cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4629231
title: Local Z Projector example dataset and parameters 03

description: Adult zebrafish brain, imaged on a laser-scanning confocal microscope. Brains were dissected in 1X solution of phosphate buffered saline (PBS - Fisher Bioreagents) and directly transferred to a 4% paraformaldehyde solution in PBS for fixation. They were fixed for 2 to 4 hours at room temperature (RT) under permanent agitation. After four washing steps in PBS, brains were dehydrated through 5 minutes series of 25%, 50% and 75% methanol diluted in 0.1% tween-20 (Sigma Life Science – P9416) PBS solution and kept in 100% methanol (Sigma-Aldrich, 322415) at -20°C. The whole-mount immunohistochemistry (IHC) started by the rehydration of the telencephali. Then, the brains were subjected to an antigen retrieval step using Histo-VT One (Nacalai Tesque) for an hour at 65°C. Brains were rinsed in a 0.1% DMSO and 0.1% Triton X-100 (Sigma Life Science– 1002135493) PBS 1X solution (PBT) and then blocked with 4% normal goat serum in PBT (blocking buffer) 4 hours at RT. The blocking buffer was later replaced by the primary antibodies solution, and the brains were kept overnight at 4°C on a rocking platform. The next day, brains were rinsed over 24 hours at room temperature with PBT and incubated in a solution of secondary antibodies diluted in PBT overnight, in the dark, and at 4°C on a rocking platform. After several washes, the telencephali were mounted in PBS on slides using a 0.7 mm-thick holder. The primary antibody anti-ZO1 was used at 1:200 (Mouse monoclonal IgG1 anti-ZO1, Thermo Fisher, cat. #33-9100, RRID: AB_2533147) and the secondary antibody anti IgG was used at 1:1000 (Goat anti-Mouse IgG (H+L) Alexa633 conjugated, Thermo Fisher, cat. #A-21052, RRID : AB_2535719). Images of whole-mounted immunostained telencephali were acquired on confocal microscope (LSM700, Carl Zeiss A.G), using a 40X oil objective. We acquired images with a z-step of 0.65 µm. We averaged each line four times with an image resolution of 1024 ×1024 pixels with a bit-depth of 12-bits. We recorded mosaics with a 15% overlap to image an entire hemisphere per fish. See the accompanying paper: <em>DProj: A toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images.</em> https://www.biorxiv.org/content/10.1101/2021.01.15.426809v2
DOI: 10.5281/zenodo.4629230
title: Local Z Projector example dataset and parameters 03

description: Adult zebrafish brain, imaged on a laser-scanning confocal microscope. Brains were dissected in 1X solution of phosphate buffered saline (PBS - Fisher Bioreagents) and directly transferred to a 4% paraformaldehyde solution in PBS for fixation. They were fixed for 2 to 4 hours at room temperature (RT) under permanent agitation. After four washing steps in PBS, brains were dehydrated through 5 minutes series of 25%, 50% and 75% methanol diluted in 0.1% tween-20 (Sigma Life Science – P9416) PBS solution and kept in 100% methanol (Sigma-Aldrich, 322415) at -20°C. The whole-mount immunohistochemistry (IHC) started by the rehydration of the telencephali. Then, the brains were subjected to an antigen retrieval step using Histo-VT One (Nacalai Tesque) for an hour at 65°C. Brains were rinsed in a 0.1% DMSO and 0.1% Triton X-100 (Sigma Life Science– 1002135493) PBS 1X solution (PBT) and then blocked with 4% normal goat serum in PBT (blocking buffer) 4 hours at RT. The blocking buffer was later replaced by the primary antibodies solution, and the brains were kept overnight at 4°C on a rocking platform. The next day, brains were rinsed over 24 hours at room temperature with PBT and incubated in a solution of secondary antibodies diluted in PBT overnight, in the dark, and at 4°C on a rocking platform. After several washes, the telencephali were mounted in PBS on slides using a 0.7 mm-thick holder. The primary antibody anti-ZO1 was used at 1:200 (Mouse monoclonal IgG1 anti-ZO1, Thermo Fisher, cat. #33-9100, RRID: AB_2533147) and the secondary antibody anti IgG was used at 1:1000 (Goat anti-Mouse IgG (H+L) Alexa633 conjugated, Thermo Fisher, cat. #A-21052, RRID : AB_2535719). Images of whole-mounted immunostained telencephali were acquired on confocal microscope (LSM700, Carl Zeiss A.G), using a 40X oil objective. We acquired images with a z-step of 0.65 µm. We averaged each line four times with an image resolution of 1024 ×1024 pixels with a bit-depth of 12-bits. We recorded mosaics with a 15% overlap to image an entire hemisphere per fish. See the accompanying paper: <em>DProj: A toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images.</em> https://www.biorxiv.org/content/10.1101/2021.01.15.426809v2
DOI: 10.6084/m9.figshare.14267651.v1
title: Supplementary Material for: Predictors of Survival in Chronic Hemodialysis Patients: A 10-Year Longitudinal Follow-Up Analysis

description: <b><i>Background:</i></b> Risk factors of mortality in chronic hemodialysis patients have not yet been sufficiently evaluated. In particular, chronological transits and interactions of the impact of risk factors have rarely been described. <b><i>Methods:</i></b> This study is a post hoc analysis of the participants in the Olme­sartan Clinical Trial in Okinawan Patients under OKIDS (OCTOPUS) study conducted between June 2006 and June 2011. We additionally followed up on the prognosis of the participants until July 31, 2018. Standardized univariable and multivariable Cox regression analyses were used to evaluate the influences of the participants’ baseline characteristics on all-cause mortality. We also evaluated chronological changes in the impacts of risk factors, interactions among predictors, and the influence of missing values using sensitivity analyses. <b><i>Results:</i></b> Of the 469 original trial participants, 461 participants were evaluated. The median time of follow-up was 10.2 years. A total of 211 (45.8%) participants were deceased. The leading causes of death were infection (<i>n</i> = 72, 34.1%) and cardiovascular disease (<i>n</i> = 66, 31.3%). Univariate and multivariate Cox regression analyses revealed that the impact of diabetes mellitus, history of coronary intervention, and hypoalbuminemia were significant risk factors for mortality during the whole follow-up period. During the early follow-up period (≤3 years), standardized univariate Cox regression analyses revealed that history of amputation (hazard ratio [HR] = 4.61, <i>p</i> &lt; 0.001), lower dry weight, higher cardiothoracic ratio, and lower potassium levels were statistically significant risks. In those who survived for longer than 3 years, a history of stroke (HR = 1.73, <i>p =</i> 0.006), higher systolic blood pressure, lower serum sodium levels, and higher levels of hemoglobin, and serum phosphate were significant risks. We also observed a stable interaction between the impacts of serum phosphate and albumin on all-cause mortality. <b><i>Conclusion:</i></b> In chronic hemodialysis patients, targets to improve the short-term prognosis and long-term prognosis are not equivalent. Hyperphosphatemia was a significant risk factor for the all-cause mortality among patients with normal serum albumin levels but not among patients with compromised albumin levels.
DOI: 10.6084/m9.figshare.14267651
title: Supplementary Material for: Predictors of Survival in Chronic Hemodialysis Patients: A 10-Year Longitudinal Follow-Up Analysis

description: <b><i>Background:</i></b> Risk factors of mortality in chronic hemodialysis patients have not yet been sufficiently evaluated. In particular, chronological transits and interactions of the impact of risk factors have rarely been described. <b><i>Methods:</i></b> This study is a post hoc analysis of the participants in the Olme­sartan Clinical Trial in Okinawan Patients under OKIDS (OCTOPUS) study conducted between June 2006 and June 2011. We additionally followed up on the prognosis of the participants until July 31, 2018. Standardized univariable and multivariable Cox regression analyses were used to evaluate the influences of the participants’ baseline characteristics on all-cause mortality. We also evaluated chronological changes in the impacts of risk factors, interactions among predictors, and the influence of missing values using sensitivity analyses. <b><i>Results:</i></b> Of the 469 original trial participants, 461 participants were evaluated. The median time of follow-up was 10.2 years. A total of 211 (45.8%) participants were deceased. The leading causes of death were infection (<i>n</i> = 72, 34.1%) and cardiovascular disease (<i>n</i> = 66, 31.3%). Univariate and multivariate Cox regression analyses revealed that the impact of diabetes mellitus, history of coronary intervention, and hypoalbuminemia were significant risk factors for mortality during the whole follow-up period. During the early follow-up period (≤3 years), standardized univariate Cox regression analyses revealed that history of amputation (hazard ratio [HR] = 4.61, <i>p</i> &lt; 0.001), lower dry weight, higher cardiothoracic ratio, and lower potassium levels were statistically significant risks. In those who survived for longer than 3 years, a history of stroke (HR = 1.73, <i>p =</i> 0.006), higher systolic blood pressure, lower serum sodium levels, and higher levels of hemoglobin, and serum phosphate were significant risks. We also observed a stable interaction between the impacts of serum phosphate and albumin on all-cause mortality. <b><i>Conclusion:</i></b> In chronic hemodialysis patients, targets to improve the short-term prognosis and long-term prognosis are not equivalent. Hyperphosphatemia was a significant risk factor for the all-cause mortality among patients with normal serum albumin levels but not among patients with compromised albumin levels.
DOI: 10.6084/m9.figshare.14267552
title: Supplementary Material for: Behçet’s Disease Is Associated with Multiple Sclerosis and Rheumatoid Arthritis: A Korean Population-Based Study

description: <b><i>Background:</i></b> No epidemiologic study has previously reported on the associations among Behçet’s disease (BD) and autoimmune disorders. <b><i>Objectives:</i></b> To investigate the association between BD and the autoimmune disorders multiple sclerosis and rheumatoid arthritis. <b><i>Methods:</i></b> Medical records of patients newly diagnosed with BD (<i>n</i> = 6,214) in 2012–2017 were analyzed using data entered into a large, nationwide database from 2007 to 2017. An age- and sex-matched control population of individuals without BD was sampled at a ratio of controls:BD cases of 3:1 (<i>n</i> = 18,642). Both cohorts were analyzed for the presence of multiple sclerosis or rheumatoid arthritis within a minimum of 5 years prior to their BD diagnosis. <b><i>Results:</i></b> Patients with BD had significantly higher odds ratios (ORs) for multiple sclerosis (8.85 [95% CI 2.36–33.17]) and rheumatoid arthritis (4.62 [95% CI 3.35–6.35]) than the control group after adjustment for diabetes mellitus, hypertension, and dyslipidemia. BD patients aged &lt;40 years had a higher proportion of rheumatoid arthritis (OR 23.91, 95% CI 5.50–103.9) than older patients (OR 3.96, 95% CI 2.83–5.54). <b><i>Conclusion:</i></b> Our results suggest that BD is associated with multiple sclerosis and rheumatoid arthritis.
DOI: 10.5281/zenodo.4629314
title: Daily Italian Deaths - 2015-2020 - ISTAT

description: Daily Italian Deaths in the period between 2015 and 2020 broken down of NUT-1 Code, Municipality, age classes, and gender.
DOI: 10.5281/zenodo.4629313
title: Daily Italian Deaths - 2015-2020 - ISTAT

description: Daily Italian Deaths in the period between 2015 and 2020 broken down of NUT-1 Code, Municipality, age classes, and gender.
DOI: 10.5281/zenodo.4628934
title: Machine Learning Dataset for Poultry Diseases Diagnostics

description: The annotated dataset of poultry disease diagnostics for small to medium-scale poultry farmers consists of poultry fecal images. The poultry fecal images were taken in Arusha and Kilimanjaro regions in Tanzania between September 2020 and February 2021 using Open Data Kit (ODK) app on mobile phones. The typical normal fecal material which is the ‘healthy’ class and Coccidiosis disease, the ‘cocci’ class were taken from poultry farms. The chickens were inoculated for Salmonella disease and fecal images taken from the diseased chickens for the ‘salmo’ class after one week. The chickens were also inoculated for Newcastle disease and fecal images for the 'ncd' class were taken within three days. All images are in the <strong>.zip files</strong>; “cocci.zip” has 2103 images, “healthy.zip” has 2057 images, “salmo.zip” has 2276 images, "ncd.zip" has 376 images. A total of 6,812 image files are labeled. The “imgObjDet_Yolo.zip” and “imgSegmentation.zip” files consist of the corresponding annotations for object detection on YOLO framework and JSON files for semantic segmentation tasks respectively. The research project is funded by the International Development Research Centre (IDRC) with IDRC Grant Number: 109187-002.
DOI: 10.6084/m9.figshare.14267327
title: Supplementary Material for: Real-Life Experience of Monoclonal Antibody Treatments in Chronic Rhinosinusitis with Nasal Polyposis

description: <b><i>Introduction:</i></b> Few studies assess biologicals such as, omalizumab, mepolizumab, benralizumab, and dupilumab in patients suffering from chronic rhinosinusitis with nasal polyposis (CRSwNP). The reported success rate in these studies differ, and it remains uncertain if there are any biomarkers to predict successful therapy. Our aim was to analyze the therapeutic outcome in a real life setting and to identify predictive biomarkers for successful treatment. <b><i>Methods:</i></b> Data from patients with CRSwNP treated with a monoclonal antibody between November 2014 and January 2020 were analyzed retrospectively. Improvement in the polyp score and clinical symptoms like nasal obstruction, sense of smell, nasal discharge, and facial pain were evaluated. Other characteristics, including use of nasal or systemic steroids, comorbidities, previous history of sinus surgery, eosinophilia tissue, blood values (eosinophils, total immunoglobulin E, eosinophilic cationic protein, and interleukin 5), and allergic sensitization in serum were also investigated to identify possible predictive biomarkers. <b><i>Results:</i></b> Forty-eight treatments in 29 patients (m/f = 15/14) aged 27–70 years were reviewed. Treatments with mepolizumab showed the best success rates (78.9%), followed by omalizumab (50%) and benralizumab treatments (50%). However, a correlation between biomarkers and treatment success could not be found. <b><i>Discussion/Conclusion:</i></b> Treatment of CRSwNP with biologicals is a promising option for severe cases not responding to conventional therapy, including difficult-to-treat patients. Predictive biomarkers for a successful treatment could not be identified, but the reduction of eosinophilic cationic protein was linked with the response.
DOI: 10.5281/zenodo.4629321
title: Safeguarding the energy transition against political backlash to carbon markets

description: Figure raw data for the manuscript titled "Safeguarding the energy transition against political backlash to carbon markets" (under review).
DOI: 10.6084/m9.figshare.13084595
title: Spatio-temporal group dynamics of snowfinches

description: Database of Snowfinch observations with coordinates, date and number of individuals recorded.
DOI: 10.6084/m9.figshare.13084595.v1
title: Spatio-temporal group dynamics of snowfinches

description: Database of Snowfinch observations with coordinates, date and number of individuals recorded.
DOI: 10.25403/upresearchdata.13309112
title: Competitive strategies for small business survival: a Gauteng township retail industry study

description: Submission of raw data and supporting documentation for a qualitative study. Datasets include non-disclosure agreements signed by the transcriber and editor, a code list, interview transcriptions and signed letter of consents from the participants.
DOI: 10.25403/upresearchdata.13309112.v1
title: Competitive strategies for small business survival: a Gauteng township retail industry study

description: Submission of raw data and supporting documentation for a qualitative study. Datasets include non-disclosure agreements signed by the transcriber and editor, a code list, interview transcriptions and signed letter of consents from the participants.
DOI: 10.6084/m9.figshare.14267738
title: Supplementary Material for: Interdigitation and Ellipsoid Zones Disruption Correlate with Visual Outcomes among Treatment-Naive Patients with Diabetic Macular Edema

description: <b><i>Introduction:</i></b> We have recently shown that defects in interdigitation and ellipsoid zones (IZ and EZ) can predict response to anti-VEGF therapy in a small group of treatment-naive diabetic macular edema (DME) patients. The aim of the current study is to further evaluate this association in a larger study group of patients over a longer follow-up time. <b><i>Methods:</i></b> Thirty eyes of 30 treatment-naive DME patients were analyzed in this retrospective study. The integrity of foveal IZ and EZ was evaluated using optical coherence tomography at the diagnosis of DME and following anti-VEGF injections. The defect size was correlated with best-corrected visual acuity (BCVA) and central macular thickness (CMT). <b><i>Results:</i></b> The mean patients’ age at baseline was 63.0 ± 10.0 years. Patients underwent 3.9 ± 2.9 anti-VEGF injections for a mean of 9.1 ± 4.8 months. Following treatment, the mean Snellen visual acuity (VA) improved from 20/52 to 20/44 (<i>p</i> = 0.05), CMT decreased from 432.5 ± 141.4 μm to 375.2 ± 121.4 µm (<i>p</i> = 0.05) and IZ/EZ defect size decreased from 259.83 ± 375.94 µm to 65.34 ± 143.97 µm (<i>p</i> = 0.001). In patients with no IZ/EZ defects at baseline, the mean Snellen VA was better when compared to those with IZ/EZ defects (20/36 vs. 20/70, <i>p</i> = 0.031). The number of eyes with IZ/EZ defects decreased from 17 (57%) at baseline to 6 (20%) at end of follow-up (<i>p</i> &lt; 0.01). BCVA gain correlated with IZ/EZ defect size reduction (<i>r</i> = 0.41, <i>p</i> = 0.02) but not with improvement in CMT (<i>r</i> = 0.28, <i>p</i> = 0.121). <b><i>Conclusions:</i></b> IZ/EZ defect size correlated not only with baseline BCVA but also predicted the change in BCVA after anti-VEGF treatment. Possible future automatic measurement of IZ/EZ defect size might prove helpful for the evaluation of treatment response.
DOI: 10.6084/m9.figshare.14267738.v1
title: Supplementary Material for: Interdigitation and Ellipsoid Zones Disruption Correlate with Visual Outcomes among Treatment-Naive Patients with Diabetic Macular Edema

description: <b><i>Introduction:</i></b> We have recently shown that defects in interdigitation and ellipsoid zones (IZ and EZ) can predict response to anti-VEGF therapy in a small group of treatment-naive diabetic macular edema (DME) patients. The aim of the current study is to further evaluate this association in a larger study group of patients over a longer follow-up time. <b><i>Methods:</i></b> Thirty eyes of 30 treatment-naive DME patients were analyzed in this retrospective study. The integrity of foveal IZ and EZ was evaluated using optical coherence tomography at the diagnosis of DME and following anti-VEGF injections. The defect size was correlated with best-corrected visual acuity (BCVA) and central macular thickness (CMT). <b><i>Results:</i></b> The mean patients’ age at baseline was 63.0 ± 10.0 years. Patients underwent 3.9 ± 2.9 anti-VEGF injections for a mean of 9.1 ± 4.8 months. Following treatment, the mean Snellen visual acuity (VA) improved from 20/52 to 20/44 (<i>p</i> = 0.05), CMT decreased from 432.5 ± 141.4 μm to 375.2 ± 121.4 µm (<i>p</i> = 0.05) and IZ/EZ defect size decreased from 259.83 ± 375.94 µm to 65.34 ± 143.97 µm (<i>p</i> = 0.001). In patients with no IZ/EZ defects at baseline, the mean Snellen VA was better when compared to those with IZ/EZ defects (20/36 vs. 20/70, <i>p</i> = 0.031). The number of eyes with IZ/EZ defects decreased from 17 (57%) at baseline to 6 (20%) at end of follow-up (<i>p</i> &lt; 0.01). BCVA gain correlated with IZ/EZ defect size reduction (<i>r</i> = 0.41, <i>p</i> = 0.02) but not with improvement in CMT (<i>r</i> = 0.28, <i>p</i> = 0.121). <b><i>Conclusions:</i></b> IZ/EZ defect size correlated not only with baseline BCVA but also predicted the change in BCVA after anti-VEGF treatment. Possible future automatic measurement of IZ/EZ defect size might prove helpful for the evaluation of treatment response.
DOI: 10.5281/zenodo.3554517
title: Data archive for paper "WRF‐TEB: Implementation and Evaluation of the Coupled Weather Research and Forecasting (WRF) and Town Energy Balance (TEB) Model"

description: <strong>WRF-TEB data archive</strong> This archive contains data and tools to reproduce results as included in Meyer et al. (2020). <strong>Prerequisites</strong> Singularity version &gt;= 3. <strong>Usage</strong> To run all models and plotting scripts included in integration test and meteorological evaluation, run the following command from your command-line interface. <pre><code>NPROC=8 TYPE=evaluate tools/singularity/run.sh</code></pre> where <code>NPROC=8</code> is the maximum number of processes to use. The output can be found in the <code>work/</code> folder. <strong>HPC</strong> If you want to use this in an HPC environment, use <code>tools/hpc</code> as a template. As an example, to run the evaluation on Imperial HPC using PBS (Portable Batch System), use: <pre><code>qsub -v REPO_ROOT=$(pwd),TYPE=evaluate tools/hpc/job_imperial.sh</code></pre> <strong>Copyright and License</strong> Copyright and licensing information are included at the top of source files or as separate files in folders. <strong>References</strong> Meyer, D., Schoetter, R., Riechert, M., Verrelle, A., Tewari, M., Dudhia, J., Masson, V., Reeuwijk, M., & Grimmond, S. (2020). WRF‐TEB: implementation and evaluation of the coupled Weather Research and Forecasting (WRF) and Town Energy Balance (TEB) model. Journal of Advances in Modeling Earth Systems. https://doi.org/10.1029/2019ms001961
DOI: 10.5281/zenodo.3554516
title: Data archive for paper "WRF‐TEB: Implementation and Evaluation of the Coupled Weather Research and Forecasting (WRF) and Town Energy Balance (TEB) Model"

description: <strong>WRF-TEB data archive</strong> This archive contains data and tools to reproduce results as included in Meyer et al. (2020). <strong>Prerequisites</strong> Singularity version &gt;= 3. <strong>Usage</strong> To run all models and plotting scripts included in integration test and meteorological evaluation, run the following command from your command-line interface. <pre><code>NPROC=8 TYPE=evaluate tools/singularity/run.sh</code></pre> where <code>NPROC=8</code> is the maximum number of processes to use. The output can be found in the <code>work/</code> folder. <strong>HPC</strong> If you want to use this in an HPC environment, use <code>tools/hpc</code> as a template. As an example, to run the evaluation on Imperial HPC using PBS (Portable Batch System), use: <pre><code>qsub -v REPO_ROOT=$(pwd),TYPE=evaluate tools/hpc/job_imperial.sh</code></pre> <strong>Copyright and License</strong> Copyright and licensing information are included at the top of source files or as separate files in folders. <strong>References</strong> Meyer, D., Schoetter, R., Riechert, M., Verrelle, A., Tewari, M., Dudhia, J., Masson, V., Reeuwijk, M., & Grimmond, S. (2020). WRF‐TEB: implementation and evaluation of the coupled Weather Research and Forecasting (WRF) and Town Energy Balance (TEB) model. Journal of Advances in Modeling Earth Systems. https://doi.org/10.1029/2019ms001961