cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11695524
title: British_India_beta_period_95sig.dat from Emergence of oscillations in a simple epidemic model with demographic data

description: A simple susceptible–infectious–removed epidemic model for smallpox, with birth and death rates based on historical data, produces oscillatory dynamics with remarkably accurate periodicity. Stochastic population data cause oscillations to be sustained rather than damped, and data analysis regarding the oscillations provides insights into the same set of population data. Notably, oscillations arise naturally from the model, instead of from a periodic forcing term or other exogenous mechanism that guarantees oscillation: the model has no such mechanism. These emergent natural oscillations display appropriate periodicity for smallpox, even when the model is applied to different locations and populations. The model and datasets, in turn, offer new observations about disease dynamics and solution trajectories. These results call for renewed attention to relatively simple models, in combination with datasets from real outbreaks.
DOI: 10.6084/m9.figshare.11695527
title: Japan_Hida_spdeaths.dat from Emergence of oscillations in a simple epidemic model with demographic data

description: A simple susceptible–infectious–removed epidemic model for smallpox, with birth and death rates based on historical data, produces oscillatory dynamics with remarkably accurate periodicity. Stochastic population data cause oscillations to be sustained rather than damped, and data analysis regarding the oscillations provides insights into the same set of population data. Notably, oscillations arise naturally from the model, instead of from a periodic forcing term or other exogenous mechanism that guarantees oscillation: the model has no such mechanism. These emergent natural oscillations display appropriate periodicity for smallpox, even when the model is applied to different locations and populations. The model and datasets, in turn, offer new observations about disease dynamics and solution trajectories. These results call for renewed attention to relatively simple models, in combination with datasets from real outbreaks.
DOI: 10.6084/m9.figshare.11695524.v1
title: British_India_beta_period_95sig.dat from Emergence of oscillations in a simple epidemic model with demographic data

description: A simple susceptible–infectious–removed epidemic model for smallpox, with birth and death rates based on historical data, produces oscillatory dynamics with remarkably accurate periodicity. Stochastic population data cause oscillations to be sustained rather than damped, and data analysis regarding the oscillations provides insights into the same set of population data. Notably, oscillations arise naturally from the model, instead of from a periodic forcing term or other exogenous mechanism that guarantees oscillation: the model has no such mechanism. These emergent natural oscillations display appropriate periodicity for smallpox, even when the model is applied to different locations and populations. The model and datasets, in turn, offer new observations about disease dynamics and solution trajectories. These results call for renewed attention to relatively simple models, in combination with datasets from real outbreaks.
DOI: 10.6084/m9.figshare.11695527.v1
title: Japan_Hida_spdeaths.dat from Emergence of oscillations in a simple epidemic model with demographic data

description: A simple susceptible–infectious–removed epidemic model for smallpox, with birth and death rates based on historical data, produces oscillatory dynamics with remarkably accurate periodicity. Stochastic population data cause oscillations to be sustained rather than damped, and data analysis regarding the oscillations provides insights into the same set of population data. Notably, oscillations arise naturally from the model, instead of from a periodic forcing term or other exogenous mechanism that guarantees oscillation: the model has no such mechanism. These emergent natural oscillations display appropriate periodicity for smallpox, even when the model is applied to different locations and populations. The model and datasets, in turn, offer new observations about disease dynamics and solution trajectories. These results call for renewed attention to relatively simple models, in combination with datasets from real outbreaks.
DOI: 10.6084/m9.figshare.11695521
title: Japan_Hida_beta_0.015714285714285715.dat from Emergence of oscillations in a simple epidemic model with demographic data

description: A simple susceptible–infectious–removed epidemic model for smallpox, with birth and death rates based on historical data, produces oscillatory dynamics with remarkably accurate periodicity. Stochastic population data cause oscillations to be sustained rather than damped, and data analysis regarding the oscillations provides insights into the same set of population data. Notably, oscillations arise naturally from the model, instead of from a periodic forcing term or other exogenous mechanism that guarantees oscillation: the model has no such mechanism. These emergent natural oscillations display appropriate periodicity for smallpox, even when the model is applied to different locations and populations. The model and datasets, in turn, offer new observations about disease dynamics and solution trajectories. These results call for renewed attention to relatively simple models, in combination with datasets from real outbreaks.
DOI: 10.6084/m9.figshare.11695518
title: wav_coi_HidaJapan.dat from Emergence of oscillations in a simple epidemic model with demographic data

description: A simple susceptible–infectious–removed epidemic model for smallpox, with birth and death rates based on historical data, produces oscillatory dynamics with remarkably accurate periodicity. Stochastic population data cause oscillations to be sustained rather than damped, and data analysis regarding the oscillations provides insights into the same set of population data. Notably, oscillations arise naturally from the model, instead of from a periodic forcing term or other exogenous mechanism that guarantees oscillation: the model has no such mechanism. These emergent natural oscillations display appropriate periodicity for smallpox, even when the model is applied to different locations and populations. The model and datasets, in turn, offer new observations about disease dynamics and solution trajectories. These results call for renewed attention to relatively simple models, in combination with datasets from real outbreaks.
DOI: 10.6084/m9.figshare.11695509
title: British_India_beta_period_power.dat from Emergence of oscillations in a simple epidemic model with demographic data

description: A simple susceptible–infectious–removed epidemic model for smallpox, with birth and death rates based on historical data, produces oscillatory dynamics with remarkably accurate periodicity. Stochastic population data cause oscillations to be sustained rather than damped, and data analysis regarding the oscillations provides insights into the same set of population data. Notably, oscillations arise naturally from the model, instead of from a periodic forcing term or other exogenous mechanism that guarantees oscillation: the model has no such mechanism. These emergent natural oscillations display appropriate periodicity for smallpox, even when the model is applied to different locations and populations. The model and datasets, in turn, offer new observations about disease dynamics and solution trajectories. These results call for renewed attention to relatively simple models, in combination with datasets from real outbreaks.
DOI: 10.6084/m9.figshare.11695509.v1
title: British_India_beta_period_power.dat from Emergence of oscillations in a simple epidemic model with demographic data

description: A simple susceptible–infectious–removed epidemic model for smallpox, with birth and death rates based on historical data, produces oscillatory dynamics with remarkably accurate periodicity. Stochastic population data cause oscillations to be sustained rather than damped, and data analysis regarding the oscillations provides insights into the same set of population data. Notably, oscillations arise naturally from the model, instead of from a periodic forcing term or other exogenous mechanism that guarantees oscillation: the model has no such mechanism. These emergent natural oscillations display appropriate periodicity for smallpox, even when the model is applied to different locations and populations. The model and datasets, in turn, offer new observations about disease dynamics and solution trajectories. These results call for renewed attention to relatively simple models, in combination with datasets from real outbreaks.
DOI: 10.6084/m9.figshare.11695479
title: Figure data for "On the use of calcium deconvolution algorithms in practical contexts"

description: Data underlying figures presented in <i>On the use of calcium deconvolution algorithms in practical contexts</i> by Mathew H. Evans, Rasmus S. Petersen and Mark D. Humphries.<br>Preprint: https://www.biorxiv.org/content/10.1101/871137v1<br>Figure code: https://github.com/mathewzilla/deconv_pitfalls<br>
DOI: 10.6084/m9.figshare.11695506
title: JapanHida_alphatot_vs_delta.dat from Emergence of oscillations in a simple epidemic model with demographic data

description: A simple susceptible–infectious–removed epidemic model for smallpox, with birth and death rates based on historical data, produces oscillatory dynamics with remarkably accurate periodicity. Stochastic population data cause oscillations to be sustained rather than damped, and data analysis regarding the oscillations provides insights into the same set of population data. Notably, oscillations arise naturally from the model, instead of from a periodic forcing term or other exogenous mechanism that guarantees oscillation: the model has no such mechanism. These emergent natural oscillations display appropriate periodicity for smallpox, even when the model is applied to different locations and populations. The model and datasets, in turn, offer new observations about disease dynamics and solution trajectories. These results call for renewed attention to relatively simple models, in combination with datasets from real outbreaks.
DOI: 10.6084/m9.figshare.11695479.v2
title: Figure data for "On the use of calcium deconvolution algorithms in practical contexts"

description: Data underlying figures presented in <i>On the use of calcium deconvolution algorithms in practical contexts</i> by Mathew H. Evans, Rasmus S. Petersen and Mark D. Humphries.<br>Preprint: https://www.biorxiv.org/content/10.1101/871137v1<br>Figure code: https://github.com/mathewzilla/deconv_pitfalls<br>
DOI: 10.6084/m9.figshare.11695440
title: Supplementary material_genotype ALSPAC FRAXA/E data.docx

description: Supplementary data of number of repeats at FRAXA/FRAXE from the ALSPAC study. This data is supplementary to the paper Clark, R., Gregory, S., Ring, S., Jacobs, P., Ennis, S., Murray, A., ... & Pembrey, M. (2019). The FRAXA and FRAXE allele repeat size of boys from the Avon Longitudinal Study of Parents and Children (ALSPAC). <i>Wellcome Open Research</i>, <i>4</i>(116), 116.<br><br><br><br><br><br><br><br><br><br><br>
DOI: 10.6084/m9.figshare.11695467
title: co-morbidities (malnutrition, diabetes, anaemia, HIV, hypertension) and quality of life in persons with tuberculosis in the Philippines

description: Full dataset available with associated meta-data for a cross-sectional study in consenting adult Filipino persons registered for tuberculosis treatment at national TB treatment clinics under the TB-DOTS programme. <br>The study protocol is available at: Malnutrition and diabetes in tuberculosis treatment programs in the Philippines ISRCTN12506117<br>Publications using this dataset are listed <br><br><br>
DOI: 10.6084/m9.figshare.11695479.v1
title: Data folder

description: Data underlying figures presented in <i>On the use of calcium deconvolution algorithms in practical contexts</i> by Mathew H. Evans, Rasmus S. Petersen and Mark D. Humphries.<br>Preprint: https://www.biorxiv.org/content/10.1101/871137v1<br>Figure code: https://github.com/mathewzilla/deconv_pitfalls<br>
DOI: 10.6084/m9.figshare.11695356
title: Spatially-referenced synthetic households for Fani-affected Districts, Bangladesh

description: Spatially-referenced synthetic households for 6 Fani-affected districts in Bangladesh: Barisal, Barguna, Khulna, Patuakhali, Pirojpur, Satkhira
DOI: 10.6084/m9.figshare.11695356.v1
title: Spatially-referenced synthetic households for Fani-affected Districts, Bangladesh

description: Spatially-referenced synthetic households for 6 Fani-affected districts in Bangladesh: Barisal, Barguna, Khulna, Patuakhali, Pirojpur, Satkhira
DOI: 10.6084/m9.figshare.11695236
title: Anatomy of the right ventricle of the heart in the young adult

description: Anatomy of the right ventricle (RV) of 89 young subjects <b> </b> <b>Cohort </b>40 Preterm and 49 Term. Age: 18 - 40 years old (average Preterm: 22.7 years, Full term: 23.6 years) Data from YACHT: https://www.rdm.ox.ac.uk/about/our-clinical-facilities-and-mrc-units/cardiovascular-clinical-research-facility/ongoing-clinical-studies/yacht <b>Terms </b>Please acknowledge this source of data, and associated publication: A Mohamed et al. “Multimodality Imaging Demonstrates Reduced Right Ventricular Function Independent of Pulmonary Physiology in Moderately Preterm-Born Adults” <b> </b> <b>Methods overview </b>RV end diastolic anatomy was reconstructed from the contours using high order interpolation meshes. The 89 meshes were then spatially aligned by their centre of mass, and by an orientation defined by their basal plane and the left to right direction set by the centre of mass of the RV and left ventricle. A statistical shape model was then built with a principal component analysis (PCA). <b>Data shared</b> <b>1. AtlasMeshData.zip</b>, where each case has 1.1 MaskLV.vtk: The mask of the left ventricular (LV) myocardium, LV blood pool and RV blood pool from the short axis magnetic resonance image in end diastole 1.2 MaskLV_mesh files (.exelem and .exnode): the cubic Hermite mesh that was personalised to the RV anatomy 1.3 Image_Initialization.jpg: image of the overlay between the template RV mesh used for personalization and the mask of the RV blood pool 1.4 ImageDistances2ClosestPointbinary_meshxxxxxxxxxx.jpg: image of the distances between the RV mesh and the mask of the RV myocardium (xxxxxxxxxx is a digit encodign for the time when the image was generated) 1.5 PersonalizationReportbinary.txt: file with metrics of mesh fitting accuracy and quality <b>2. VTKMeshes.zip</b>: the collection of all the LV shapes in VTK format, after correction of centre of mass and left to right orientation. <b>3. AtlasModesHG5s4_s4_c2.pdf</b>: illustration of all the 20 first modes of anatomical variation, together with the boxplots of the two subgroups.<br>
DOI: 10.6084/m9.figshare.11695152
title: Non-typhoidal Salmonella intestinal carriage in a Schistosoma mansoni endemic community in a rural area of the Democratic Republic of Congo

description: This database presents the results of a study on the presence of non-typhoidal Salmonella intestinal carriage in a <i>Schistosoma mansoni </i>community infected in a rural area of the Democratic Republic of Congo.<br>During a cross-sectional community-wide study conducted in a rural area in the Democratic Republic of Congo, stool samples were analyzed for <i>Salmonella</i> intestinal carriage by culture and <i>Schistosoma mansoni</i> infection by microscopy after preparation using the Kato Katz. <i><br></i><i>Salmonella</i> Typhimurium and Enteritidis isolates were compared to blood culture isolates obtained during the same period in a neighboring hospital using multi-locus variable-numbers tandem repeat analysis (MLVA).<br><br>The proportion of <i>Salmonella</i> carriage among participants with a heavy <i>Schistosoma mansoni </i>infection intensity was significantly higher compared to those with a light and moderate infection intensity and compared to <i>Schistosoma mansoni</i> negative. <br>The <i>Salmonella</i> isolates comprised five and four Enteritidis and Typhimurium serotypes respectively, the majority of them had MLVA types identical or similar to those observed among blood culture isolates.<br>
DOI: 10.6084/m9.figshare.11695089
title: Gaussian_inputs_archives_XYZ.zip

description: Part of Supporting Information for "A Spherically Shielded Triphenylamine and Its Persistent Radical Cation" published in Chemistry - A European Journal (https://doi.org/10.1002/chem.202000355). Output archives of geometry optimizations of all species in S0 and S1 states with the Gaussian 09 program package provided together with the respective input files and XYZ coordinates of optimized species.
DOI: 10.6084/m9.figshare.11695089.v1
title: Gaussian_inputs_archives_XYZ.zip

description: Part of Supporting Information for "A Spherically Shielded Triphenylamine and Its Persistent Radical Cation" published in Chemistry - A European Journal (https://doi.org/10.1002/chem.202000355). Output archives of geometry optimizations of all species in S0 and S1 states with the Gaussian 09 program package provided together with the respective input files and XYZ coordinates of optimized species.
DOI: 10.6084/m9.figshare.11694807
title: Trace SLR Primary Study List

description: Primary Studies Data set
DOI: 10.6084/m9.figshare.11692740
title: MOESM2 of Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota

description: Additional file 1: Table S1. Statistics for 346 SAGs obtained from the mouse fecal microbiome Table S2. Taxonomic annotation for 346 SAGs and 28 SAGCs obtained from the mouse fecal microbiome Table S3. Comparison of OTU detection between 16S rRNA gene amplicon sequencing and single-cell sequencing Table S4. Statistics for 28 composite SAGs (IMSAGCs) obtained from the mouse fecal microbiome. Table S5. Detailed statistics for medium and high-quality draft genomes obtained from the mouse fecal microbiome Table S6. Statistics for Bacteroides genomes used in comparative genome analysis Table S7. Numbers of signal peptide-containing predicted glycoside hydrolases/polysaccharide lyases Table S8. Statistics for high completeness SAGs (&gt; 80%) associated with inulin uptake and TCA cycle-mediated metabolism Table S9. Statistics for conserved metabolic modules in qualified draft genomes and known Bacteroides spp. reference genomes.
DOI: 10.6084/m9.figshare.11692740.v1
title: MOESM2 of Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota

description: Additional file 1: Table S1. Statistics for 346 SAGs obtained from the mouse fecal microbiome Table S2. Taxonomic annotation for 346 SAGs and 28 SAGCs obtained from the mouse fecal microbiome Table S3. Comparison of OTU detection between 16S rRNA gene amplicon sequencing and single-cell sequencing Table S4. Statistics for 28 composite SAGs (IMSAGCs) obtained from the mouse fecal microbiome. Table S5. Detailed statistics for medium and high-quality draft genomes obtained from the mouse fecal microbiome Table S6. Statistics for Bacteroides genomes used in comparative genome analysis Table S7. Numbers of signal peptide-containing predicted glycoside hydrolases/polysaccharide lyases Table S8. Statistics for high completeness SAGs (&gt; 80%) associated with inulin uptake and TCA cycle-mediated metabolism Table S9. Statistics for conserved metabolic modules in qualified draft genomes and known Bacteroides spp. reference genomes.
DOI: 10.6084/m9.figshare.11692674
title: MOESM7 of Genomics-based epidemiology of bovine Mycoplasma bovis strains in Israel

description: Additional file 7. WGS-SNP-based phylogenetic analysis of all M. bovis isolates performed in comparison to a reference genome M. bovis PG45 as described in Materials and Methods. The phylogenetic tree was constructed by using the Maximum-Likelihood method, and bootstrapped 500 times to assess support for the different branches using MEGA-X [25]. The designation of the isolates includes serial number or sequencing identifier (for isolates sequenced in this study), name of the isolate, anatomical site of isolation, year and country of isolation. For additional information about particular strain, see Additional file 1: Table S1. E – eye; FT – fetal tissue; J – joint; L – lung; Lr – larynx; M – milk; N – nasal cavity; P – pharynx; S – semen; V – vulva. Total SNP count resulted in 7203 SNPs. Phylogenetic tree received by comparison of 224 M. bovis isolates to the reference genome M. bovis PG45 supported a separation on the geographical origin. This file can be opened using MEGA software [25] or via public available servers, e.g. the NCBI Tree Viewer (https://www.ncbi.nlm.nih.gov/tools/treeviewer/), ETE Toolkit (http://etetoolkit.org/treeview/) etc.
DOI: 10.6084/m9.figshare.11692674.v1
title: MOESM7 of Genomics-based epidemiology of bovine Mycoplasma bovis strains in Israel

description: Additional file 7. WGS-SNP-based phylogenetic analysis of all M. bovis isolates performed in comparison to a reference genome M. bovis PG45 as described in Materials and Methods. The phylogenetic tree was constructed by using the Maximum-Likelihood method, and bootstrapped 500 times to assess support for the different branches using MEGA-X [25]. The designation of the isolates includes serial number or sequencing identifier (for isolates sequenced in this study), name of the isolate, anatomical site of isolation, year and country of isolation. For additional information about particular strain, see Additional file 1: Table S1. E – eye; FT – fetal tissue; J – joint; L – lung; Lr – larynx; M – milk; N – nasal cavity; P – pharynx; S – semen; V – vulva. Total SNP count resulted in 7203 SNPs. Phylogenetic tree received by comparison of 224 M. bovis isolates to the reference genome M. bovis PG45 supported a separation on the geographical origin. This file can be opened using MEGA software [25] or via public available servers, e.g. the NCBI Tree Viewer (https://www.ncbi.nlm.nih.gov/tools/treeviewer/), ETE Toolkit (http://etetoolkit.org/treeview/) etc.
DOI: 10.6084/m9.figshare.11692665
title: MOESM6 of Genomics-based epidemiology of bovine Mycoplasma bovis strains in Israel

description: Additional file 6. WGS-SNP-based phylogenetic analysis of local M. bovis mastitis-associated isolates (n = 89) performed in comparison to a reference genome M. bovis PG45 as described in Materials and Methods. The phylogenetic tree was constructed by using the Maximum-Likelihood method, and bootstrapped 500 times to assess support for the different branches using MEGA-X [25]. The designation of the isolates includes serial number or sequencing identifier (for isolates sequenced in this study), name of the isolate, type of mastitis (clinical (CM) or subclinical (SM)) and year isolation. For additional information about particular strain, see Additional file 1: Table S1. Total SNP count resulted in 16,910 SNPs. Comparison between phylogenetic trees obtained by total-genome-based SNP analysis with (Additional file 6) and without (Fig. 3a) comparison to the reference genome revealed almost the same intergroup clustering of the isolates. However, the clade distribution of isolates was slightly different between these two comparisons. This file can be opened using MEGA software [25] or via public available servers, e.g. the NCBI Tree Viewer (https://www.ncbi.nlm.nih.gov/tools/treeviewer/), ETE Toolkit (http://etetoolkit.org/treeview/) etc.