cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5882437
title: System loss assessment of bridge networks accounting for multi-hazard interactions

description: This paper details an integrated method for the multi-hazard risk assessment of road infrastructure systems exposed to potential earthquake and flood events. A harmonisation effort is required to reconcile bridge fragility models and damage scales from different hazard types: this is achieved by the derivation of probabilistic functionality curves, which express the probability of reaching or exceeding a loss level given the seismic intensity measure. Such probabilistic tools are essential for the loss assessment of infrastructure systems, since they directly provide the functionality losses instead of the physical damage states. Multi-hazard interactions at the vulnerability level are ensured by the functionality loss curves, which result from the assembly of hazard-specific fragility curves for local damage mechanisms. At the hazard level, the potential overlap between earthquake and flood events is represented by a time window during which the effects of one hazard type on the infrastructure may still be present: the value of this temporal parameter is based on the repair duration estimates provided by the functionality loss curves. The proposed framework is implemented through Bayesian Networks, thus enabling the propagation of uncertainties and the computation of joint probabilities. The procedure is demonstrated on a bridge example and a hypothetical road network.
DOI: 10.6084/m9.figshare.5882437.v1
title: System loss assessment of bridge networks accounting for multi-hazard interactions

description: This paper details an integrated method for the multi-hazard risk assessment of road infrastructure systems exposed to potential earthquake and flood events. A harmonisation effort is required to reconcile bridge fragility models and damage scales from different hazard types: this is achieved by the derivation of probabilistic functionality curves, which express the probability of reaching or exceeding a loss level given the seismic intensity measure. Such probabilistic tools are essential for the loss assessment of infrastructure systems, since they directly provide the functionality losses instead of the physical damage states. Multi-hazard interactions at the vulnerability level are ensured by the functionality loss curves, which result from the assembly of hazard-specific fragility curves for local damage mechanisms. At the hazard level, the potential overlap between earthquake and flood events is represented by a time window during which the effects of one hazard type on the infrastructure may still be present: the value of this temporal parameter is based on the repair duration estimates provided by the functionality loss curves. The proposed framework is implemented through Bayesian Networks, thus enabling the propagation of uncertainties and the computation of joint probabilities. The procedure is demonstrated on a bridge example and a hypothetical road network.
DOI: 10.6084/m9.figshare.5882431
title: Supplementary Material for: Effect of the Opioid Crisis on the Donor Pool for Kidney Transplantation: An Analysis of National Kidney Deceased Donor Trends from 2010–2016

description: <b><i>Background:</i></b> The opioid crisis has led to a dramatic increase in the number of drug overdose deaths in the United States. Little is known about the effect of the opioid crisis on the kidney transplant donor pool, particularly on hepatitis C virus (HCV)-infected donors. <b><i>Methods:</i></b> This is a retrospective analysis of the data from the Organ Procurement and Transplantation Network from 2010 to 2016. We determined the changes in characteristics of kidney transplant donors and evaluated which changes may be directly related to the opioid crisis. <b><i>Results:</i></b> Between 2010 and 2016, we found a 26% increase in overall donors, including a 277% increase in the number of donors who died from drug overdose. Nineteen percent of donors who died of drug overdose had HCV infection. Donors who die from drug overdose and donors with HCV infection are younger, less likely to have diabetes or hypertension, and have favorable kidney donor profile index scores compared to average donors. Despite these favorable characteristics, HCV-infected donors appear to be notably underutilized, with substantially lower kidneys per donor being transplanted compared to HCV uninfected donors. <b><i>Conclusion:</i></b> The opioid crisis in the United States has substantially altered the kidney donor pool. Strategies to increase utilization of all potentially viable kidneys for transplant are needed, particularly in this era of new, highly effective, direct-acting antiviral therapy for HCV infection.
DOI: 10.6084/m9.figshare.5882431.v1
title: Supplementary Material for: Effect of the Opioid Crisis on the Donor Pool for Kidney Transplantation: An Analysis of National Kidney Deceased Donor Trends from 2010–2016

description: <b><i>Background:</i></b> The opioid crisis has led to a dramatic increase in the number of drug overdose deaths in the United States. Little is known about the effect of the opioid crisis on the kidney transplant donor pool, particularly on hepatitis C virus (HCV)-infected donors. <b><i>Methods:</i></b> This is a retrospective analysis of the data from the Organ Procurement and Transplantation Network from 2010 to 2016. We determined the changes in characteristics of kidney transplant donors and evaluated which changes may be directly related to the opioid crisis. <b><i>Results:</i></b> Between 2010 and 2016, we found a 26% increase in overall donors, including a 277% increase in the number of donors who died from drug overdose. Nineteen percent of donors who died of drug overdose had HCV infection. Donors who die from drug overdose and donors with HCV infection are younger, less likely to have diabetes or hypertension, and have favorable kidney donor profile index scores compared to average donors. Despite these favorable characteristics, HCV-infected donors appear to be notably underutilized, with substantially lower kidneys per donor being transplanted compared to HCV uninfected donors. <b><i>Conclusion:</i></b> The opioid crisis in the United States has substantially altered the kidney donor pool. Strategies to increase utilization of all potentially viable kidneys for transplant are needed, particularly in this era of new, highly effective, direct-acting antiviral therapy for HCV infection.
DOI: 10.6084/m9.figshare.5882401
title: Sci-Hub download data 2017 for Ukraine, Belarus and Russia

description: The data set include full 2017 download log of Sci-Hub (only Ukrainian, Belarusian and Russian users requests). This is part of the data from: https://twitter.com/Sci_Hub/status/954095639859814402<br>
DOI: 10.6084/m9.figshare.5882377
title: Dataset for the paper Item Response Theory Modeling of High-School Students’ Behavior in a High-Stake Exam

description: Dataset for the paper Item Response Theory Modeling of High-School Students’ Behavior in a High-Stake Exam
DOI: 10.6084/m9.figshare.5882377.v1
title: Dataset for the paper Item Response Theory Modeling of High-School Students’ Behavior in a High-Stake Exam

description: Dataset for the paper Item Response Theory Modeling of High-School Students’ Behavior in a High-Stake Exam
DOI: 10.6084/m9.figshare.5882344
title: Sector length vs. sector width from Emergence of evolutionary driving forces in pattern-forming microbial populations

description: Table of data shown in Fig. 3c
DOI: 10.6084/m9.figshare.5882344.v1
title: Sector length vs. sector width from Emergence of evolutionary driving forces in pattern-forming microbial populations

description: Table of data shown in Fig. 3c
DOI: 10.6084/m9.figshare.5882305
title: Supplementary Material for: Posterior Hyaloid Dissection: Let’s Make It Easy with Blue

description: <b><i>Purpose:</i></b> Our aim is to present in this online supplementa ry video (see www.karger.com/doi/10.1159/000486348) an easy new surgical technique using blue dye to dissect the posterior hyaloid when performing pars plana vitrectomy. <b><i>Procedures:</i></b> Dual-Blue stain is injected in vitreous cavity just after central vitrectomy is performed. The distribution of the blue stain will allow us to know if there is a posterior vitreous detachment or not (“blue lake fashion” or “blue jelly fashion,” respectively) and as an excellent visualization of the vitreous fibers is accomplished, dissection of the posterior hyaloid can be performed without difficulty. <b><i>Results:</i></b> This procedure allows a much more simple, fast, and safe dissection of posterior hyaloid even for an inexperienced vitreoretinal surgeon. The cleavage plane between the retina and the posterior hyaloid is easily differentiated. <b><i>Conclusions:</i></b> A more controlled and easy dissection of posterior hyaloid during vitrectomy is accomplished with this simple technique without adding any extra cost. <b><i>Message of the paper:</i></b> An easy technique that allows a much easier dissection of the posterior hyaloid during vitrectomy improving visualization and decreasing risks. No extra cost, nor time is needed.
DOI: 10.6084/m9.figshare.5882305.v1
title: Supplementary Material for: Posterior Hyaloid Dissection: Let’s Make It Easy with Blue

description: <b><i>Purpose:</i></b> Our aim is to present in this online supplementa ry video (see www.karger.com/doi/10.1159/000486348) an easy new surgical technique using blue dye to dissect the posterior hyaloid when performing pars plana vitrectomy. <b><i>Procedures:</i></b> Dual-Blue stain is injected in vitreous cavity just after central vitrectomy is performed. The distribution of the blue stain will allow us to know if there is a posterior vitreous detachment or not (“blue lake fashion” or “blue jelly fashion,” respectively) and as an excellent visualization of the vitreous fibers is accomplished, dissection of the posterior hyaloid can be performed without difficulty. <b><i>Results:</i></b> This procedure allows a much more simple, fast, and safe dissection of posterior hyaloid even for an inexperienced vitreoretinal surgeon. The cleavage plane between the retina and the posterior hyaloid is easily differentiated. <b><i>Conclusions:</i></b> A more controlled and easy dissection of posterior hyaloid during vitrectomy is accomplished with this simple technique without adding any extra cost. <b><i>Message of the paper:</i></b> An easy technique that allows a much easier dissection of the posterior hyaloid during vitrectomy improving visualization and decreasing risks. No extra cost, nor time is needed.
DOI: 10.6084/m9.figshare.5882290
title: Supplementary Material for: Chromosome Nomenclature and Cytological Characterization of Sacred Lotus

description: Sacred lotus is a basal eudicot plant that has been cultivated in Asia for over 7,000 years for its agricultural, ornamental, religious, and medicinal importance. A notable characteristic of lotus is the seed longevity. Extensive endeavors have been devoted to dissect its genome assembly, including the variety China Antique, which germinated from a 1,300-year-old seed. Here, cytogenetic markers representing the 10 largest megascaffolds, which constitute approximately 70% of the lotus genome assembly, were developed. These 10 megascaffolds were then anchored to the corresponding lotus chromosomes by fluorescence in situ hybridization using these cytogenetic markers, and a set of chromosome-specific cytogenetic markers that could unambiguously identify each of the 8 chromosomes was generated. Karyotyping was conducted, and a nomenclature based on chromosomal length was established for the 8 chromosomes of China Antique. Comparative karyotyping revealed relatively conserved chromosomal structures between China Antique and 3 modern cultivars. Interestingly, significant variations in the copy number of 45S rDNA were detected between China Antique and modern cultivars. Our results provide a comprehensive view on the chromosomal structure of sacred lotus and will facilitate further studies and the genome assembly of lotus.
DOI: 10.6084/m9.figshare.5882290.v1
title: Supplementary Material for: Chromosome Nomenclature and Cytological Characterization of Sacred Lotus

description: Sacred lotus is a basal eudicot plant that has been cultivated in Asia for over 7,000 years for its agricultural, ornamental, religious, and medicinal importance. A notable characteristic of lotus is the seed longevity. Extensive endeavors have been devoted to dissect its genome assembly, including the variety China Antique, which germinated from a 1,300-year-old seed. Here, cytogenetic markers representing the 10 largest megascaffolds, which constitute approximately 70% of the lotus genome assembly, were developed. These 10 megascaffolds were then anchored to the corresponding lotus chromosomes by fluorescence in situ hybridization using these cytogenetic markers, and a set of chromosome-specific cytogenetic markers that could unambiguously identify each of the 8 chromosomes was generated. Karyotyping was conducted, and a nomenclature based on chromosomal length was established for the 8 chromosomes of China Antique. Comparative karyotyping revealed relatively conserved chromosomal structures between China Antique and 3 modern cultivars. Interestingly, significant variations in the copy number of 45S rDNA were detected between China Antique and modern cultivars. Our results provide a comprehensive view on the chromosomal structure of sacred lotus and will facilitate further studies and the genome assembly of lotus.
DOI: 10.6084/m9.figshare.12854002
title: Surveying coastal cliffs using two UAV platforms (multirotor and fixed-wing) and three different approaches for the estimation of volumetric changes

description: The increasing availability of highly detailed and accurate three-dimensional (3D) geospatial data are currently pushing the 3D change detection analysis towards a new 3D mapping frame. In this paper, medium-term changes (8 years) at a coastal rocky cliff are quantified using and comparing 2.5D and 3D methods to estimate the volume of rockfalls and three datasets: one Terrestrial Laser Scanner (TLS) acquired in 2010 and two coincident Unmanned Aerial Vehicles (UAV: multirotor and fixed-wing) datasets acquired in 2018. Advantages and limitations of these techniques, platforms and methods are discussed and the role of Ground Control Points (GCPs) distribution was analysed. Maps of 3D changes were produced by means of the Multiscale-Model-to-Model Cloud-Comparison algorithm (M3C2). The volume of the eroded-deposited material was estimated using two 2.5D and one 3D approaches: 1) rasterizing M3C2 distances using a conventional top-view perspective, 2) rasterizing the M3C2 distances rotated and orientated with the <b><i>z</i></b> vector normal and, 3) for the largest rockfalls, the volume was estimated using the Poisson Surface Reconstruction (PSR) algorithm (3D). The 3D models produced using both UAV platforms showed cm-level accuracies with Root Mean Square Error (RMSE) of 0.02 and 0.03 m for the multirotor and the fixed-wing, respectively, and faithfully represented cliff geometry. GCP configuration analysis showed that, at least, two stripes of GCPs evenly distributed at different heights are necessary, but three are recommended. The spatial pattern of change between the TLS and the two UAVs datasets was similar. The quantification of the volume of the eroded-accumulated material (using the M3C2 distances and the two UAV datasets) resulted in significant differences as the fixed-wing underestimated the values calculated using the multirotor dataset. The 2.5D strategies used to quantify the volume of change underestimated the eroded volume of the largest rockfalls (compared to the PSR 3D method), which provided the most accurate volume estimates.
DOI: 10.6084/m9.figshare.12854002.v1
title: Surveying coastal cliffs using two UAV platforms (multirotor and fixed-wing) and three different approaches for the estimation of volumetric changes

description: The increasing availability of highly detailed and accurate three-dimensional (3D) geospatial data are currently pushing the 3D change detection analysis towards a new 3D mapping frame. In this paper, medium-term changes (8 years) at a coastal rocky cliff are quantified using and comparing 2.5D and 3D methods to estimate the volume of rockfalls and three datasets: one Terrestrial Laser Scanner (TLS) acquired in 2010 and two coincident Unmanned Aerial Vehicles (UAV: multirotor and fixed-wing) datasets acquired in 2018. Advantages and limitations of these techniques, platforms and methods are discussed and the role of Ground Control Points (GCPs) distribution was analysed. Maps of 3D changes were produced by means of the Multiscale-Model-to-Model Cloud-Comparison algorithm (M3C2). The volume of the eroded-deposited material was estimated using two 2.5D and one 3D approaches: 1) rasterizing M3C2 distances using a conventional top-view perspective, 2) rasterizing the M3C2 distances rotated and orientated with the <b><i>z</i></b> vector normal and, 3) for the largest rockfalls, the volume was estimated using the Poisson Surface Reconstruction (PSR) algorithm (3D). The 3D models produced using both UAV platforms showed cm-level accuracies with Root Mean Square Error (RMSE) of 0.02 and 0.03 m for the multirotor and the fixed-wing, respectively, and faithfully represented cliff geometry. GCP configuration analysis showed that, at least, two stripes of GCPs evenly distributed at different heights are necessary, but three are recommended. The spatial pattern of change between the TLS and the two UAVs datasets was similar. The quantification of the volume of the eroded-accumulated material (using the M3C2 distances and the two UAV datasets) resulted in significant differences as the fixed-wing underestimated the values calculated using the multirotor dataset. The 2.5D strategies used to quantify the volume of change underestimated the eroded volume of the largest rockfalls (compared to the PSR 3D method), which provided the most accurate volume estimates.
DOI: 10.6084/m9.figshare.5882242
title: CitySounds2017train annotations

description: Annotations of sound events in the CitySounds2017<i><sub>train</sub></i> dataset created using AudioTagger software (https://github.com/groakat/AudioTagger).
DOI: 10.6084/m9.figshare.5882239
title: Dataset for: Comparing hierarchical models via the marginalized deviance information criterion

description: Hierarchical models are extensively used in pharmacokinetics and longitudinal studies. When the estimation is carried out from a Bayesian approach, model comparison is often based on the deviance information criterion (DIC). In hierarchical models with latent variables there are several versions of this statistic, specifically: the conditional DIC (cDIC) that incorporates the latent variables in the focus of the analysis and the marginalized DIC (mDIC) which integrates them out. Regardless of the asymptotic and coherency difficulties of cDIC, this alternative is usually employed in Markov chain Monte Carlo (MCMC) methods for hierarchical models due to practical convenience. The mDIC criterion is more appropriate in most cases but requires integration of the likelihood which is computationally demanding and not implemented in Bayesian software. Therefore, we consider a method to compute mDIC by generating replicate samples of the latent variables that need to be integrated out. This alternative can be easily conducted from the MCMC output of Bayesian packages and is widely applicable to hierarchical models in general. Additionally, we propose some approximations in order to reduce the computational complexity for large-sample situations. The method is illustrated with simulated data sets and two medical studies, evidencing that cDIC may be misleading whilst mDIC appears pertinent.
DOI: 10.6084/m9.figshare.5882239.v1
title: Dataset for: Comparing hierarchical models via the marginalized deviance information criterion

description: Hierarchical models are extensively used in pharmacokinetics and longitudinal studies. When the estimation is carried out from a Bayesian approach, model comparison is often based on the deviance information criterion (DIC). In hierarchical models with latent variables there are several versions of this statistic, specifically: the conditional DIC (cDIC) that incorporates the latent variables in the focus of the analysis and the marginalized DIC (mDIC) which integrates them out. Regardless of the asymptotic and coherency difficulties of cDIC, this alternative is usually employed in Markov chain Monte Carlo (MCMC) methods for hierarchical models due to practical convenience. The mDIC criterion is more appropriate in most cases but requires integration of the likelihood which is computationally demanding and not implemented in Bayesian software. Therefore, we consider a method to compute mDIC by generating replicate samples of the latent variables that need to be integrated out. This alternative can be easily conducted from the MCMC output of Bayesian packages and is widely applicable to hierarchical models in general. Additionally, we propose some approximations in order to reduce the computational complexity for large-sample situations. The method is illustrated with simulated data sets and two medical studies, evidencing that cDIC may be misleading whilst mDIC appears pertinent.
DOI: 10.6084/m9.figshare.5882230
title: OpenML R Bot Benchmark Data (final subset)

description: This is a clean subset of the data that was created by the OpenML R Bot that executed benchmark experiments on binary classification task of the OpenML100 benchmarking suite with six R algorithms: glmnet, rpart, kknn, svm, ranger and xgboost. The hyperparameters of these algorithms were drawn randomly. In total it contains more than 2.6 million benchmark experiments and can be used by other researchers. <br><br>The subset was created by taking 500000 results of each learner (except of kknn for which only 1140 results are available). <br><br>The csv-file for each learner is a table that for each benchmark experiment has a row that contains: OpenML-Data ID, hyperparameter values, performance measures (AUC, accuracy, brier score), runtime, scimark (runtime reference of the machine), and some meta features of the dataset.<br><br>OpenMLRandomBotResults.RData (format for R) contains all data in seperate tables for the results, the hyperparameters, the meta features, the runtime, the scimark results and reference results.<br>
DOI: 10.6084/m9.figshare.5882230.v1
title: OpenML R Bot Benchmark Data (final subset)

description: This is a clean subset of the data that was created by the OpenML R Bot that executed benchmark experiments on binary classification task of the OpenML100 benchmarking suite with six R algorithms: glmnet, rpart, kknn, <br>svm, ranger and xgboost. The hyperparameters of these algorithms were drawn randomly. In total it contains more than 2.6 million benchmark experiments and can be used by other researchers. <br><br>The subset was created by taking 500000 results of each learner (except of kknn for which only ~125000 results are available). <br><br>The csv-file for each learner is a table that for each benchmark experiment has a row that contains: OpenML-Data ID, hyperparameter values, performance measures (AUC, accuracy, brier score), runtime, scimark (runtime reference of the machine), and some meta features of the dataset.<br><br>OpenMLRandomBotResults.RData (format for R) contains all data in seperate tables for the results, the hyperparameters, the meta features, the runtime, the scimark results and reference results.<br>