cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5257298
title: Results of the Web-Delphi process to INAMI stakeholders (three rounds)

description: IMPACT HTA, WP7 (Methodological tools using multi-criteria value methods for HTA decision-making), Task 3 (Testing the framework with empirical applications), Results of the Web-Delphi process to INAMI stakeholders (three rounds), about the views of stakeholders regarding “The relevance of the following value aspects for the evaluation of new medicines in this disease context is” (2020) For details on the Web-Delphi process, see: IMPACT HTA, Work Package 7 (Methodological tools using multi-criteria value methods for HTA decision-making), Task 3, Deliverable 7.3 (Testing the framework with empirical applications), Testing the IMPACT-HTA Value Framework in collaboration with HTA agencies: Case studies on Non-Small Cell Lung Cancer and Spinal Muscular Atrophy (2021), Aris Angelis (LSHTM, LSE), Mónica Oliveira (IST), Teresa Rodrigues (IST), Liliana Freitas (IST), Carlos Bana e Costa (IST), Panos Kanavos (LSE)
DOI: 10.5281/zenodo.5257297
title: Results of the Web-Delphi process to INAMI stakeholders (three rounds)

description: IMPACT HTA, WP7 (Methodological tools using multi-criteria value methods for HTA decision-making), Task 3 (Testing the framework with empirical applications), Results of the Web-Delphi process to INAMI stakeholders (three rounds), about the views of stakeholders regarding “The relevance of the following value aspects for the evaluation of new medicines in this disease context is” (2020) For details on the Web-Delphi process, see: IMPACT HTA, Work Package 7 (Methodological tools using multi-criteria value methods for HTA decision-making), Task 3, Deliverable 7.3 (Testing the framework with empirical applications), Testing the IMPACT-HTA Value Framework in collaboration with HTA agencies: Case studies on Non-Small Cell Lung Cancer and Spinal Muscular Atrophy (2021), Aris Angelis (LSHTM, LSE), Mónica Oliveira (IST), Teresa Rodrigues (IST), Liliana Freitas (IST), Carlos Bana e Costa (IST), Panos Kanavos (LSE)
DOI: 10.5281/zenodo.5257425
title: Results of the Web-Delphi process to YLV stakeholders (three rounds)

description: IMPACT HTA, WP7 (Methodological tools using multi-criteria value methods for HTA decision-making), Task 3 (Testing the framework with empirical applications), Results of the Web-Delphi process to TLV stakeholders (three rounds), about the views of stakeholders regarding “The relevance of the following value aspects for the evaluation of new medicines in this disease context is” (2020) For details on the Web-Delphi process, see: IMPACT HTA, Work Package 7 (Methodological tools using multi-criteria value methods for HTA decision-making), Task 3, Deliverable 7.3 (Testing the framework with empirical applications), Testing the IMPACT-HTA Value Framework in collaboration with HTA agencies: Case studies on Non-Small Cell Lung Cancer and Spinal Muscular Atrophy (2021), Aris Angelis (LSHTM, LSE), Mónica Oliveira (IST), Teresa Rodrigues (IST), Liliana Freitas (IST), Carlos Bana e Costa (IST), Panos Kanavos (LSE)
DOI: 10.5281/zenodo.5257424
title: Results of the Web-Delphi process to YLV stakeholders (three rounds)

description: IMPACT HTA, WP7 (Methodological tools using multi-criteria value methods for HTA decision-making), Task 3 (Testing the framework with empirical applications), Results of the Web-Delphi process to TLV stakeholders (three rounds), about the views of stakeholders regarding “The relevance of the following value aspects for the evaluation of new medicines in this disease context is” (2020) For details on the Web-Delphi process, see: IMPACT HTA, Work Package 7 (Methodological tools using multi-criteria value methods for HTA decision-making), Task 3, Deliverable 7.3 (Testing the framework with empirical applications), Testing the IMPACT-HTA Value Framework in collaboration with HTA agencies: Case studies on Non-Small Cell Lung Cancer and Spinal Muscular Atrophy (2021), Aris Angelis (LSHTM, LSE), Mónica Oliveira (IST), Teresa Rodrigues (IST), Liliana Freitas (IST), Carlos Bana e Costa (IST), Panos Kanavos (LSE)
DOI: 10.5281/zenodo.5248340
title: #elxn42 web crawl

description: Consists of a web crawl of unique URLs tweeted with the #elxn42 hashtag. #elxn42 collection took place from August 3, 2015 - November 5, 2015. Unique URLs were extracted from the dataset, and harvested with Heritrix on January 29, 2016 - February 8, 2016.
description: This research was supported by a research grant -- 435-2015-0011 -- issued by Social Sciences and Humanities Research Council.
DOI: 10.5281/zenodo.5248339
title: #elxn42 web crawl

description: Consists of a web crawl of unique URLs tweeted with the #elxn42 hashtag. #elxn42 collection took place from August 3, 2015 - November 5, 2015. Unique URLs were extracted from the dataset, and harvested with Heritrix on January 29, 2016 - February 8, 2016.
description: This research was supported by a research grant -- 435-2015-0011 -- issued by Social Sciences and Humanities Research Council.
DOI: 10.5281/zenodo.1246025
title: BugRepo

description: Datasets from the paper: Generating duplicate bug datasets, MSR 2014.
DOI: 10.5281/zenodo.1144098
title: BugRepo

description: Datasets from the paper: Generating duplicate bug datasets, MSR 2014.
DOI: 10.6084/m9.figshare.16438797.v1
title: File for visualization in Paraview

description: This dataset is to visualize in Paraview the Model CM at 20 Myr described in the paper Lo Bue et al. 2021, JGR: “The role of Adria plate lithospheric structures on the recent dynamics of the Central Mediterranean region”. The datasets saved in files named *.h5 can be loaded on PARAVIEW with the corresponding files *.xmf. For further material and information, please contact the authors directly.
DOI: 10.6084/m9.figshare.14995314.v12
title: Effect of behavioural sampling methods on local and global social network metrics: A case-study of three macaque species

description: Data set and R-codes
DOI: 10.6084/m9.figshare.16438947
title: Microplastics Ingested per Daphnid per Timestep (Including No MPs group)

description: Microplastics ingested per Daphnid per timestep which included the no microplastics (control) group
DOI: 10.6084/m9.figshare.16438947.v1
title: Microplastics Ingested per Daphnid per Timestep (Including No MPs group)

description: Microplastics ingested per Daphnid per timestep which included the no microplastics (control) group
DOI: 10.5281/zenodo.5148664
title: The influence of the gut microbiome on BCG-induced trained immunity

description: This repository contains the code to reproduce the analysis in the study investigating the effects of gut microbiota on Bacillus Calmette-Guerin (BCG) vaccination of 321 healthy Dutch individuals. The results are presented in the paper <em>The influence of the gut microbiome on BCG-induced trained immunity</em> by Martin Stražar, Vera P. Mourits, Valerie A.C.M. Koeken, L. Charlotte J. de Bree, Simone J.C.F.M. Moorlag, Leo A.B. Joosten, Reinout van Crevel, Hera Vlamakis, Mihai G. Netea, Ramnik J. Xavier (2021) The bacillus Calmette-Guérin (BCG) vaccine protects against tuberculosis and heterologous infections but elicits high interindividual variation in specific and nonspecific (trained) immune responses. While the gut microbiome is increasingly recognized as an important modulator of vaccine responses and immunity in general, its potential role in BCG-induced protection is largely unknown. Stool and blood were collected from 321 healthy adults before BCG vaccination, followed by blood sampling two weeks and three months afterwards. Metagenomics based on de novo genome assembly revealed 43 immunomodulatory taxa. The nonspecific, trained immune response was detected by altered production of cytokines IL-6, IL-1β, and TNF-α upon ex vivo blood restimulation with Staphylococcus aureus and negatively correlated with abundance of Roseburia. The specific response, measured by IFN-γ production upon Mycobacterium tuberculosis stimulation, was associated positively with Ruminococcus and Eggerthella lenta. The immunomodulatory taxa identified also had the strongest effects on circulating metabolites, with Roseburia predominantly affecting phenylalanine metabolism. This was corroborated by abundances of relevant enzymes, suggesting alternate phenylalanine metabolism modules are activated in a Roseburia species-dependent manner. <br> Variability in cytokine production after BCG vaccination was associated with the abundance of microbial genomes, which in turn affect or produce metabolites in circulation. Roseburia was found to alter both trained immune responses and phenylalanine metabolism, revealing microbes and microbial products that may alter BCG-induced immunity. Together, our findings contribute to the understanding of specific and trained immune responses after BCG vaccination. The analysis and dataset details are further described in README.md and https://gitlab.com/xavier-lab-computation/public/bcg300 .
DOI: 10.5281/zenodo.5148663
title: The influence of the gut microbiome on BCG-induced trained immunity

description: This repository contains the code to reproduce the analysis in the study investigating the effects of gut microbiota on Bacillus Calmette-Guerin (BCG) vaccination of 321 healthy Dutch individuals. The results are presented in the paper <em>The influence of the gut microbiome on BCG-induced trained immunity</em> by Martin Stražar, Vera P. Mourits, Valerie A.C.M. Koeken, L. Charlotte J. de Bree, Simone J.C.F.M. Moorlag, Leo A.B. Joosten, Reinout van Crevel, Hera Vlamakis, Mihai G. Netea, Ramnik J. Xavier (2021) The bacillus Calmette-Guérin (BCG) vaccine protects against tuberculosis and heterologous infections but elicits high interindividual variation in specific and nonspecific (trained) immune responses. While the gut microbiome is increasingly recognized as an important modulator of vaccine responses and immunity in general, its potential role in BCG-induced protection is largely unknown. Stool and blood were collected from 321 healthy adults before BCG vaccination, followed by blood sampling two weeks and three months afterwards. Metagenomics based on de novo genome assembly revealed 43 immunomodulatory taxa. The nonspecific, trained immune response was detected by altered production of cytokines IL-6, IL-1β, and TNF-α upon ex vivo blood restimulation with Staphylococcus aureus and negatively correlated with abundance of Roseburia. The specific response, measured by IFN-γ production upon Mycobacterium tuberculosis stimulation, was associated positively with Ruminococcus and Eggerthella lenta. The immunomodulatory taxa identified also had the strongest effects on circulating metabolites, with Roseburia predominantly affecting phenylalanine metabolism. This was corroborated by abundances of relevant enzymes, suggesting alternate phenylalanine metabolism modules are activated in a Roseburia species-dependent manner. <br> Variability in cytokine production after BCG vaccination was associated with the abundance of microbial genomes, which in turn affect or produce metabolites in circulation. Roseburia was found to alter both trained immune responses and phenylalanine metabolism, revealing microbes and microbial products that may alter BCG-induced immunity. Together, our findings contribute to the understanding of specific and trained immune responses after BCG vaccination. The analysis and dataset details are further described in README.md and https://gitlab.com/xavier-lab-computation/public/bcg300 .
DOI: 10.6084/m9.figshare.16438959
title: Microplastics Ingested per Daphnid (accounting for control group)

description: Micorplastics ingested per daphnid per timestep accounting for the no microplastics (control) group
DOI: 10.6084/m9.figshare.16438959.v1
title: Microplastics Ingested per Daphnid (accounting for control group)

description: Micorplastics ingested per daphnid per timestep accounting for the no microplastics (control) group
DOI: 10.5281/zenodo.5257698
title: Crowdsourced air traffic data from The OpenSky Network 2020 [CC-BY]

description: <strong>Motivation</strong> The data in this dataset is derived and cleaned from the full OpenSky dataset to illustrate the development of air traffic during the COVID-19 pandemic. It spans all flights seen by the network's more than 2500 members since 1 January 2019. More data will be periodically included in the dataset until the end of the COVID-19 pandemic. <strong>License</strong> Creative Commons CC-BY The only difference with the original dataset comes from anonymised aircraft information. <strong>Disclaimer</strong> The data provided in the files is provided as is. Despite our best efforts at filtering out potential issues, some information could be erroneous. Origin and destination airports are computed online based on the ADS-B trajectories on approach/takeoff: no crosschecking with external sources of data has been conducted.<br> Fields <strong>origin</strong> or <strong>destination</strong> are empty when no airport could be found. Aircraft information come from the OpenSky aircraft database. Fields <strong>typecode</strong> and <strong>registration</strong> are empty when the aircraft is not present in the database. <strong>Description of the dataset</strong> One file per month is provided as a csv file with the following features: <strong>callsign</strong>: the identifier of the flight displayed on ATC screens (usually the first three letters are reserved for an airline: AFR for Air France, DLH for Lufthansa, etc.) <strong>number</strong>: the commercial number of the flight, when available (the matching with the callsign comes from public open API) <strong>aircraft_uid</strong>: a unique anonymised identifier for aircraft; <strong>typecode</strong>: the aircraft model type (when available); <strong>origin</strong>: a four letter code for the origin airport of the flight (when available); <strong>destination</strong>: a four letter code for the destination airport of the flight (when available); <strong>firstseen</strong>: the UTC timestamp of the first message received by the OpenSky Network; <strong>lastseen</strong>: the UTC timestamp of the last message received by the OpenSky Network; <strong>day</strong>: the UTC day of the last message received by the OpenSky Network; <strong>latitude_1</strong>, <strong>longitude_1</strong>, <strong>altitude_1</strong>: the first detected position of the aircraft; <strong>latitude_2</strong>, <strong>longitude_2</strong>, <strong>altitude_2</strong>: the last detected position of the aircraft. <strong>Examples</strong> Possible visualisations and a more detailed description of the data are available at the following page:<br> &lt;https://traffic-viz.github.io/scenarios/covid19.html&gt; <strong>Credit</strong> Martin Strohmeier, Xavier Olive, Jannis Lübbe, Matthias Schäfer, and Vincent Lenders<br> <strong>"</strong>Crowdsourced air traffic data from the OpenSky Network 2019–2020<strong>"</strong><br> <em>Earth System Science Data</em> 13(2), 2021<br> https://doi.org/10.5194/essd-13-357-2021
DOI: 10.6084/m9.figshare.16438977
title: Statistical Analysis Methods

description: All statistics were done in R Studio
DOI: 10.6084/m9.figshare.16304922.v1
title: SELECTIVE FORCES ON THE MAINTENANCE OF OUTCROSSING IN AN ALMOST EXCLUSIVELY CLEISTOGAMOUS VIOLET SPECIES

description: PREMISE OF THE STUDY: Cleistogamous species constitute interesting study systems to resolve the longstanding question of how outcrossing is maintained given that seed production is assured through selfing. In this work, we investigate the selective forces that allow the persistence of producing self-pollinated cleistogamous (CL) and chasmogamous (CH) flowers in Viola jaubertiana Marès & Vigin.<br>METHODS: We monitored three populations at different elevation for two years, and studied the flowering phenology and the relative contribution of each flower morph to parental fitness. We tested whether allocation to CH and CL flowers differed across populations and if it covaried with herbivory and water stress conditions. We also performed hand-pollination and bagging experiments in CH flowers to estimate inbreeding depression and heterosis.<br>KEY RESULTS: CH flowers open in winter, under unfavorable conditions for pollination, show high pollen limitation and no-delayed selfing, and thus produce a low amount of seeds. Conversely, CL flowers appear in early spring, are physiologically cheaper to produce (i.e. dry weight 3.4 times lower than that of CH flowers), and yield c. 100 times more seeds than CH flowers. CH flowers were favored under water stress and low herbivory. Crosses between populations showed up to 25% greater fitness than those within populations.<br>CONCLUSIONS: Despite the great pollen limitation in CH flowers, we suggest that the interaction among different environmental determinants and heterosis are probably sufficient forces to maintain chasmogamy in this long-lived species, reducing deleterious fixed mutations in the selfed lines.<br>
DOI: 10.6084/m9.figshare.16304922
title: SELECTIVE FORCES ON THE MAINTENANCE OF OUTCROSSING IN AN ALMOST EXCLUSIVELY CLEISTOGAMOUS VIOLET SPECIES

description: PREMISE OF THE STUDY: Cleistogamous species constitute interesting study systems to resolve the longstanding question of how outcrossing is maintained given that seed production is assured through selfing. In this work, we investigate the selective forces that allow the persistence of producing self-pollinated cleistogamous (CL) and chasmogamous (CH) flowers in Viola jaubertiana Marès & Vigin.<br>METHODS: We monitored three populations at different elevation for two years, and studied the flowering phenology and the relative contribution of each flower morph to parental fitness. We tested whether allocation to CH and CL flowers differed across populations and if it covaried with herbivory and water stress conditions. We also performed hand-pollination and bagging experiments in CH flowers to estimate inbreeding depression and heterosis.<br>KEY RESULTS: CH flowers open in winter, under unfavorable conditions for pollination, show high pollen limitation and no-delayed selfing, and thus produce a low amount of seeds. Conversely, CL flowers appear in early spring, are physiologically cheaper to produce (i.e. dry weight 3.4 times lower than that of CH flowers), and yield c. 100 times more seeds than CH flowers. CH flowers were favored under water stress and low herbivory. Crosses between populations showed up to 25% greater fitness than those within populations.<br>CONCLUSIONS: Despite the great pollen limitation in CH flowers, we suggest that the interaction among different environmental determinants and heterosis are probably sufficient forces to maintain chasmogamy in this long-lived species, reducing deleterious fixed mutations in the selfed lines.<br>
DOI: 10.5281/zenodo.5060008
title: Bayesian Analysis of Quasar Lightcurves with a Running Optimal Average: PyROA Fits to COSMOGRAIL Data

description: Available as .zip files are the data/results of using PyROA to fit to the COSMOGRAIL gravitationally lensed quasar data. In each .zip are the individual lightcurves for each image as a .dat file, a plot of the results, a corner plot of the sampled parameters and three pickle objects. These are samples.obj, samples_flat.obj and X_t.obj. The first of these, samples.obj, contains all the MCMC samples in an array with shape (Nsamples, Nwalkers, Ndim). The second, samples_flat.obj, contains the flattened samples, where the burn-in has been removed and is an array with shape (Nsamples_final, Ndim), where Nsamples_final is the number of samples with burn-in removed. This was used to generate the corner plot and obtain the best fit parameters. The last, X_t.obj, contains the driving lightcurve, X(t), as described in Donnan et al. 2021. This is an array of the form [t, X, X_errs], where X is the value of the driving lightcurve at time, t, with errors, X_errs. For objects with more than two images, folders where other images were the reference are included. The sigma parameter in the corner plot is the extra error added to the flux data which is labelled as <em>s<sub>i</sub></em> in the paper. The original data file downloaded from the COSMOGRAIL website is also included as a csv file.
DOI: 10.5281/zenodo.5060007
title: Bayesian Analysis of Quasar Lightcurves with a Running Optimal Average: PyROA Fits to COSMOGRAIL Data

description: Available as .zip files are the data/results of using PyROA to fit to the COSMOGRAIL gravitationally lensed quasar data. In each .zip are the individual lightcurves for each image as a .dat file, a plot of the results, a corner plot of the sampled parameters and three pickle objects. These are samples.obj, samples_flat.obj and X_t.obj. The first of these, samples.obj, contains all the MCMC samples in an array with shape (Nsamples, Nwalkers, Ndim). The second, samples_flat.obj, contains the flattened samples, where the burn-in has been removed and is an array with shape (Nsamples_final, Ndim), where Nsamples_final is the number of samples with burn-in removed. This was used to generate the corner plot and obtain the best fit parameters. The last, X_t.obj, contains the driving lightcurve, X(t), as described in Donnan et al. 2021. This is an array of the form [t, X, X_errs], where X is the value of the driving lightcurve at time, t, with errors, X_errs. For objects with more than two images, folders where other images were the reference are included. The sigma parameter in the corner plot is the extra error added to the flux data which is labelled as <em>s<sub>i</sub></em> in the paper. The original data file downloaded from the COSMOGRAIL website is also included as a csv file.
DOI: 10.6084/m9.figshare.16438998.v1
title: Graphs

description: All graphs displayed in this paper were created in R studio
DOI: 10.6084/m9.figshare.16438998
title: Graphs

description: All graphs displayed in this paper were created in R studio
DOI: 10.5281/zenodo.5257247
title: Flow cytometry data of "The impact of storage on extracellular vesicles: a systematic study" experiments

description: Flow cytometry raw data acquired for the pubblication of "The impact of storage on extracellular vesicles: a systematic study"
DOI: 10.5281/zenodo.5257246
title: Flow cytometry data of "The impact of storage on extracellular vesicles: a systematic study" experiments

description: Flow cytometry raw data acquired for the pubblication of "The impact of storage on extracellular vesicles: a systematic study"
DOI: 10.5517/ccdc.csd.cc2176s9
title: CCDC 1883770: Experimental Crystal Structure Determination

description: Related Article: Guoying Zhang, Torsten Irrgang, Martin Schlagbauer, Rhett Kempe|2021|Chem Cat.|1|681|doi:10.1016/j.checat.2021.05.007
DOI: 10.5517/ccdc.csd.cc269ps0
title: CCDC 2035112: Experimental Crystal Structure Determination

description: Related Article: Bettina Wagner, Johanna Heine|2021|Z.Anorg.Allg.Chem.|647|663|doi:10.1002/zaac.202000422
DOI: 10.5517/ccdc.csd.cc269pt1
title: CCDC 2035113: Experimental Crystal Structure Determination

description: Related Article: Bettina Wagner, Johanna Heine|2021|Z.Anorg.Allg.Chem.|647|663|doi:10.1002/zaac.202000422
DOI: 10.5517/ccdc.csd.cc25yn82
title: CCDC 2024494: Experimental Crystal Structure Determination

description: Related Article: Juan Hong, Xuxian Xiao, Haoliang Liu, Lin Fu, Xin-Chang Wang, Long Zhou, Xiao-Ye Wang, Zijie Qiu, Xiao-Yu Cao, Akimitsu Narita, Klaus Müllen, Yunbin Hu|2021|Chem.Commun.|57|5566|doi:10.1039/D1CC01631H
DOI: 10.5517/ccdc.csd.cc27j7st
title: CCDC 2071196: Experimental Crystal Structure Determination

description: Related Article: Ricardo A. Peralta, Michael T. Huxley, Jorge Albalad, Christopher J. Sumby, Christian J. Doonan|2021|Inorg.Chem.|60|11775|doi:10.1021/acs.inorgchem.1c00849
DOI: 10.5517/ccdc.csd.cc27j7tv
title: CCDC 2071197: Experimental Crystal Structure Determination

description: Related Article: Ricardo A. Peralta, Michael T. Huxley, Jorge Albalad, Christopher J. Sumby, Christian J. Doonan|2021|Inorg.Chem.|60|11775|doi:10.1021/acs.inorgchem.1c00849