cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8290199
title: Data; Single Photon, Time-Gated, Phasor-based Fluorescence Lifetime Imaging Through Highly Scattering Medium

description: This data contains: i) time gated fluorescence images for dyes and A459 cells behind tissue-like phantoms. ii) phasor plots of the time-gated fluorescence images. iii) Alligator notebooks which detailed description of the data analysis processes.iv) Files that were used for 3D printing of our samples order. v) Region of interests (ROIs) files that were used for each analysis set.
DOI: 10.6084/m9.figshare.8290622.v1
title: Distribution of Wetlands in Inner Mongolia Plateau, China

description: The dataset includes spatial distribution of wetlands in 1993, 2002 and 2013 of Inner Mongolia Plateau, which is derived from Landsat ETM+, TM and OLI images. Calculation of normalized difference water index (NDWI) combined with manual interpretation are adopted to extract wetland information with Albers equal-area projection. Based on field investigation, the relationships between each wetland type and the corresponding imagery features in terms of color, shape, location and texture are established, combining with the ancillary data included Google Earth images, topographic map (1:100,000) and digital elevation model (DEM, 1:100,000), the complete wetland information (with patch area&gt;0.01km<sup>2</sup>) was finally extracted by visual interpretation.
DOI: 10.6084/m9.figshare.8290199.v1
title: Data; Single Photon, Time-Gated, Phasor-based Fluorescence Lifetime Imaging Through Highly Scattering Medium

description: This data contains: i) time gated fluorescence images for dyes and A459 cells behind tissue-like phantoms. ii) phasor plots of the time-gated fluorescence images. iii) Alligator notebooks which detailed description of the data analysis processes.iv) Files that were used for 3D printing of our samples order. v) Region of interests (ROIs) files that were used for each analysis set.
DOI: 10.6084/m9.figshare.8290199.v2
title: Data; Single Photon, Time-Gated, Phasor-based Fluorescence Lifetime Imaging Through Highly Scattering Medium

description: This data contains: i) time gated fluorescence images for dyes and A459 cells behind tissue-like phantoms. ii) phasor plots of the time-gated fluorescence images. iii) Alligator notebooks which detailed description of the data analysis processes.iv) Files that were used for 3D printing of our samples order. v) Region of interests (ROIs) files that were used for each analysis set.
DOI: 10.6084/m9.figshare.8290121
title: GAD67 & Iba1 abutments measurements 8212 GP 1

description: GAD67 & Iba1 abutments measurements 8212 GP 2 2019 paper
DOI: 10.6084/m9.figshare.8290121.v1
title: GAD67 & Iba1 abutments measurements 8212 GP 1

description: GAD67 & Iba1 abutments measurements 8212 GP 2 2019 paper
DOI: 10.6084/m9.figshare.8289881.v1
title: Tana1.pep.filter.fas

description: This fasta file contains the sequences of full-length Tana1 transposase. Gene position is shown in the &gt;gene ID of the fasta file.
DOI: 10.6084/m9.figshare.8289869
title: Images of mouse popliteal lymph node vascular structure derived using phase-contrast synchrotron micro-computed tomography (µCT)

description: This data record consists of a zipped folder <b>LN image stacks.zip. </b>The folder contains four other folders named <b>LN1</b>, <b>LN2</b>, <b>LN3</b> and <b>LN4</b> respectively. Each of these folders consists of a collection of images in <b>.tif file format.</b> These images were derived using phase-contrast synchrotron micro-computed tomography (µCT) and show details of lymph node (LN) vascular structure. Folders LN1-LN4 represent lymph node blood vessels of four mouse LNs that varied in overall nominal diameter from 1.0 – 1.4 mm.<br>The related study aimed to establish a corrosion casting <br>technique in combination with phase-contrast synchrotron micro-computed tomography (µCT) to quantify the details of lymph node vascular structure with the emphasis on the quantification of surface area distribution. By providing spatially-resolved 3D data on the distribution of blood vessels in lymph nodes, the eventual goal of the study was to understand LN transport phenomena down to the cell-level scale.<br>All experiments were undertaken with the approval of the Imperial College’s Animal Ethics Committee and were in accordance with its guidelines and the requirements of the United Kingdom Home Office regulations (ASPA 1986).<br>The blood in LN vasculature was flushed out and replaced with Mercox II resin to cast the lumen of the vasculature. The LN was then surgically excised and placed in a pipette tip before dissolving the tissue with potassium hydroxide. The freeze-dried samples were scanned with high-resolution synchrotron tomography and the radiographs were reconstructed into stack images using a phase-retrieval algorithm. The images were pre-processed by removing the pipette tip image using a cone crop before intensity-based segmentation and manual artefact processing. The binary data were then skeletonized and diameters and length of the vessels as well as the surface area density were calculated. Pressures and velocities of blood flow were estimated in each vessel based on an assumption of Poiseuille flow. The results were visualized with Imaris and further parameters quantified and plotted with Matlab. Please refer to the published article for more details on the methodology.<br>
DOI: 10.6084/m9.figshare.8289869.v1
title: Images of mouse popliteal lymph node vascular structure derived using phase-contrast synchrotron micro-computed tomography (µCT)

description: This data record consists of a zipped folder <b>LN image stacks.zip. </b>The folder contains four other folders named <b>LN1</b>, <b>LN2</b>, <b>LN3</b> and <b>LN4</b> respectively. Each of these folders consists of a collection of images in <b>.tif file format.</b> These images were derived using phase-contrast synchrotron micro-computed tomography (µCT) and show details of lymph node (LN) vascular structure. Folders LN1-LN4 represent lymph node blood vessels of four mouse LNs that varied in overall nominal diameter from 1.0 – 1.4 mm.<br>The related study aimed to establish a corrosion casting <br>technique in combination with phase-contrast synchrotron micro-computed tomography (µCT) to quantify the details of lymph node vascular structure with the emphasis on the quantification of surface area distribution. By providing spatially-resolved 3D data on the distribution of blood vessels in lymph nodes, the eventual goal of the study was to understand LN transport phenomena down to the cell-level scale.<br>All experiments were undertaken with the approval of the Imperial College’s Animal Ethics Committee and were in accordance with its guidelines and the requirements of the United Kingdom Home Office regulations (ASPA 1986).<br>The blood in LN vasculature was flushed out and replaced with Mercox II resin to cast the lumen of the vasculature. The LN was then surgically excised and placed in a pipette tip before dissolving the tissue with potassium hydroxide. The freeze-dried samples were scanned with high-resolution synchrotron tomography and the radiographs were reconstructed into stack images using a phase-retrieval algorithm. The images were pre-processed by removing the pipette tip image using a cone crop before intensity-based segmentation and manual artefact processing. The binary data were then skeletonized and diameters and length of the vessels as well as the surface area density were calculated. Pressures and velocities of blood flow were estimated in each vessel based on an assumption of Poiseuille flow. The results were visualized with Imaris and further parameters quantified and plotted with Matlab. Please refer to the published article for more details on the methodology.<br>
DOI: 10.6084/m9.figshare.8289827
title: ddPCR raw data - part 2

description: ddPCR raw data for both calibration curve and single-cell measurements
DOI: 10.6084/m9.figshare.8289728
title: ddPCR raw data - part 1

description: ddPCR raw data for both calibration curves and single-cell measurements
DOI: 10.6084/m9.figshare.8289650
title: Distribution data for 40 bryophyte species in Europe

description: Distribution data for 40 bryophyte species in Europe used for ecological modelling
DOI: 10.6084/m9.figshare.8289563
title: JupyterView.zip

description: Viewer for vertical stuff<br>
DOI: 10.6084/m9.figshare.8289650.v1
title: Distribution data for 40 bryophyte species in Europe

description: Distribution data for 40 bryophyte species in Europe used for ecological modelling
DOI: 10.6084/m9.figshare.8289536.v1
title: Sterlet.repeats.gff

description: <br>This file is a gff file contains a list of repeat sequences annotated from the sterlet genome
DOI: 10.6084/m9.figshare.8289563.v1
title: JupyterView.zip

description: Viewer for vertical stuff<br>
DOI: 10.6084/m9.figshare.8289308
title: Modelling disease risk for amyloid A (AA) amyloidosis in non-human primates using machine learning

description: <b>Objective:</b> Amyloid A (AA) amyloidosis is found in humans and non-human primates, but quantifying disease risk prior to clinical symptoms is challenging. We applied machine learning to identify the best predictors of amyloidosis in rhesus macaques from available clinical and pathology records. To explore potential biomarkers, we also assessed whether changes in circulating serum amyloid A (SAA) or lipoprotein profiles accompany the disease. <b>Methods:</b> We conducted a retrospective study using 86 cases and 163 controls matched for age and sex. We performed data reduction on 62 clinical, pathological and demographic variables, and applied multivariate modelling and model selection with cross-validation. To test the performance of our final model, we applied it to a replication cohort of 2,775 macaques. <b>Results:</b> The strongest predictors of disease were colitis, gastrointestinal adenocarcinoma, endometriosis, arthritis, trauma, diarrhoea and number of pregnancies. Sensitivity and specificity of the risk model were predicted to be 82%, and were assessed at 79 and 72%, respectively. Total, low density lipoprotein and high density lipoprotein cholesterol levels were significantly lower, and SAA levels and triglyceride-to-HDL ratios were significantly higher in cases versus controls. <b>Conclusion:</b> Machine learning is a powerful approach to identifying macaques at risk of AA amyloidosis, which is accompanied by increased circulating SAA and altered lipoprotein profiles.
DOI: 10.6084/m9.figshare.8289269
title: Ageing does not correlate with the formation of misfolded protein aggregates

description: a) Brightness profile along the length of two pairs of old and new pole daughters at the 24th generation of growth in a mother machine seeded with an overnight E. coli culture and of individual E. coli expressing exogenous GFP and loaded in a different mother machine from a different overnight culture. Only the latter exhibit significant depth in brightness in proximity of the bacterial poles resembling previously reported misfolded protein aggregates . Formal statistical comparisons of brightness profiles showed that (i) the wild type E. coli cells displayed significantly less evidence of pole-associated dark foci than E. coli expressing exogenous GFP (N=30 cells; p-value=0.005); (ii) wild type E. coli old pole daughters did not show significantly stronger evidence of pole-associated dark foci than same-generation new pole daughters (a paired t-test of N=10 pairs returned a p-value=0.4). <br>b) Thioflavin T (ThT) fluorescence profile along the length of two pairs of old and new pole daughters at the 24th generation of growth in a mother machine seeded with an overnight E. coli culture and of individual E. coli expressing exogenous misfolded proteins after 4h induction with IPTG dissolved in LB (to stimulate amyloid beta 42 production) in the mother machine from an overnight culture. Only the latter exhibit significant peaks in ThT fluorescence in proximity of the bacterial poles. Formal statistical comparisons of ThT fluorescence profiles revealed that (i) the wild type E. coli cells showed significantly less evidence of pole-associated ThT staining than E. coli expressing exogenous misfolded protein aggregates (N=30 cells; p-value=0.002); (ii) wild type E. coli old pole daughters did not show significantly stronger evidence of pole-associated ThT staining than same-generation new pole daughters (a paired t-test of N=10 pairs returned a p-value=0.2).
DOI: 10.6084/m9.figshare.8289308.v1
title: Modelling disease risk for amyloid A (AA) amyloidosis in non-human primates using machine learning

description: <b>Objective:</b> Amyloid A (AA) amyloidosis is found in humans and non-human primates, but quantifying disease risk prior to clinical symptoms is challenging. We applied machine learning to identify the best predictors of amyloidosis in rhesus macaques from available clinical and pathology records. To explore potential biomarkers, we also assessed whether changes in circulating serum amyloid A (SAA) or lipoprotein profiles accompany the disease. <b>Methods:</b> We conducted a retrospective study using 86 cases and 163 controls matched for age and sex. We performed data reduction on 62 clinical, pathological and demographic variables, and applied multivariate modelling and model selection with cross-validation. To test the performance of our final model, we applied it to a replication cohort of 2,775 macaques. <b>Results:</b> The strongest predictors of disease were colitis, gastrointestinal adenocarcinoma, endometriosis, arthritis, trauma, diarrhoea and number of pregnancies. Sensitivity and specificity of the risk model were predicted to be 82%, and were assessed at 79 and 72%, respectively. Total, low density lipoprotein and high density lipoprotein cholesterol levels were significantly lower, and SAA levels and triglyceride-to-HDL ratios were significantly higher in cases versus controls. <b>Conclusion:</b> Machine learning is a powerful approach to identifying macaques at risk of AA amyloidosis, which is accompanied by increased circulating SAA and altered lipoprotein profiles.
DOI: 10.6084/m9.figshare.8289269.v1
title: Ageing does not correlate with the formation of misfolded protein aggregates

description: a) Brightness profile along the length of two pairs of old and new pole daughters at the 24th generation of growth in a mother machine seeded with an overnight E. coli culture and of individual E. coli expressing exogenous GFP and loaded in a different mother machine from a different overnight culture. Only the latter exhibit significant depth in brightness in proximity of the bacterial poles resembling previously reported misfolded protein aggregates . Formal statistical comparisons of brightness profiles showed that (i) the wild type E. coli cells displayed significantly less evidence of pole-associated dark foci than E. coli expressing exogenous GFP (N=30 cells; p-value=0.005); (ii) wild type E. coli old pole daughters did not show significantly stronger evidence of pole-associated dark foci than same-generation new pole daughters (a paired t-test of N=10 pairs returned a p-value=0.4). <br>b) Thioflavin T (ThT) fluorescence profile along the length of two pairs of old and new pole daughters at the 24th generation of growth in a mother machine seeded with an overnight E. coli culture and of individual E. coli expressing exogenous misfolded proteins after 4h induction with IPTG dissolved in LB (to stimulate amyloid beta 42 production) in the mother machine from an overnight culture. Only the latter exhibit significant peaks in ThT fluorescence in proximity of the bacterial poles. Formal statistical comparisons of ThT fluorescence profiles revealed that (i) the wild type E. coli cells showed significantly less evidence of pole-associated ThT staining than E. coli expressing exogenous misfolded protein aggregates (N=30 cells; p-value=0.002); (ii) wild type E. coli old pole daughters did not show significantly stronger evidence of pole-associated ThT staining than same-generation new pole daughters (a paired t-test of N=10 pairs returned a p-value=0.2).
DOI: 10.6084/m9.figshare.8289251
title: GAD67 & Iba1 abutments measurements 8210 GP 2

description: GAD67 & Iba1 abutments measurements 8210 GP 2 2019 paper
DOI: 10.6084/m9.figshare.8289053
title: Data and R scripts

description: Complete data and R scripts corresponding to submitted Dexter et al. manuscript.
DOI: 10.6084/m9.figshare.8289044
title: d'Hondt et. al (2019) - Persuasive message elements

description: This dataset includes the list of persuasive message elements implemented in the APMS as discussed in the study '<i>Evaluation of computer-tailored motivational messaging in a health promotion context'</i> by d'Hondt et. al (2019).
DOI: 10.6084/m9.figshare.8289053.v1
title: Data and R scripts

description: Complete data and R scripts corresponding to submitted Dexter et al. manuscript.
DOI: 10.6084/m9.figshare.8289053.v2
title: Data and R scripts

description: Complete data and R scripts corresponding to submitted Dexter et al. manuscript.
DOI: 10.6084/m9.figshare.8289053.v4
title: Data and R scripts

description: Complete data and R scripts corresponding to submitted Dexter et al. manuscript.
DOI: 10.6084/m9.figshare.8289053.v3
title: Data and R scripts

description: Complete data and R scripts corresponding to submitted Dexter et al. manuscript.
DOI: 10.6084/m9.figshare.8288981
title: Dataset: Impact of a structured HIV testing program in a hospital emergency department and a primary care center

description: Dataset: Impact of a structured HIV testing program in a hospital emergency department and a primary care center
DOI: 10.6084/m9.figshare.8288981.v1
title: Dataset: Impact of a structured HIV testing program in a hospital emergency department and a primary care center

description: Dataset: Impact of a structured HIV testing program in a hospital emergency department and a primary care center
DOI: 10.6084/m9.figshare.8288882
title: d'Hondt et. al (2019) - Challenge list

description: This dataset includes the list of challenges/activities available to participants in the intervention discussed in the study '<i>Evaluation of computer-tailored motivational messaging in a health promotion context'</i> by d'Hondt et. al (2019).
DOI: 10.6084/m9.figshare.8288882.v1
title: d'Hondt et. al (2019) - Challenge list

description: This dataset includes the list of challenges/activities (including the amount of points rewarded upon completion) available to the participants of the study '<i>Evaluation of computer-tailored motivational messaging in a health promotion context'</i> by d'Hondt et. al (2019).
DOI: 10.6084/m9.figshare.8288858
title: Standing centre of pressure alters the vibration transmissibility response of the foot

description: Vibration-white foot as an occupational disease has underscored the need to better understand the vibration response of the foot. While vibration transmissibility data exist for a natural standing position, it is anticipated that weight distribution will affect the response. The purpose of this study was to determine the effects of changes in centre of pressure (COP) on the foot’s biomechanical response. Twenty-one participants were exposed to vertical vibration of 30 mm/s, with a sine sweep from 10–200 Hz. <i>Z</i>-axis (vertical) vibration was measured at 24 locations on the right foot, with the COP shifted forward or toward the heel. A mixed model analysis at each location revealed significant differences (<i>p</i> <b>Practitioner Summary</b>: Altering the centre of pressure location resulted in changes in the transmission of vibration through the foot. The forward lean position was associated with the greatest amplitude of vibration transmissibility at the toes. This information is relevant for clinicians studying vibration-induced white-foot and engineers designing protective equipment.
DOI: 10.6084/m9.figshare.8288858.v1
title: Standing centre of pressure alters the vibration transmissibility response of the foot

description: Vibration-white foot as an occupational disease has underscored the need to better understand the vibration response of the foot. While vibration transmissibility data exist for a natural standing position, it is anticipated that weight distribution will affect the response. The purpose of this study was to determine the effects of changes in centre of pressure (COP) on the foot’s biomechanical response. Twenty-one participants were exposed to vertical vibration of 30 mm/s, with a sine sweep from 10–200 Hz. <i>Z</i>-axis (vertical) vibration was measured at 24 locations on the right foot, with the COP shifted forward or toward the heel. A mixed model analysis at each location revealed significant differences (<i>p</i> <b>Practitioner Summary</b>: Altering the centre of pressure location resulted in changes in the transmission of vibration through the foot. The forward lean position was associated with the greatest amplitude of vibration transmissibility at the toes. This information is relevant for clinicians studying vibration-induced white-foot and engineers designing protective equipment.
DOI: 10.6084/m9.figshare.8288846
title: GAD67 & Iba1 abutments measurements 8210 GP 1

description: GAD67 & Iba1 abutments measurements 8210 GP 1 2019 paper
DOI: 10.6084/m9.figshare.8288882.v2
title: d'Hondt et. al (2019) - Persuasive message elements

description: This dataset includes the list of persuasive message elements implemented in the APMS as discussed in the study '<i>Evaluation of computer-tailored motivational messaging in a health promotion context'</i> by d'Hondt et. al (2019).
DOI: 10.6084/m9.figshare.8288846.v1
title: GAD67 & Iba1 abutments measurements 8210 GP 1

description: GAD67 & Iba1 abutments measurements 8210 GP 1 2019 paper
DOI: 10.6084/m9.figshare.8288807
title: Global spatio-temporally harmonised datasets for producing high-resolution gridded population distribution datasets

description: Multi-temporal, globally consistent, high-resolution human population datasets provide consistent and comparable population distributions in support of mapping sub-national heterogeneities in health, wealth, and resource access, and monitoring change in these over time. The production of more reliable and spatially detailed population datasets is increasingly necessary due to the importance of improving metrics at sub-national and multi-temporal scales. This is in support of measurement and monitoring of UN Sustainable Development Goals and related agendas. In response to these agendas, a method has been developed to assemble and harmonise a unique, open access, archive of geospatial datasets. Datasets are provided as global, annual time series, where pertinent at the timescale of population analyses and where data is available, for use in the construction of population distribution layers. The archive includes sub-national census-based population estimates, matched to a geospatial layer denoting administrative unit boundaries, and a number of co-registered gridded geospatial factors that correlate strongly with population presence and density. Here, we describe these harmonised datasets and their limitations, along with the production workflow. Further, we demonstrate applications of the archive by producing multi-temporal gridded population outputs for Africa and using these to derive health and development metrics. The geospatial archive is available at https://doi.org/10.5258/SOTON/WP00650.