cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24297103.v1
title: Supplementary Material for: The balance of CD8-positive T cells and PD-L1 expression in the myocardium predicts prognosis in lymphocytic fulminant myocarditis

description: Introduction: The clinical significance and prognostic value of T cell involvement and programmed cell death-1 (PD-1)/programmed cell death ligand-1 (PD-L1) have not been established in lymphocytic fulminant myocarditis (FM). We investigated the prognostic impact of the number of CD4+, CD8+, FoxP3+, and PD-1+ T cells, as well as PD-L1 expression, in cardiomyocytes in lymphocytic FM. Methods: This is a single-center observational cohort study. Myocardial tissue was obtained from 16 consecutive patients at lymphocytic FM onset. The median follow-up was 140 days. Cardiac events were defined as a composite of cardiac death and left ventricular-assist device implantation. CD4, CD8, FoxP3, PD-1, and PD-L1 immunostaining was performed on myocardial specimens. Results: The median age of the patients was 52 years (seven men and nine women). There was no significant difference in the number of CD4+ cells. The number of CD8+ cells and the CD8+/CD4+ T cell ratio were higher in the cardiac event group (Event+) than in the group without cardiac events (Event−) (P = 0.048 and P = 0.022, respectively). The number of FoxP3+ T cells was higher in the Event+ group (P = 0.049). Although there was no difference in the number of PD-1+ cells, cardiomyocyte PD-L1 expression was higher in the Event+ group (P = 0.112). Event-free survival was worse in the group with a high CD8+ cell count (P = 0.012) and high PD-L1 expression (P = 0.049). When divided into three groups based on the number of CD8+ cells and PD-L1 expression (CD8highPD-L1high [n = 8], CD8lowPD-L1high [n = 1], and CD8lowPD-L1low [n = 7]), the CD8highPD-L1high group demonstrated the worst event-free survival, while the CD8lowPD-L1high group had a favorable prognosis without cardiac events (P = 0.041). Conclusion: High myocardial expression of CD8+ T cells and PD-L1 may predict a poor prognosis in lymphocytic FM.
DOI: 10.5281/zenodo.10024117
title: PENELLOPE - X-Shooter spectra of targets in the Taurus and CrA regions (survey targets)

description: Spectra of the targets in the Taurus and CrA regions observed with the VLT/X-Shooter spectrograph. These spectra are part of the PENELLOPE Large Program and are obtained close in time to the HST/ULLYSES spectra of the same targets. 
Here one can find the 1D absolute flux-calibrated and telluric corrected spectra. Each object is observed simultaneously in three arms, UVB, VIS, and NIR, and the spectrum of each arm is saved in one file. The units of the spectra are: Flux [erg/s/cm2/nm]; Wavelength [nm]. In some cases, multiple observations for one target have been taken.
Data are public, we ask to ask to the authors of this release, who contributed to the observation preparation and data reduction, whether they want to be included in any publication using these data. The data reduction procedure is presented in Manara et al. (2021). Please quote this paper in any related publication. Please contact Carlo Manara for estimates of the stellar and accretion properties of these targets based on this data. 
For questions or comments please contact Carlo Manara, cmanara@eso.org
DOI: 10.5281/zenodo.10024118
title: PENELLOPE - X-Shooter spectra of targets in the Taurus and CrA regions (survey targets)

description: Spectra of the targets in the Taurus and CrA regions observed with the VLT/X-Shooter spectrograph. These spectra are part of the PENELLOPE Large Program and are obtained close in time to the HST/ULLYSES spectra of the same targets. 
Here one can find the 1D absolute flux-calibrated and telluric corrected spectra. Each object is observed simultaneously in three arms, UVB, VIS, and NIR, and the spectrum of each arm is saved in one file. The units of the spectra are: Flux [erg/s/cm2/nm]; Wavelength [nm]. In some cases, multiple observations for one target have been taken.
Data are public, we ask to ask to the authors of this release, who contributed to the observation preparation and data reduction, whether they want to be included in any publication using these data. The data reduction procedure is presented in Manara et al. (2021). Please quote this paper in any related publication. Please contact Carlo Manara for estimates of the stellar and accretion properties of these targets based on this data. 
For questions or comments please contact Carlo Manara, cmanara@eso.org
DOI: 10.5281/zenodo.10024072
title: PENELLOPE - X-Shooter spectra of targets in Lupus (all survey targets)

description: Spectra of the targets in the Lupus star-forming region observed with the VLT/X-Shooter spectrograph. These spectra are part of the PENELLOPE Large Program and are obtained close in time to the HST/ULLYSES spectra of the same targets. 
Here one can find the 1D absolute flux-calibrated and telluric corrected spectra. Each object is observed simultaneously in three arms, UVB, VIS, and NIR, and the spectrum of each arm is saved in one file. The units of the spectra are: Flux [erg/s/cm2/nm]; Wavelength [nm]. In some cases, multiple observations for one target have been taken.
Data are public, we ask to ask to the authors of this release, who contributed to the observation preparation and data reduction, whether they want to be included in any publication using these data. The data reduction procedure is presented in Manara et al. (2021). Please quote this paper in any related publication. Please contact Carlo Manara for estimates of the stellar and accretion properties of these targets based on this data. 
For questions or comments please contact Carlo Manara, cmanara@eso.org
DOI: 10.5281/zenodo.10024073
title: PENELLOPE - X-Shooter spectra of targets in Lupus (all survey targets)

description: Spectra of the targets in the Lupus star-forming region observed with the VLT/X-Shooter spectrograph. These spectra are part of the PENELLOPE Large Program and are obtained close in time to the HST/ULLYSES spectra of the same targets. 
Here one can find the 1D absolute flux-calibrated and telluric corrected spectra. Each object is observed simultaneously in three arms, UVB, VIS, and NIR, and the spectrum of each arm is saved in one file. The units of the spectra are: Flux [erg/s/cm2/nm]; Wavelength [nm]. In some cases, multiple observations for one target have been taken.
Data are public, we ask to ask to the authors of this release, who contributed to the observation preparation and data reduction, whether they want to be included in any publication using these data. The data reduction procedure is presented in Manara et al. (2021). Please quote this paper in any related publication. Please contact Carlo Manara for estimates of the stellar and accretion properties of these targets based on this data. 
For questions or comments please contact Carlo Manara, cmanara@eso.org
DOI: 10.5281/zenodo.10024001
title: PENELLOPE - X-Shooter spectra of targets in the Chamaeleon I, eta Cha, and eps Cha regions

description: Spectra of the targets in the Chamaeleon I, eps-Cha and eta-Cha regions observed with the VLT/X-Shooter spectrograph. These spectra are part of the PENELLOPE Large Program and are obtained close in time to the HST/ULLYSES spectra of the same targets. 
Here one can find the 1D absolute flux-calibrated and telluric corrected spectra. Each object is observed simultaneously in three arms, UVB, VIS, and NIR, and the spectrum of each arm is saved in one file. The units of the spectra are: Flux [erg/s/cm2/nm]; Wavelength [nm]. In some cases, multiple observations for one target have been taken.
Data are public, we ask to ask to the authors of this release, who contributed to the observation preparation and data reduction, whether they want to be included in any publication using these data. The data reduction procedure is presented in Manara et al. (2021). Please quote this paper in any related publication. Please contact Carlo Manara for estimates of the stellar and accretion properties of these targets based on this data. 
For questions or comments please contact Carlo Manara, cmanara@eso.org
DOI: 10.21227/a241-gm35
title: TARTAN Traceroute Data Set

description: The Transport-level pAcket RouTing ANalysis Tool for Cloud-native Applications (TARTAN) Dataset contains TARTAN/HiPerConTracer Traceroute runs between an endpoint in Oslo, Norway and the public Comprehensive TeX Archive Network (CTAN, https://www.ctan.org) and Comprehensive R Archive Network (CRAN, https://cran.r-project.org) mirror web servers, using ICMP and TCP as Transport Layer protocols. The data has been collected between August and October 2023. 3 rounds of Traceroute runs have been performed every 300 s. Both, IPv4 and IPv6 data have been collected. The purpose of the dataset is to show the changes of routes over time between a private endpoint and public web servers in different countries.
DOI: 10.5281/zenodo.10024000
title: PENELLOPE - X-Shooter spectra of targets in the Chamaeleon I, eta Cha, and eps Cha regions

description: Spectra of the targets in the Chamaeleon I, eps-Cha and eta-Cha regions observed with the VLT/X-Shooter spectrograph. These spectra are part of the PENELLOPE Large Program and are obtained close in time to the HST/ULLYSES spectra of the same targets. 
Here one can find the 1D absolute flux-calibrated and telluric corrected spectra. Each object is observed simultaneously in three arms, UVB, VIS, and NIR, and the spectrum of each arm is saved in one file. The units of the spectra are: Flux [erg/s/cm2/nm]; Wavelength [nm]. In some cases, multiple observations for one target have been taken.
Data are public, we ask to ask to the authors of this release, who contributed to the observation preparation and data reduction, whether they want to be included in any publication using these data. The data reduction procedure is presented in Manara et al. (2021). Please quote this paper in any related publication. Please contact Carlo Manara for estimates of the stellar and accretion properties of these targets based on this data. 
For questions or comments please contact Carlo Manara, cmanara@eso.org
DOI: 10.5281/zenodo.10091653
title: The role and risks of selective adaptation in extreme coral habitats

description: This data repository contains the raw data used in the morphological analyses for the study "The role and risks of selective adaptation in extreme coral habitats". These include data from X-Ray tomography, electron microscopy, skeletal morphometrics (density, porosity) and material structural analyses (hardness).
DOI: 10.5281/zenodo.7454381
title: The role and risks of selective adaptation in extreme coral habitats

description: This data repository contains the raw data used in the morphological analyses for the study "The role and risks of selective adaptation in extreme coral habitats". These include data from X-Ray tomography, electron microscopy, skeletal morphometrics (density, porosity) and material structural analyses (hardness).
DOI: 10.5281/zenodo.10091479
title: Benchmarking of Apps for Early Childhood: Comparing Public and Educators' Evaluation

description: Children frequently encounter content that may not be developmentally appropriate or are exposed to commercials that incite a desire to acquire superfluous products. Therefore, it is advantageous to use safety filters on personal devices in order to curate age-appropriate content and, in all circumstances, to closely monitor children's usage of these technologies. In this particular context, it is crucial to ascertain the calibre of early childhood applications and the extent to which parents and education professionals contribute to facilitating children's understanding of the digital realm. Some ideas include looking into how useful educational apps for babies and toddlers really are and what could go wrong if they are used in the wrong way, especially when it comes to safety, privacy, and ethical concerns.
This record introduces a sample of thirty applications commonly used by families, which are available for download on the 'Google Play' store. The primary objective of the study carried out over this data was to elucidate intriguing perspectives on the notions of quality, privacy, and the correlation between children and technology. The benchmarking tool utilised in this study was developed under the framework of the DataChild Map project. Its purpose was to assess several attributes of mobile applications, including the examination of their privacy policies.
The record is composed of three main elements:
1. The instrument adopted, English and Italian Version
2: The R script used to carry out the analysis
3: The dataset
DOI: 10.5281/zenodo.10091478
title: Benchmarking of Apps for Early Childhood: Comparing Public and Educators' Evaluation

description: Children frequently encounter content that may not be developmentally appropriate or are exposed to commercials that incite a desire to acquire superfluous products. Therefore, it is advantageous to use safety filters on personal devices in order to curate age-appropriate content and, in all circumstances, to closely monitor children's usage of these technologies. In this particular context, it is crucial to ascertain the calibre of early childhood applications and the extent to which parents and education professionals contribute to facilitating children's understanding of the digital realm. Some ideas include looking into how useful educational apps for babies and toddlers really are and what could go wrong if they are used in the wrong way, especially when it comes to safety, privacy, and ethical concerns.
This record introduces a sample of thirty applications commonly used by families, which are available for download on the 'Google Play' store. The primary objective of the study carried out over this data was to elucidate intriguing perspectives on the notions of quality, privacy, and the correlation between children and technology. The benchmarking tool utilised in this study was developed under the framework of the DataChild Map project. Its purpose was to assess several attributes of mobile applications, including the examination of their privacy policies.
The record is composed of three main elements:
1. The instrument adopted, English and Italian Version
2: The R script used to carry out the analysis
3: The dataset
DOI: 10.5281/zenodo.10087862
title: Impact of Convective Parameterizations on Atmospheric Mesoscale Kinetic Energy Spectra in Global High-resolution Simulations
DOI: 10.5281/zenodo.10089166
title: Supplementary Information BeXY

description: These are all the input files that were used in the publication.
S1 Table: contains a list of all samples, their respective publication and ENA project number analyzed in this paper (there are 4 sheets for whole-genome sequencing of ancient humans (WGS), high-depth subset of ancient WGS, 1240k target enrichment capture samples of ancient humans, and modern human WGS from the Simons Genome Diversity Project).
Capture1240k: contains the counts and the number of targets per scaffold for all ancient humans sequenced with 1240k target enrichment capture sequencing (see S1 table)
downsampling_aneuploids: contains all downsampled counts for simulated aneuploid invididuals as well as scripts to generate those. Also contains our implementation of the method seGMM.
downsampling_trisomy: contains all downsampled counts for simulated invididuals with trisomy 21 (factor21_1.5) and without trisomy 21 (factor_21_1) as well as scripts to generate those.
downsampling_euploids: contains all downsampled counts for euploid individuals as well as scripts to generate those.
lowQualityReference: contains all downsampled counts for the simulated low-quality reference genome assembly, as well as the scripts that were used to generate such an assembly based on the human reference genome.
WGS_ancient: contains the counts and the chromosome lengths for all ancient humans sequenced with whole-genome shotgun sequencing (see S1 table)
WGS_ancient_samples_lt_2x: contains the counts and the chromosome lengths for the 116 high-depth WGS samples (see S1 table)
WGS_modern_SGDP: contains the counts and the chromosome lengths for the 276 modern human samples downloaded from the Simons Genome Diversity Project (see S1 table). wgs_modern_SGDP_original_counts_withoutSeqTypes.txt corresponds to the counts obtained from the downloaded CRAM files, without considering differences in sequencing types. wgs_modern_SGDP_original_counts_withSeqTypes.txt corresponds to the same counts, but the sequencing type per sample is specified in the second column. wgs_modern_SGDP_filteredMQ30_counts.txt corresponds to the counts obtained by filtering on a mapping quality of 30.
non_model_organisms_posterior_probabilities_t: contains the posterior probabilities for each scaffold to be autosomal, Y-linked, X-linked or different as inferred by BeXY, for each of the six non-model organism species published in Nursyifa et al. 2021 ( https://doi.org/10.1111/1755-0998.13491).
DOI: 10.5281/zenodo.8366963
title: Supplementary Information BeXY

description: These are all the input files that were used in the publication. S1 Table: contains a list of all samples, their respective publication and ENA project number analyzed in this paper (there are 3 sheets for whole-genome sequencing (WGS), high-depth subset of WGS and capture samples). Capture1240k: contains the counts and the number of targets per scaffold for all ancient humans sequenced with 1240k target enrichment capture sequencing (see S1 table) downsampling_aneuploids: contains all downsampled counts for simulated aneuploid invididuals as well as scripts to generate those. Also contains our implementation of the method seGMM. downsampling_euploids: contains all downsampled counts for euploid individuals as well as scripts to generate those. lowQualityReference: contains all downsampled counts for the simulated low-quality reference genome assembly, as well as the scripts that were used to generate such an assembly based on the human reference genome. WGS_ancient: contains the counts and the chromosome lengths for all ancient humans sequenced with whole-genome shotgun sequencing (see S1 table) WGS_ancient_samples_lt_2x: contains the counts and the chromosome lengths for the 116 high-depth WGS samples (see S1 table) non_model_organisms_posterior_probabilities_t: contains the posterior probabilities for each scaffold to be autosomal, Y-linked, X-linked or different as inferred by BeXY, for each of the six non-model organism species published in Nursyifa et al. 2021 ( https://doi.org/10.1111/1755-0998.13491).
DOI: 10.5281/zenodo.8344991
title: Supplementary Information BeXY

description: These are all the input files that were used in the publication.
S1 Table: contains a list of all samples, their respective publication and ENA project number analyzed in this paper (there are 4 sheets for whole-genome sequencing of ancient humans (WGS), high-depth subset of ancient WGS, 1240k target enrichment capture samples of ancient humans, and modern human WGS from the Simons Genome Diversity Project).
Capture1240k: contains the counts and the number of targets per scaffold for all ancient humans sequenced with 1240k target enrichment capture sequencing (see S1 table)
downsampling_aneuploids: contains all downsampled counts for simulated aneuploid invididuals as well as scripts to generate those. Also contains our implementation of the method seGMM.
downsampling_trisomy: contains all downsampled counts for simulated invididuals with trisomy 21 (factor21_1.5) and without trisomy 21 (factor_21_1) as well as scripts to generate those.
downsampling_euploids: contains all downsampled counts for euploid individuals as well as scripts to generate those.
lowQualityReference: contains all downsampled counts for the simulated low-quality reference genome assembly, as well as the scripts that were used to generate such an assembly based on the human reference genome.
WGS_ancient: contains the counts and the chromosome lengths for all ancient humans sequenced with whole-genome shotgun sequencing (see S1 table)
WGS_ancient_samples_lt_2x: contains the counts and the chromosome lengths for the 116 high-depth WGS samples (see S1 table)
WGS_modern_SGDP: contains the counts and the chromosome lengths for the 276 modern human samples downloaded from the Simons Genome Diversity Project (see S1 table). wgs_modern_SGDP_original_counts_withoutSeqTypes.txt corresponds to the counts obtained from the downloaded CRAM files, without considering differences in sequencing types. wgs_modern_SGDP_original_counts_withSeqTypes.txt corresponds to the same counts, but the sequencing type per sample is specified in the second column. wgs_modern_SGDP_filteredMQ30_counts.txt corresponds to the counts obtained by filtering on a mapping quality of 30.
non_model_organisms_posterior_probabilities_t: contains the posterior probabilities for each scaffold to be autosomal, Y-linked, X-linked or different as inferred by BeXY, for each of the six non-model organism species published in Nursyifa et al. 2021 ( https://doi.org/10.1111/1755-0998.13491).
DOI: 10.5281/zenodo.8344992
title: Supplementary Information BeXY

description: These are all the input files that were used in the publication. S1 Table: contains a list of all samples and their respective publication analyzed in this paper (there are 3 sheets for whole-genome sequencing (WGS), high-depth subset of WGS and capture samples). Capture1240k: contains the counts and the number of targets per scaffold for all ancient humans sequenced with 1240k target enrichment capture sequencing (see S1 table) downsampling_aneuploids: contains all downsampled counts for simulated aneuploid invididuals as well as scripts to generate those. Also contains our implementation of the method seGMM. downsampling_euploids: contains all downsampled counts for euploid individuals as well as scripts to generate those. lowQualityReference: contains all downsampled counts for the simulated low-quality reference genome assembly, as well as the scripts that were used to generate such an assembly based on the human reference genome. WGS_ancient: contains the counts and the chromosome lengths for all ancient humans sequenced with whole-genome shotgun sequencing (see S1 table) WGS_ancient_samples_lt_2x: contains the counts and the chromosome lengths for the 116 high-depth WGS samples (see S1 table)
DOI: 10.5519/qd.kzrhd0y6
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (62051 records)
DOI: 10.6084/m9.figshare.24534774
title: Script 3: supplementary graphs and inaccuracy simulation (Supplementary figures) from The efficiency of varying methods and degrees of time-compensation for the solar azimuth

description: The additional calculations and visualisations included in the supplementary text, demonstrated in R Markdown. Includes additional results of a pilot study simulating migration inaccuracy, showing that it does not interact with time compensation. Dependencies: Sun position detail.csv, Radar weighting data.csv.
DOI: 10.6084/m9.figshare.24534774.v1
title: Script 3: supplementary graphs and inaccuracy simulation (Supplementary figures) from The efficiency of varying methods and degrees of time-compensation for the solar azimuth

description: The additional calculations and visualisations included in the supplementary text, demonstrated in R Markdown. Includes additional results of a pilot study simulating migration inaccuracy, showing that it does not interact with time compensation. Dependencies: Sun position detail.csv, Radar weighting data.csv.
DOI: 10.6084/m9.figshare.24534777
title: Script 1: virtual flight path and azimuth visualisation (Figure 1) from The efficiency of varying methods and degrees of time-compensation for the solar azimuth

description: The process of calculating and visualising migratory tracks and the estimated azimuths of different compensation strategies, demonstrated in R Markdown. Dependencies: Sun position detail.csv.