cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4288499.v1
title: Superfund Locations and Potential Associations with Cancer Incidence in Florida

description: <i>Background</i>: Uncontrolled hazardous wastes sites have the potential to adversely impact human health and damage or disrupt ecological systems and the greater environment. Four decades have passed since the Superfund law was enacted, allowing increased exposure time to these potential health hazards while also allowing advancement of analysis techniques. Florida has the sixth highest number of Superfund sites in the US and, in 2016, Florida was projected to have the second largest number of new cancer cases in the US. <i>Objectives</i>: We explore statewide cancer incidence in Florida from 1986 to 2010 to determine if differences or associations exist in counties containing Superfund sites compared to counties that do not. <i>Methods</i>: To investigate potential environmental associations with cancer incidence; results using spatial and non-spatial mixed models were compared. <i>Results</i>: Using a Poisson-Gamma generalized linear mixture model, our results provide some evidence of an association between cancer incidence rates and Superfund site hazard levels, as well as proxy measures of water contamination around Superfund sites. In addition, results build upon previously observed gender differences in cancer incidence rates and further indicate <i>spatial</i> differences for cancer incidence. <i>Conclusions</i>: Results indicate strong evidence of heterogeneity among cancer incidence rates across Florida with some mild association with Superfund exposure proxies.
DOI: 10.6084/m9.figshare.4288499.v3
title: Superfund Locations and Potential Associations with Cancer Incidence in Florida

description: <i>Background</i>: Uncontrolled hazardous wastes sites have the potential to adversely impact human health and damage or disrupt ecological systems and the greater environment. Four decades have passed since the Superfund law was enacted, allowing increased exposure time to these potential health hazards while also allowing advancement of analysis techniques. Florida has the sixth highest number of Superfund sites in the US and, in 2016, Florida was projected to have the second largest number of new cancer cases in the US. <i>Objectives</i>: We explore statewide cancer incidence in Florida from 1986 to 2010 to determine if differences or associations exist in counties containing Superfund sites compared to counties that do not. <i>Methods</i>: To investigate potential environmental associations with cancer incidence; results using spatial and non-spatial mixed models were compared. <i>Results</i>: Using a Poisson-Gamma generalized linear mixture model, our results provide some evidence of an association between cancer incidence rates and Superfund site hazard levels, as well as proxy measures of water contamination around Superfund sites. In addition, results build upon previously observed gender differences in cancer incidence rates and further indicate <i>spatial</i> differences for cancer incidence. <i>Conclusions</i>: Results indicate strong evidence of heterogeneity among cancer incidence rates across Florida with some mild association with Superfund exposure proxies.
DOI: 10.6084/m9.figshare.4288499.v2
title: Superfund Locations and Potential Associations with Cancer Incidence in Florida

description: <i>Background</i>: Uncontrolled hazardous wastes sites have the potential to adversely impact human health and damage or disrupt ecological systems and the greater environment. Four decades have passed since the Superfund law was enacted, allowing increased exposure time to these potential health hazards while also allowing advancement of analysis techniques. Florida has the sixth highest number of Superfund sites in the US and, in 2016, Florida was projected to have the second largest number of new cancer cases in the US. <i>Objectives</i>: We explore statewide cancer incidence in Florida from 1986 to 2010 to determine if differences or associations exist in counties containing Superfund sites compared to counties that do not. <i>Methods</i>: To investigate potential environmental associations with cancer incidence; results using spatial and non-spatial mixed models were compared. <i>Results</i>: Using a Poisson-Gamma generalized linear mixture model, our results provide some evidence of an association between cancer incidence rates and Superfund site hazard levels, as well as proxy measures of water contamination around Superfund sites. In addition, results build upon previously observed gender differences in cancer incidence rates and further indicate <i>spatial</i> differences for cancer incidence. <i>Conclusions</i>: Results indicate strong evidence of heterogeneity among cancer incidence rates across Florida with some mild association with Superfund exposure proxies.
DOI: 10.6084/m9.figshare.4288466
title: DOTmark v1.0

description: This benchmark for testing discrete optimal transport algorithms consists of 10 classes. Each class contains 10 images in each of the 5 different resolutions from 32×32 to 512×512 (in doubling steps per dimension). This allows for a total of 45 computations of Wasserstein distances between two images for any one class at any fixed resolution.<br><br>Classes 1–7 are random simulations based on various probability distributions. Images at different resolutions are generated independently from each other but according to the same laws. Classes 8–10 were obtained by ad-hoc choices of simple geometric shapes, classic test images and images of mitochondria acquired using STED super-resolution microscopy. For geometric shapes and classic test<br> images the various resolutions available are coarsenings of a single image. For the microscopy images different clippings of various sizes have been selected from larger images to obtain the various resolutions. <br>
DOI: 10.6084/m9.figshare.4288466.v1
title: DOTmark v1.0

description: This benchmark for testing discrete optimal transport algorithms consists of 10 classes. Each class contains 10 images in each of the 5 different resolutions from 32×32 to 512×512 (in doubling steps per dimension). This allows for a total of 45 computations of Wasserstein distances between two images for any one class at any fixed resolution.<br><br>Classes 1–7 are random simulations based on various probability distributions. Images at different resolutions are generated independently from each other but according to the same laws. Classes 8–10 were obtained by ad-hoc choices of simple geometric shapes, classic test images and images of mitochondria acquired using STED super-resolution microscopy. For geometric shapes and classic test<br> images the various resolutions available are coarsenings of a single image. For the microscopy images different clippings of various sizes have been selected from larger images to obtain the various resolutions. <br>
DOI: 10.6084/m9.figshare.4288448
title: High-Dimensional Multivariate Time Series With Additional Structure

description: High-dimensional multivariate time series are challenging due to the dependent and high-dimensional nature of the data, but in many applications there is additional structure that can be exploited to reduce computing time along with statistical error. We consider high-dimensional vector autoregressive processes with spatial structure, a simple and common form of additional structure. We propose novel high-dimensional methods that take advantage of such structure without making model assumptions about how distance affects dependence. We provide nonasymptotic bounds on the statistical error of parameter estimators in high-dimensional settings and show that the proposed approach reduces the statistical error. An application to air pollution in the USA demonstrates that the estimation approach reduces both computing time and prediction error and gives rise to results that are meaningful from a scientific point of view, in contrast to high-dimensional methods that ignore spatial structure. In practice, these high-dimensional methods can be used to decompose high-dimensional multivariate time series into lower-dimensional multivariate time series that can be studied by other methods in more depth. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.4288448.v1
title: High-Dimensional Multivariate Time Series With Additional Structure

description: High-dimensional multivariate time series are challenging due to the dependent and high-dimensional nature of the data, but in many applications there is additional structure that can be exploited to reduce computing time along with statistical error. We consider high-dimensional vector autoregressive processes with spatial structure, a simple and common form of additional structure. We propose novel high-dimensional methods that take advantage of such structure without making model assumptions about how distance affects dependence. We provide non-asymptotic bounds on the statistical error of parameter estimators in high-dimensional settings and show that the proposed approach reduces the statistical error. An application to air pollution in the U.S.A. demonstrates that the estimation approach reduces both computing time and prediction error and gives rise to results that are meaningful from a scientific point of view, in contrast to high-dimensional methods that ignore spatial structure. In practice, these high-dimensional methods can be used to decompose high-dimensional multivariate time series into lower-dimensional multivariate time series that can be studied by other methods in more depth.
DOI: 10.6084/m9.figshare.4288442
title: Trend analysis of nutrient loadings in a large prairie catchment

description: Nutrient loadings in many river catchments continue to increase due to rapid expansion of agriculture, urban and industrial development, and population growth. Nutrient enrichment of water bodies has intensified eutrophication which degrades water quality and ecosystem health. In this study, we carried out a trend analysis of total phosphorus and total nitrogen loads in the South Saskatchewan River (SSR) catchment using a novel approach to analyse nutrient time series. Seasonal analysis of trends at each of the water quality stations was performed to determine the relationships between annual flow regimes and nutrient loads in the catchment, in particular, the influence of the high spring runoff on nutrient export. Decadal analysis was also performed to determine the long-term relationships of nutrients with anthropogenic changes in the catchment. Although it was found that seasonal and historical variability of nutrient load trends is mainly determined by streamflow regime changes, there is evidence that increases in nitrogen concentration can also be attributed to anthropogenic changes.
DOI: 10.6084/m9.figshare.4288442.v1
title: Trend analysis of nutrient loadings in a large prairie catchment

description: Nutrient loadings in many river catchments continue to increase due to rapid expansion of agriculture, urban and industrial development, and population growth. Nutrient enrichment of water bodies has intensified eutrophication which degrades water quality and ecosystem health. In this study, we carried out a trend analysis of total phosphorus and total nitrogen loads in the South Saskatchewan River (SSR) catchment using a novel approach to analyse nutrient time series. Seasonal analysis of trends at each of the water quality stations was performed to determine the relationships between annual flow regimes and nutrient loads in the catchment, in particular, the influence of the high spring runoff on nutrient export. Decadal analysis was also performed to determine the long-term relationships of nutrients with anthropogenic changes in the catchment. Although it was found that seasonal and historical variability of nutrient load trends is mainly determined by streamflow regime changes, there is evidence that increases in nitrogen concentration can also be attributed to anthropogenic changes.
DOI: 10.6084/m9.figshare.4288415
title: Formation and exudation of non-volatile products of the arabidiol triterpenoid degradation pathway in <i>Arabidopsis</i> roots

description: Triterpenoids produced by plants play important roles in the protection against biotic stress. Roots of <i>Arabidopsis thaliana</i> produce different triterpenoids, which include the tricyclic triterpene diol, arabidiol. In a degradation reaction induced by infection with the oomycete pathogen, <i>Pythium irregulare</i>, arabidiol is cleaved to the 11-carbon volatile homoterpene, (<i>E</i>)-4,8-dimethyl-1,3,7-nonatriene (DMNT), and the 19-carbon ketone, apo-arabidiol. The arabidiol pathway and its volatile breakdown product DMNT have been implicated in the defense against <i>P. irregulare</i> infection. Here we show that the non-volatile breakdown product apo-arabidiol is further converted to the acetylated derivative α−14-acetyl-apo-arabidiol via a presumed epimerization and subsequent acetylation reaction. α−14-acetyl-apo-arabidiol and the detected intermediates in the derivatization pathway are partially exuded from the root indicating possible defensive activities of these molecules in the rhizosphere. The conversion steps of apo-arabidiol vary among different <i>Arabidopsis</i> accessions and are present in only rudimentary form in the close relative <i>Arabidopsis lyrata</i>, which supports an intra- and inter-specific modularity in triterpenoid metabolism.
DOI: 10.6084/m9.figshare.4288418
title: Formation and exudation of non-volatile products of the arabidiol triterpenoid degradation pathway in <i>Arabidopsis</i> roots

description: Triterpenoids produced by plants play important roles in the protection against biotic stress. Roots of <i>Arabidopsis thaliana</i> produce different triterpenoids, which include the tricyclic triterpene diol, arabidiol. In a degradation reaction induced by infection with the oomycete pathogen, <i>Pythium irregulare</i>, arabidiol is cleaved to the 11-carbon volatile homoterpene, (<i>E</i>)-4,8-dimethyl-1,3,7-nonatriene (DMNT), and the 19-carbon ketone, apo-arabidiol. The arabidiol pathway and its volatile breakdown product DMNT have been implicated in the defense against <i>P. irregulare</i> infection. Here we show that the non-volatile breakdown product apo-arabidiol is further converted to the acetylated derivative α−14-acetyl-apo-arabidiol via a presumed epimerization and subsequent acetylation reaction. α−14-acetyl-apo-arabidiol and the detected intermediates in the derivatization pathway are partially exuded from the root indicating possible defensive activities of these molecules in the rhizosphere. The conversion steps of apo-arabidiol vary among different <i>Arabidopsis</i> accessions and are present in only rudimentary form in the close relative <i>Arabidopsis lyrata</i>, which supports an intra- and inter-specific modularity in triterpenoid metabolism.
DOI: 10.6084/m9.figshare.4288415.v1
title: Formation and exudation of non-volatile products of the arabidiol triterpenoid degradation pathway in <i>Arabidopsis</i> roots

description: Triterpenoids produced by plants play important roles in the protection against biotic stress. Roots of <i>Arabidopsis thaliana</i> produce different triterpenoids, which include the tricyclic triterpene diol, arabidiol. In a degradation reaction induced by infection with the oomycete pathogen, <i>Pythium irregulare</i>, arabidiol is cleaved to the 11-carbon volatile homoterpene, (<i>E</i>)-4,8-dimethyl-1,3,7-nonatriene (DMNT), and the 19-carbon ketone, apo-arabidiol. The arabidiol pathway and its volatile breakdown product DMNT have been implicated in the defense against <i>P. irregulare</i> infection. Here we show that the non-volatile breakdown product apo-arabidiol is further converted to the acetylated derivative α−14-acetyl-apo-arabidiol via a presumed epimerization and subsequent acetylation reaction. α−14-acetyl-apo-arabidiol and the detected intermediates in the derivatization pathway are partially exuded from the root indicating possible defensive activities of these molecules in the rhizosphere. The conversion steps of apo-arabidiol vary among different <i>Arabidopsis</i> accessions and are present in only rudimentary form in the close relative <i>Arabidopsis lyrata</i>, which supports an intra- and inter-specific modularity in triterpenoid metabolism.
DOI: 10.6084/m9.figshare.4288418.v1
title: Formation and exudation of non-volatile products of the arabidiol triterpenoid degradation pathway in <i>Arabidopsis</i> roots

description: Triterpenoids produced by plants play important roles in the protection against biotic stress. Roots of <i>Arabidopsis thaliana</i> produce different triterpenoids, which include the tricyclic triterpene diol, arabidiol. In a degradation reaction induced by infection with the oomycete pathogen, <i>Pythium irregulare</i>, arabidiol is cleaved to the 11-carbon volatile homoterpene, (<i>E</i>)-4,8-dimethyl-1,3,7-nonatriene (DMNT), and the 19-carbon ketone, apo-arabidiol. The arabidiol pathway and its volatile breakdown product DMNT have been implicated in the defense against <i>P. irregulare</i> infection. Here we show that the non-volatile breakdown product apo-arabidiol is further converted to the acetylated derivative α−14-acetyl-apo-arabidiol via a presumed epimerization and subsequent acetylation reaction. α−14-acetyl-apo-arabidiol and the detected intermediates in the derivatization pathway are partially exuded from the root indicating possible defensive activities of these molecules in the rhizosphere. The conversion steps of apo-arabidiol vary among different <i>Arabidopsis</i> accessions and are present in only rudimentary form in the close relative <i>Arabidopsis lyrata</i>, which supports an intra- and inter-specific modularity in triterpenoid metabolism.
DOI: 10.6084/m9.figshare.4288412
title: Formation and exudation of non-volatile products of the arabidiol triterpenoid degradation pathway in <i>Arabidopsis</i> roots

description: Triterpenoids produced by plants play important roles in the protection against biotic stress. Roots of <i>Arabidopsis thaliana</i> produce different triterpenoids, which include the tricyclic triterpene diol, arabidiol. In a degradation reaction induced by infection with the oomycete pathogen, <i>Pythium irregulare</i>, arabidiol is cleaved to the 11-carbon volatile homoterpene, (<i>E</i>)-4,8-dimethyl-1,3,7-nonatriene (DMNT), and the 19-carbon ketone, apo-arabidiol. The arabidiol pathway and its volatile breakdown product DMNT have been implicated in the defense against <i>P. irregulare</i> infection. Here we show that the non-volatile breakdown product apo-arabidiol is further converted to the acetylated derivative α-14-acetyl-apo-arabidiol via a presumed epimerization and subsequent acetylation reaction. α-14-acetyl-apo-arabidiol and the detected intermediates in the derivatization pathway are partially exuded from the root indicating possible defensive activities of these molecules in the rhizosphere. The conversion steps of apo-arabidiol vary among different <i>Arabidopsis</i> accessions and are present in only rudimentary form in the close relative <i>Arabidopsis lyrata</i>, which supports an intra- and inter-specific modularity in triterpenoid metabolism.
DOI: 10.6084/m9.figshare.4288412.v1
title: Formation and exudation of non-volatile products of the arabidiol triterpenoid degradation pathway in <i>Arabidopsis</i> roots

description: Triterpenoids produced by plants play important roles in the protection against biotic stress. Roots of <i>Arabidopsis thaliana</i> produce different triterpenoids, which include the tricyclic triterpene diol, arabidiol. In a degradation reaction induced by infection with the oomycete pathogen, <i>Pythium irregulare</i>, arabidiol is cleaved to the 11-carbon volatile homoterpene, (<i>E</i>)-4,8-dimethyl-1,3,7-nonatriene (DMNT), and the 19-carbon ketone, apo-arabidiol. The arabidiol pathway and its volatile breakdown product DMNT have been implicated in the defense against <i>P. irregulare</i> infection. Here we show that the non-volatile breakdown product apo-arabidiol is further converted to the acetylated derivative α-14-acetyl-apo-arabidiol via a presumed epimerization and subsequent acetylation reaction. α-14-acetyl-apo-arabidiol and the detected intermediates in the derivatization pathway are partially exuded from the root indicating possible defensive activities of these molecules in the rhizosphere. The conversion steps of apo-arabidiol vary among different <i>Arabidopsis</i> accessions and are present in only rudimentary form in the close relative <i>Arabidopsis lyrata</i>, which supports an intra- and inter-specific modularity in triterpenoid metabolism.
DOI: 10.6084/m9.figshare.4288394
title: Modeling the effect of succimer (DMSA; dimercaptosuccinic acid) chelation therapy in patients poisoned by lead

description: <b>Context:</b> Kinetic models could assist clinicians potentially in managing cases of lead poisoning. Several models exist that can simulate lead kinetics but none of them can predict the effect of chelation in lead poisoning. Our aim was to devise a model to predict the effect of succimer (dimercaptosuccinic acid; DMSA) chelation therapy on blood lead concentrations. <b>Materials and methods:</b> We integrated a two-compartment kinetic succimer model into an existing PBPK lead model and produced a Chelation Lead Therapy (CLT) model. The accuracy of the model’s predictions was assessed by simulating clinical observations in patients poisoned by lead and treated with succimer. The CLT model calculates blood lead concentrations as the sum of the background exposure and the acute or chronic lead poisoning. The latter was due either to ingestion of traditional remedies or occupational exposure to lead-polluted ambient air. The exposure duration was known. The blood lead concentrations predicted by the CLT model were compared to the measured blood lead concentrations. <b>Results:</b> Pre-chelation blood lead concentrations ranged between 99 and 150 μg/dL. The model was able to simulate accurately the blood lead concentrations during and after succimer treatment. The pattern of urine lead excretion was successfully predicted in some patients, while poorly predicted in others. <b>Conclusions:</b> Our model is able to predict blood lead concentrations after succimer therapy, at least, in situations where the duration of lead exposure is known.
DOI: 10.6084/m9.figshare.4288394.v2
title: Modeling the effect of succimer (DMSA; dimercaptosuccinic acid) chelation therapy in patients poisoned by lead

description: <b>Context:</b> Kinetic models could assist clinicians potentially in managing cases of lead poisoning. Several models exist that can simulate lead kinetics but none of them can predict the effect of chelation in lead poisoning. Our aim was to devise a model to predict the effect of succimer (dimercaptosuccinic acid; DMSA) chelation therapy on blood lead concentrations. <b>Materials and methods:</b> We integrated a two-compartment kinetic succimer model into an existing PBPK lead model and produced a Chelation Lead Therapy (CLT) model. The accuracy of the model’s predictions was assessed by simulating clinical observations in patients poisoned by lead and treated with succimer. The CLT model calculates blood lead concentrations as the sum of the background exposure and the acute or chronic lead poisoning. The latter was due either to ingestion of traditional remedies or occupational exposure to lead-polluted ambient air. The exposure duration was known. The blood lead concentrations predicted by the CLT model were compared to the measured blood lead concentrations. <b>Results:</b> Pre-chelation blood lead concentrations ranged between 99 and 150 μg/dL. The model was able to simulate accurately the blood lead concentrations during and after succimer treatment. The pattern of urine lead excretion was successfully predicted in some patients, while poorly predicted in others. <b>Conclusions:</b> Our model is able to predict blood lead concentrations after succimer therapy, at least, in situations where the duration of lead exposure is known.