cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17839324.v1
title: Time-to-Event Analysis with Unknown Time Origins via Longitudinal Biomarker Registration

description: In observational studies, the time origin of interest for time-to-event analysis is often unknown, such as the time of disease onset. Existing approaches to estimating the time origins are commonly built on extrapolating a parametric longitudinal model, which rely on rigid assumptions that can lead to biased inferences. In this paper, we introduce a flexible semiparametric curve registration model. It assumes the longitudinal trajectories follow a flexible common shape function with person-specific disease progression pattern characterized by a random curve registration function, which is further used to model the unknown time origin as a random start time. This random time is used as a link to jointly model the longitudinal and survival data where the unknown time origins are integrated out in the joint likelihood function, which facilitates unbiased and consistent estimation. Since the disease progression pattern naturally predicts time-to-event, we further propose a new functional survival model using the registration function as a predictor of the time-to-event. The asymptotic consistency and semiparametric efficiency of the proposed models are proved. Simulation studies and two real data applications demonstrate the effectiveness of this new approach. Supplementary materials for this article are available online.
DOI: 10.5281/zenodo.6306026
title: Significant differences between MT and Rahlfs' text of LXX in the non–kaige section of Kings

description: A listing of most cases of verse-level differences between the Masoretic Text and The Septuagint in Kings, most importantly in the non-kaige section of 1 Kings. Also a cursory search of cases in 2 Kings is included. This file forms an appendix to chapter “4. Textual history of the Books of Kings” in the <em>Oxford Handbook of Kings</em> (forthcoming).
DOI: 10.5281/zenodo.6306025
title: Significant differences between MT and Rahlfs' text of LXX in the non–kaige section of Kings

description: A listing of most cases of verse-level differences between the Masoretic Text and The Septuagint in Kings, most importantly in the non-kaige section of 1 Kings. Also a cursory search of cases in 2 Kings is included. This file forms an appendix to chapter “4. Textual history of the Books of Kings” in the <em>Oxford Handbook of Kings</em> (forthcoming).
DOI: 10.13140/rg.2.2.34682.57281
title: Prescription drugs 22-02-28
DOI: 10.5255/ukda-sn-855415
title: Fairwork Scores: Decent Work Standards on Platforms in South Africa, 2021

description: Work on digital labour platforms has been shown to frequently fall short of decent labour standards. Platform work takes place in a highly unregulated context, and in most countries platform workers are not protected by minimum labour standards governing pay, health and safety, fair due process, and representation. Platform work has rapidly expanded as an anticipated engine of job creation in the Global South, however, there is a lack of data to enable policymakers to evaluate job quality in the platform economy, and the potential of platform work to provide sustainable livelihoods. This project gathered data in South Africa against a set of criteria of decent platform work (the Fairwork Principles). The Principles were established through a process of consultation and consensus building with platform workers, platforms and other stakeholders from several regions, at meetings held at the ILO in 2018. Drawing on evidence provided by platform managers, research interviews with platform workers, and desk research, the resultant data took the form of 'scores' for prominent platforms in South Africa against five principles, and ten thresholds of decent work. We now share annual fairness scorecards for key platforms operating in the South African market, for 2019, 2020 and 2021.
DOI: 10.5281/zenodo.5898012
title: Vasculature Segmentation Validation Dataset - Part I - Simulated Tubes and Filter Responses

description: Dataset to allow exploration of data enhancement, segmentation, and validation for: https://www.biorxiv.org/content/10.1101/2020.07.21.213843v1 and associated future publications <strong>Dataset description:</strong> <em><strong>SimulatedTubes</strong></em>: Computationally produced tubes (3 different sizes) that are hollow, filled, or filled with Gaussian distribution. To study filter responses, artificial noise and blurring were added. <em><strong>DataExFilterResponse</strong></em>: Example data of the head vasculature of 4dpf of zebrafish, where the response to different filters is tested (i.e. GF - general filtering and TF - tubular filtering / Sato enhancement; for TF also different scale sizes are examined; see also: https://www.mdpi.com/2313-433X/5/1/14). <em><strong>Data acquisition:</strong></em><br> Experiments were performed according to the rules and guidelines of institutional and UK Home Office regulations under the Home Office Project Licence 70/8588 held by TC. Maintenance of adult zebrafish Tg(kdrl:HRAS-mCherry)s916 (Chi et al., 2008) was performed as described in standard husbandry protocols (Westerfield, 1993). Embryos, obtained from controlled mating, were kept in E3 medium buffer with methylene blue and staged as previously described (Kimmel et al., 1995). Embryos were embedded in 2% LMP-agarose with 0.01% Tricaine in E3 (MS-222, Sigma). Data were acquired using a Zeiss Z.1 light sheet microscope, Plan-Apochromat 20x/1.0 Corr nd=1.38 objective, dual-side illumination with online fusion, activated Pivot Scan, image acquisition chamber incubation at 28°C, with a scientific complementary metal-oxide semiconductor (sCMOS) detection unit. Data properties can be summarised as: 16bit image depth, voxel dimensions in x, y and z of 1920 x 1920 x 400-600, respectively, giving a voxel size of 0.33 x 0.33 x 0.5 µm). <em><strong>Contact</strong></em>: kugler.elisabeth[at]gmail.com <em><strong>Useful code links</strong></em>: https://github.com/ElisabethKugler/ZFVascularQuantification https://github.com/ElisabethKugler/Matlab3D-ImageAnalysis
DOI: 10.5281/zenodo.5898011
title: Vasculature Segmentation Validation Dataset - Part I - Simulated Tubes and Filter Responses

description: Dataset to allow exploration of data enhancement, segmentation, and validation for: https://www.biorxiv.org/content/10.1101/2020.07.21.213843v1 and associated future publications <strong>Dataset description:</strong> <em><strong>SimulatedTubes</strong></em>: Computationally produced tubes (3 different sizes) that are hollow, filled, or filled with Gaussian distribution. To study filter responses, artificial noise and blurring were added. <em><strong>DataExFilterResponse</strong></em>: Example data of the head vasculature of 4dpf of zebrafish, where the response to different filters is tested (i.e. GF - general filtering and TF - tubular filtering / Sato enhancement; for TF also different scale sizes are examined; see also: https://www.mdpi.com/2313-433X/5/1/14). <em><strong>Data acquisition:</strong></em><br> Experiments were performed according to the rules and guidelines of institutional and UK Home Office regulations under the Home Office Project Licence 70/8588 held by TC. Maintenance of adult zebrafish Tg(kdrl:HRAS-mCherry)s916 (Chi et al., 2008) was performed as described in standard husbandry protocols (Westerfield, 1993). Embryos, obtained from controlled mating, were kept in E3 medium buffer with methylene blue and staged as previously described (Kimmel et al., 1995). Embryos were embedded in 2% LMP-agarose with 0.01% Tricaine in E3 (MS-222, Sigma). Data were acquired using a Zeiss Z.1 light sheet microscope, Plan-Apochromat 20x/1.0 Corr nd=1.38 objective, dual-side illumination with online fusion, activated Pivot Scan, image acquisition chamber incubation at 28°C, with a scientific complementary metal-oxide semiconductor (sCMOS) detection unit. Data properties can be summarised as: 16bit image depth, voxel dimensions in x, y and z of 1920 x 1920 x 400-600, respectively, giving a voxel size of 0.33 x 0.33 x 0.5 µm). <em><strong>Contact</strong></em>: kugler.elisabeth[at]gmail.com <em><strong>Useful code links</strong></em>: https://github.com/ElisabethKugler/ZFVascularQuantification https://github.com/ElisabethKugler/Matlab3D-ImageAnalysis
DOI: 10.5281/zenodo.5910316
title: Vasculature Segmentation Validation Dataset - Part II - Decreasing Contrast-To-Noise Ratio

description: Dataset to allow exploration of data enhancement, segmentation, and validation for: https://www.biorxiv.org/content/10.1101/2020.07.21.213843v1 and associated future publications <strong>Dataset description:</strong> <em><strong>LaserForNoise</strong></em>: Example data of the head vasculature of 4dpf of zebrafish. The data were consecutively acquired with 1.2%, 0.8%, and 0.4% laser power (LP), respectively. This allowed us to produce data with decreasing contrast-to-noise ratio, and thus study robustness over a range of signal distributions. <em><strong>Data acquisition</strong></em>:<br> Experiments were performed according to the rules and guidelines of institutional and UK Home Office regulations under the Home Office Project Licence 70/8588 held by TC. Maintenance of adult zebrafish Tg(kdrl: HRAS-mCherry)s916 (Chi et al., 2008) was performed as described in standard husbandry protocols (Westerfield, 1993). Embryos, obtained from controlled mating, were kept in E3 medium buffer with methylene blue and staged as previously described (Kimmel et al., 1995). Embryos were embedded in 2% LMP-agarose with 0.01% Tricaine in E3 (MS-222, Sigma). Data were acquired using a Zeiss Z.1 light sheet microscope, Plan-Apochromat 20x/1.0 Corr nd=1.38 objective, dual-side illumination with online fusion, activated Pivot Scan, image acquisition chamber incubation at 28°C, with a scientific complementary metal-oxide-semiconductor (sCMOS) detection unit. Data properties can be summarised as: 16bit image depth, voxel dimensions in x, y and z of 1920 x 1920 x 400-600, respectively, giving a voxel size of 0.33 x 0.33 x 0.5 µm). <strong>Contact</strong>: kugler.elisabeth[at]gmail.com <strong>Useful code links</strong>: https://github.com/ElisabethKugler/ZFVascularQuantification https://github.com/ElisabethKugler/Matlab3D-ImageAnalysis
DOI: 10.5281/zenodo.5910315
title: Vasculature Segmentation Validation Dataset - Part II - Decreasing Contrast-To-Noise Ratio

description: Dataset to allow exploration of data enhancement, segmentation, and validation for: https://www.biorxiv.org/content/10.1101/2020.07.21.213843v1 and associated future publications <strong>Dataset description:</strong> <em><strong>LaserForNoise</strong></em>: Example data of the head vasculature of 4dpf of zebrafish. The data were consecutively acquired with 1.2%, 0.8%, and 0.4% laser power (LP), respectively. This allowed us to produce data with decreasing contrast-to-noise ratio, and thus study robustness over a range of signal distributions. <em><strong>Data acquisition</strong></em>:<br> Experiments were performed according to the rules and guidelines of institutional and UK Home Office regulations under the Home Office Project Licence 70/8588 held by TC. Maintenance of adult zebrafish Tg(kdrl: HRAS-mCherry)s916 (Chi et al., 2008) was performed as described in standard husbandry protocols (Westerfield, 1993). Embryos, obtained from controlled mating, were kept in E3 medium buffer with methylene blue and staged as previously described (Kimmel et al., 1995). Embryos were embedded in 2% LMP-agarose with 0.01% Tricaine in E3 (MS-222, Sigma). Data were acquired using a Zeiss Z.1 light sheet microscope, Plan-Apochromat 20x/1.0 Corr nd=1.38 objective, dual-side illumination with online fusion, activated Pivot Scan, image acquisition chamber incubation at 28°C, with a scientific complementary metal-oxide-semiconductor (sCMOS) detection unit. Data properties can be summarised as: 16bit image depth, voxel dimensions in x, y and z of 1920 x 1920 x 400-600, respectively, giving a voxel size of 0.33 x 0.33 x 0.5 µm). <strong>Contact</strong>: kugler.elisabeth[at]gmail.com <strong>Useful code links</strong>: https://github.com/ElisabethKugler/ZFVascularQuantification https://github.com/ElisabethKugler/Matlab3D-ImageAnalysis
DOI: 10.5281/zenodo.5914725
title: Vasculature Segmentation Validation Dataset - Part III - Biological Difference Dataset 1/2 (Exsanguination)

description: Dataset to allow exploration of data enhancement, segmentation, and validation for: https://www.biorxiv.org/content/10.1101/2020.07.21.213843v1 and associated future publications <strong>Dataset description</strong> <strong>Exsanguination</strong>: Example data of the head vasculature of 4dpf of zebrafish. Data acquisition before and after exsanguination by opening of the heart cavity with forceps in Tg(kdrl:HRAS-mCherry)s916 (4dpf; n=16 embryos from 2 experimental repeats). <br> <strong>Data acquisition</strong>:<br> Experiments were performed according to the rules and guidelines of institutional and UK Home Office regulations under the Home Office Project Licence 70/8588 held by TC. Maintenance of adult zebrafish Tg(kdrl:HRAS-mCherry)s916 (Chi et al., 2008) was performed as described in standard husbandry protocols (Westerfield, 1993). Embryos, obtained from controlled mating, were kept in E3 medium buffer with methylene blue and staged as previously described (Kimmel et al., 1995). Embryos were embedded in 2% LMP-agarose with 0.01% Tricaine in E3 (MS-222, Sigma). Data were acquired using a Zeiss Z.1 light sheet microscope, Plan-Apochromat 20x/1.0 Corr nd=1.38 objective, dual-side illumination with online fusion, activated Pivot Scan, image acquisition chamber incubation at 28°C, with a scientific complementary metal-oxide semiconductor (sCMOS) detection unit. Data properties can be summarised as: 16bit image depth, voxel dimensions in x, y and z of 1920 x 1920 x 400-600, respectively, giving a voxel size of 0.33 x 0.33 x 0.5 µm). <strong>Contact</strong>: kugler.elisabeth[at]gmail.com <strong>Useful code links</strong>: https://github.com/ElisabethKugler/ZFVascularQuantification<br> https://github.com/ElisabethKugler/Matlab3D-ImageAnalysis
DOI: 10.5281/zenodo.5914749
title: Vasculature Segmentation Validation Dataset - Part IV - Biological Difference Dataset 2/2 (Development)

description: Dataset to allow exploration of data enhancement, segmentation, and validation for: https://www.biorxiv.org/content/10.1101/2020.07.21.213843v1 and associated future publications<br> <strong>Dataset description</strong>: <strong>Development</strong>: Example data of the head vasculature of developing zebrafish. <br> <strong>Data acquisition</strong>:<br> Experiments were performed according to the rules and guidelines of institutional and UK Home Office regulations under the Home Office Project Licence 70/8588 held by TC. Maintenance of adult zebrafish Tg(kdrl:HRAS-mCherry)s916 (Chi et al., 2008) was performed as described in standard husbandry protocols (Westerfield, 1993). Embryos, obtained from controlled mating, were kept in E3 medium buffer with methylene blue and staged as previously described (Kimmel et al., 1995). Embryos were embedded in 2% LMP-agarose with 0.01% Tricaine in E3 (MS-222, Sigma). Data were acquired using a Zeiss Z.1 light sheet microscope, Plan-Apochromat 20x/1.0 Corr nd=1.38 objective, dual-side illumination with online fusion, activated Pivot Scan, image acquisition chamber incubation at 28°C, with a scientific complementary metal-oxide semiconductor (sCMOS) detection unit. Data properties can be summarised as: 16bit image depth, voxel dimensions in x, y and z of 1920 x 1920 x 400-600, respectively, giving a voxel size of 0.33 x 0.33 x 0.5 µm). <strong>Contact</strong>: kugler.elisabeth[at]gmail.com <strong>Useful code links</strong>: https://github.com/ElisabethKugler/ZFVascularQuantification https://github.com/ElisabethKugler/Matlab3D-ImageAnalysis<br>
DOI: 10.5281/zenodo.5914724
title: Vasculature Segmentation Validation Dataset - Part III - Biological Difference Dataset 1/2 (Exsanguination)

description: Dataset to allow exploration of data enhancement, segmentation, and validation for: https://www.biorxiv.org/content/10.1101/2020.07.21.213843v1 and associated future publications <strong>Dataset description</strong> <strong>Exsanguination</strong>: Example data of the head vasculature of 4dpf of zebrafish. Data acquisition before and after exsanguination by opening of the heart cavity with forceps in Tg(kdrl:HRAS-mCherry)s916 (4dpf; n=16 embryos from 2 experimental repeats). <br> <strong>Data acquisition</strong>:<br> Experiments were performed according to the rules and guidelines of institutional and UK Home Office regulations under the Home Office Project Licence 70/8588 held by TC. Maintenance of adult zebrafish Tg(kdrl:HRAS-mCherry)s916 (Chi et al., 2008) was performed as described in standard husbandry protocols (Westerfield, 1993). Embryos, obtained from controlled mating, were kept in E3 medium buffer with methylene blue and staged as previously described (Kimmel et al., 1995). Embryos were embedded in 2% LMP-agarose with 0.01% Tricaine in E3 (MS-222, Sigma). Data were acquired using a Zeiss Z.1 light sheet microscope, Plan-Apochromat 20x/1.0 Corr nd=1.38 objective, dual-side illumination with online fusion, activated Pivot Scan, image acquisition chamber incubation at 28°C, with a scientific complementary metal-oxide semiconductor (sCMOS) detection unit. Data properties can be summarised as: 16bit image depth, voxel dimensions in x, y and z of 1920 x 1920 x 400-600, respectively, giving a voxel size of 0.33 x 0.33 x 0.5 µm). <strong>Contact</strong>: kugler.elisabeth[at]gmail.com <strong>Useful code links</strong>: https://github.com/ElisabethKugler/ZFVascularQuantification<br> https://github.com/ElisabethKugler/Matlab3D-ImageAnalysis
DOI: 10.5281/zenodo.5914748
title: Vasculature Segmentation Validation Dataset - Part IV - Biological Difference Dataset 2/2 (Development)

description: Dataset to allow exploration of data enhancement, segmentation, and validation for: https://www.biorxiv.org/content/10.1101/2020.07.21.213843v1 and associated future publications<br> <strong>Dataset description</strong>: <strong>Development</strong>: Example data of the head vasculature of developing zebrafish. <br> <strong>Data acquisition</strong>:<br> Experiments were performed according to the rules and guidelines of institutional and UK Home Office regulations under the Home Office Project Licence 70/8588 held by TC. Maintenance of adult zebrafish Tg(kdrl:HRAS-mCherry)s916 (Chi et al., 2008) was performed as described in standard husbandry protocols (Westerfield, 1993). Embryos, obtained from controlled mating, were kept in E3 medium buffer with methylene blue and staged as previously described (Kimmel et al., 1995). Embryos were embedded in 2% LMP-agarose with 0.01% Tricaine in E3 (MS-222, Sigma). Data were acquired using a Zeiss Z.1 light sheet microscope, Plan-Apochromat 20x/1.0 Corr nd=1.38 objective, dual-side illumination with online fusion, activated Pivot Scan, image acquisition chamber incubation at 28°C, with a scientific complementary metal-oxide semiconductor (sCMOS) detection unit. Data properties can be summarised as: 16bit image depth, voxel dimensions in x, y and z of 1920 x 1920 x 400-600, respectively, giving a voxel size of 0.33 x 0.33 x 0.5 µm). <strong>Contact</strong>: kugler.elisabeth[at]gmail.com <strong>Useful code links</strong>: https://github.com/ElisabethKugler/ZFVascularQuantification https://github.com/ElisabethKugler/Matlab3D-ImageAnalysis<br>
DOI: 10.6073/pasta/6f08a2f716eec881b544ee06750544ab
title: Influence of soil amendment and crop species on nutrient cycling in a St. Paul urban garden

description: An experiment was conducted from 2017-2021 at the University of St. Thomas research garden (Saint Paul, MN) to determine rates of nutrient recycling and loss from compost applied to urban gardens. Thirty-two 4 square-meter study plots received one of six different soil amendment treatments, with four different crops growing on each plot. Meteorological data includes hourly measurements of rainfall, solar radiation, temperature and relative humidity, and wind speed and direction, from June 2017-August 2021. Hourly soil moisture measurements were recorded at depths of 10 cm, 20 cm, and 30 cm, from June-December 2021. Annual crop harvest totals from each subplot are reported for 2017-2021. Leachate was collected from lysimeters installed in each of the 132 subplots weekly from June-October of each year (2017-2021), recording total volume. Leachate subsamples were analyzed for NO 3 -N, NH 4 -N, and PO 4 -P. Soil samples were collected at the beginning and end of the growing season in 2017, and every two weeks during the growing season from 2018-2021, and analyzed for pH, organic matter, Bray-1 extractable P, available K, nitrate, and ammonium, at the University of Minnesota Analytical Research Laboratory.
DOI: 10.5281/zenodo.5513825
title: Data for "Spurious forces can dominate the vorticity budget of ocean gyres on the C-grid"

description: This contains data for the submitted paper "Spurious forces can dominate the vorticity budget of ocean gyres on the C-grid" which has been submitted to JAMES.
description: This work was financially supported by the Natural Environment Research Council NE/S007474/1. This work used Monsoon2, a collaborative High-Performance Computing facility funded by the Met Office and the Natural Environment Research Council and used JASMIN, the UK collaborative data analysis facility.
DOI: 10.5281/zenodo.5513824
title: Data for "Spurious forces can dominate the vorticity budget of ocean gyres on the C-grid"

description: This contains data for the submitted paper "Spurious forces can dominate the vorticity budget of ocean gyres on the C-grid" which has been submitted to JAMES.
description: This work was financially supported by the Natural Environment Research Council NE/S007474/1. This work used Monsoon2, a collaborative High-Performance Computing facility funded by the Met Office and the Natural Environment Research Council and used JASMIN, the UK collaborative data analysis facility.
DOI: 10.17632/cytx9tt93b.1
title: Condensate liquid viscosity data-bank for modelling and optimizing gas-condensate reservoirs below the saturation pressure. 

description: The gas-condensate liquid viscosity is recorded as a function of Pressure, Temperature and Solution gas to oil ratio (GOR) or normally presented as Rs using constant volume depletion experiment. All three aforementioned parameters of pressure, temperature and GOR strongly define the true characteristics of gas-condensate reservoir fluid below the saturation pressure, hence condensate liquid viscosity. 

The units for each factor are as follow:
The pressure recorded in Pounds per square inch absolute (psia), Temperature recorded in degree Fahrenheit (F), solution gas to oil ratio corrected from Standing correlation and recorded in standard cubic foot per stock tank barrel (scf/STB) and condensate liquid viscosity is measured and recorded in centipoise (cp). 

The data can be used in modelling condensate liquid viscosity as a predominant factor in modelling and simulation of gas-condensate reservoirs below the saturation pressure. This also helps better performance modelling of such reservoirs and increase production efficiency.