.org/index.php/ELN_vendor", "Rubacha, M., Rattan, A. K. & Hosselet, S. C. A Review of Electronic Laboratory Notebooks Available in the Market Today. JALA J. Assoc. Lab. Autom. 16, 90\u201398 (2011).", "Kanza, S. et al. Electronic lab notebooks: can they replace paper? J. Cheminformatics 9, 31 (2017)."]}
DOI: 10.5281/zenodo.5524200
title: Syntheses of aircraft noise obtained by computational methods

description: In ANIMA WP4, where focus is put on toolset development, a benchmark on three partners’ auralization tools was performed. These tools are used to reproduce the sound of an aircraft flyover from either physical modelling of noise, a prediction based on measurement or a combination of both. As the chosen methodologies and the modelling hypotheses are different between partners, a benchmark was performed to assess the impact of these strategies on the produced sound synthesis. The realism of each auralization was evaluated through comparison to experimental recordings. For propriety reasons, only the synthesized sounds are available here, and can be compared between each other. Two of the three tools were further used in the WP3 task dedicated to Virtual Reality, see "Virtual reality simulated aircraft flyovers: Influence of the landscape on the overall pleasantness of the environment" The sounds represent three flight configurations, one landing, and two take-offs with different engine speeds. Two aircraft are considered, one single-aisle and one double-aisle aircraft. The synthesis is performed at a receiver position below the aircraft trajectory. For more information, please contact: Ingrid.legriffon@onera.fr (ONERA) isabelle.boullet@airbus.com (Airbus Aviation) jean-michel.boiteux@safrangroup.com (Safran Aircraft Engine)
description: This dataset contains twelve sounds under the form of .wav files. The dataset is compressed in a .z format and may be decompressed, for instance using the 7-zip software (https://www.7-zip.org/) Nomenclature of the files and corresponding informations are available through the associated pdf file named "Metadata.pdf".
DOI: 10.5281/zenodo.5524199
title: Syntheses of aircraft noise obtained by computational methods

description: In ANIMA WP4, where focus is put on toolset development, a benchmark on three partners’ auralization tools was performed. These tools are used to reproduce the sound of an aircraft flyover from either physical modelling of noise, a prediction based on measurement or a combination of both. As the chosen methodologies and the modelling hypotheses are different between partners, a benchmark was performed to assess the impact of these strategies on the produced sound synthesis. The realism of each auralization was evaluated through comparison to experimental recordings. For propriety reasons, only the synthesized sounds are available here, and can be compared between each other. Two of the three tools were further used in the WP3 task dedicated to Virtual Reality, see "Virtual reality simulated aircraft flyovers: Influence of the landscape on the overall pleasantness of the environment" The sounds represent three flight configurations, one landing, and two take-offs with different engine speeds. Two aircraft are considered, one single-aisle and one double-aisle aircraft. The synthesis is performed at a receiver position below the aircraft trajectory. For more information, please contact: Ingrid.legriffon@onera.fr (ONERA) isabelle.boullet@airbus.com (Airbus Aviation) jean-michel.boiteux@safrangroup.com (Safran Aircraft Engine)
description: This dataset contains twelve sounds under the form of .wav files. The dataset is compressed in a .z format and may be decompressed, for instance using the 7-zip software (https://www.7-zip.org/) Nomenclature of the files and corresponding informations are available through the associated pdf file named "Metadata.pdf".
DOI: 10.18746/bmth.data.00000198
title: Anti-Fascist Autobiography (1930-1936)
DOI: 10.6084/m9.figshare.14864344
title: Semen sampling as a simple, noninvasive surrogate for prostate health screening

description: The detection rates for prostate cancer (pCa) by invasive biopsy are high, fully justifying its use in confirmatory testing. False-positive results of prior, relatively insensitive screening tests, however, can lead to expensive and often unnecessary surgery. Several reports have suggested the potential use of the ejaculate to screen for prostate conditions. Hitherto, the potential impact of sterilization on the diagnostic potential of seminal plasma screening has not been examined. Herein, we report cellular and molecular comparisons of semen samples obtained from normal (N = 5), vasectomized (N = 5) and prostate pathology patients (N = 4; confirmed by a biopsy) that were centrifuged over 60% PureSperm cushions. Non-penetrating cells were washed prior to immunocytochemistry with prostatic epithelial cell markers including PSMA, NKX3.1 and CD24. KRT18 was used to highlight epithelial cells in these samples. RNA sequencing was then used to identify differentially expressed small RNAs associated with vasectomy and prostate pathology. Specific gene transcripts were confirmed by RT-qPCR. PMSA<sup>+</sup>/KRT18<sup>+</sup>, CD24<sup>+</sup>/KRT18<sup>+</sup> and NKX3.1/<sup>+</sup>KRT18<sup>+</sup> cells were observed, albeit infrequently in most processed semen samples by indirect immunocytochemistry. Targeted RT-qPCR supported their enrichment, along with their putative designation as prostatic luminal cells. Small RNAs in seminal plasma were highly heterogeneous, with tRNAs and miRNAs being the dominant forms. Hsa-miR-143 and hsa-miR-199 were among the most prominent of the differentially expressed miRNAs upregulated in samples with prostate pathology but not vasectomy. The targets of these small RNAs illustrate biological processes involved among others in transcription regulation and collagen metabolism. Our outcomes strongly support an appraisal of selected biologically meaningful small RNAs of ejaculate semen for prostate health screening. A long-term goal would be a simple, routine, noninvasive test for monitoring prostate health, potentially among younger men.
DOI: 10.6084/m9.figshare.14864344.v2
title: Semen sampling as a simple, noninvasive surrogate for prostate health screening

description: The detection rates for prostate cancer (pCa) by invasive biopsy are high, fully justifying its use in confirmatory testing. False-positive results of prior, relatively insensitive screening tests, however, can lead to expensive and often unnecessary surgery. Several reports have suggested the potential use of the ejaculate to screen for prostate conditions. Hitherto, the potential impact of sterilization on the diagnostic potential of seminal plasma screening has not been examined. Herein, we report cellular and molecular comparisons of semen samples obtained from normal (N = 5), vasectomized (N = 5) and prostate pathology patients (N = 4; confirmed by a biopsy) that were centrifuged over 60% PureSperm cushions. Non-penetrating cells were washed prior to immunocytochemistry with prostatic epithelial cell markers including PSMA, NKX3.1 and CD24. KRT18 was used to highlight epithelial cells in these samples. RNA sequencing was then used to identify differentially expressed small RNAs associated with vasectomy and prostate pathology. Specific gene transcripts were confirmed by RT-qPCR. PMSA<sup>+</sup>/KRT18<sup>+</sup>, CD24<sup>+</sup>/KRT18<sup>+</sup> and NKX3.1/<sup>+</sup>KRT18<sup>+</sup> cells were observed, albeit infrequently in most processed semen samples by indirect immunocytochemistry. Targeted RT-qPCR supported their enrichment, along with their putative designation as prostatic luminal cells. Small RNAs in seminal plasma were highly heterogeneous, with tRNAs and miRNAs being the dominant forms. Hsa-miR-143 and hsa-miR-199 were among the most prominent of the differentially expressed miRNAs upregulated in samples with prostate pathology but not vasectomy. The targets of these small RNAs illustrate biological processes involved among others in transcription regulation and collagen metabolism. Our outcomes strongly support an appraisal of selected biologically meaningful small RNAs of ejaculate semen for prostate health screening. A long-term goal would be a simple, routine, noninvasive test for monitoring prostate health, potentially among younger men.
DOI: 10.6084/m9.figshare.14864344.v1
title: Semen sampling as a simple, noninvasive surrogate for prostate health screening

description: The detection rates for prostate cancer (pCa) by invasive biopsy are high, fully justifying its use in confirmatory testing. False-positive results of prior, relatively insensitive screening tests, however, can lead to expensive and often unnecessary surgery. Several reports have suggested the potential use of the ejaculate to screen for prostate conditions. Hitherto, the potential impact of sterilization on the diagnostic potential of seminal plasma screening has not been examined. Herein, we report cellular and molecular comparisons of semen samples obtained from normal (N = 5), vasectomized (N = 5) and prostate pathology patients (N = 4; confirmed by a biopsy) that were centrifuged over 60% PureSperm cushions. Non-penetrating cells were washed prior to immunocytochemistry with prostatic epithelial cell markers including PSMA, NKX3.1 and CD24. KRT18 was used to highlight epithelial cells in these samples. RNA sequencing was then used to identify differentially expressed small RNAs associated with vasectomy and prostate pathology. Specific gene transcripts were confirmed by RT-qPCR. PMSA<sup>+</sup>/KRT18<sup>+</sup>, CD24<sup>+</sup>/KRT18<sup>+</sup> and NKX3.1/<sup>+</sup>KRT18<sup>+</sup> cells were observed, albeit infrequently in most processed semen samples by indirect immunocytochemistry. Targeted RT-qPCR supported their enrichment, along with their putative designation as prostatic luminal cells. Small RNAs in seminal plasma were highly heterogeneous, with tRNAs and miRNAs being the dominant forms. Hsa-miR-143 and hsa-miR-199 were among the most prominent of the differentially expressed miRNAs upregulated in samples with prostate pathology but not vasectomy. The targets of these small RNAs illustrate biological processes involved among others in transcription regulation and collagen metabolism. Our outcomes strongly support an appraisal of selected biologically meaningful small RNAs of ejaculate semen for prostate health screening. A long-term goal would be a simple, routine, noninvasive test for monitoring prostate health, potentially among younger men.
DOI: 10.6084/m9.figshare.12844692
title: Operational research applied to decisions in home health care: A systematic literature review

description: The efficient deployment of resources in home-based care is considered crucial for the sustainability of health and social care systems worldwide. The aim of this study was to identify and review operational research approaches to support decision-making in home health care. We identified a set of linked decisions at different planning levels (strategic, tactical, operational) and conducted a systematic review of operational research approaches used to address these decisions. We also sampled OR literature applied to analogous decisions in other settings. The 77 papers selected focused predominantly on solutions for staff-to-patient allocation, visit scheduling and staff routing, few of which were adopted by organisations. Few studies dealt with tactical decisions of team size and composition or strategic decisions of districting, and we found no studies on contract design for commissioning home health care, on staff role definitions or on reassessment of patient need. Integrative work is scarce and the aspects of system performance considered are variable and diverse. For these reasons the literature does not provide guidance for home health care services aspiring to effective and coherent decisions across planning levels. OR approaches from other areas of application provide some insights for future research aimed at addressing this shortfall.
DOI: 10.6084/m9.figshare.12844692.v2
title: Operational research applied to decisions in home health care: A systematic literature review

description: The efficient deployment of resources in home-based care is considered crucial for the sustainability of health and social care systems worldwide. The aim of this study was to identify and review operational research approaches to support decision-making in home health care. We identified a set of linked decisions at different planning levels (strategic, tactical, operational) and conducted a systematic review of operational research approaches used to address these decisions. We also sampled OR literature applied to analogous decisions in other settings. The 77 papers selected focused predominantly on solutions for staff-to-patient allocation, visit scheduling and staff routing, few of which were adopted by organisations. Few studies dealt with tactical decisions of team size and composition or strategic decisions of districting, and we found no studies on contract design for commissioning home health care, on staff role definitions or on reassessment of patient need. Integrative work is scarce and the aspects of system performance considered are variable and diverse. For these reasons the literature does not provide guidance for home health care services aspiring to effective and coherent decisions across planning levels. OR approaches from other areas of application provide some insights for future research aimed at addressing this shortfall.
DOI: 10.6084/m9.figshare.12844692.v1
title: Operational research applied to decisions in home health care: A systematic literature review

description: The efficient deployment of resources in home-based care is considered crucial for the sustainability of health and social care systems worldwide. The aim of this study was to identify and review operational research approaches to support decision-making in home health care. We identified a set of linked decisions at different planning levels (strategic, tactical, operational) and conducted a systematic review of operational research approaches used to address these decisions. We also sampled OR literature applied to analogous decisions in other settings. The 77 papers selected focused predominantly on solutions for staff-to-patient allocation, visit scheduling and staff routing, few of which were adopted by organisations. Few studies dealt with tactical decisions of team size and composition or strategic decisions of districting, and we found no studies on contract design for commissioning home health care, on staff role definitions or on reassessment of patient need. Integrative work is scarce and the aspects of system performance considered are variable and diverse. For these reasons the literature does not provide guidance for home health care services aspiring to effective and coherent decisions across planning levels. OR approaches from other areas of application provide some insights for future research aimed at addressing this shortfall.