cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11734566
title: Uncertainty calculation methods in dose assessment for dicentric chromosome assay

description: <b>Purpose:</b> To present the impact in coverage of different methods for Poisson confidence intervals and the impact in dose coverage of different uncertainty factors. A detailed explanation of the uncertainty sources in the Bayesian method is also presented. <b>Materials and methods:</b> The exact coverage of uncertainty Poisson confidence intervals and the dose uncertainty interval coverage were performed by simulations using R-based scripts. <b>Results:</b> The Poisson exact calibration interval via the Modified Crow and Gardner method resulted in coverage quite close to the nominal level of confidence; additionally, the method retains the shortest property of Crow and Gardner, and gains the property of a lower limit strictly increasing in the mean of dicentrics. The unlimited simultaneous calibration interval seems to be the method of choice to preserve the coverage at 95% under parametric and nonparametric conditions but is a conservative method. When samples came from a Poisson distribution, the ISO propagation of errors and Bayesian approaches seem to be the closest to the 95% coverage. <b>Conclusions:</b> The Modified Crow and Gardner method should be preferred over the Garwood method for Poisson exact confidence intervals. The unlimited simultaneous calibration interval did not lose its property to preserve the coverage at 95% applying a regression coverage factor of value 2.02 at the point of doses studied in the simulation.
DOI: 10.6084/m9.figshare.11734572.v1
title: Matlab Reading Function Example

description: Matlab Reading Function Example
DOI: 10.6084/m9.figshare.11734551
title: Driving simulator experiments to study drowsiness: A systematic review

description: <b>Objective:</b> The National Highway Traffic Safety Administration in the USA estimated that the effects of drowsiness while driving led to approximately 72,000 crashes, 44,000 injuries, and 800 deaths in 2013. Keeping this in mind, the risk and injuries of drowsy driving remain a major safety issue that clearly needs to be studied. Our purpose was to conduct a systematic review of international literature including studies on driving behavior associated to drowsy and fatigued drivers. The research focused on the prediction and effects of drowsiness, and particularly on studies based on driving in simulated environments. Additionally, we searched for studies related to driving simulators, in general, to better understand the tool’s efficacy and its advantages and disadvantages. <b>Methods:</b> This review was made in accordance with PRISMA statement guidelines. After conducting in-depth research in targeted databases, 23 studies met the inclusion criteria; the papers were analyzed regarding the type of experiment and procedures and driving performance of 690 participants was studied. <b>Results:</b> Studies revealed that drowsiness have effects on driving performance and these effects become more relevant with time-on-task and in monotonous scenarios and landscapes. In addition, some documents include validations of several technologies to detect and predict sleepiness. <b>Conclusions:</b> Overall, we can conclude that drowsiness and fatigue impair driving performance, resulting in drivers who are more exposed to risky situations.
DOI: 10.6084/m9.figshare.11734566.v2
title: Uncertainty calculation methods in dose assessment for dicentric chromosome assay

description: <b>Purpose:</b> To present the impact in coverage of different methods for Poisson confidence intervals and the impact in dose coverage of different uncertainty factors. A detailed explanation of the uncertainty sources in the Bayesian method is also presented. <b>Materials and methods:</b> The exact coverage of uncertainty Poisson confidence intervals and the dose uncertainty interval coverage were performed by simulations using R-based scripts. <b>Results:</b> The Poisson exact calibration interval via the Modified Crow and Gardner method resulted in coverage quite close to the nominal level of confidence; additionally, the method retains the shortest property of Crow and Gardner, and gains the property of a lower limit strictly increasing in the mean of dicentrics. The unlimited simultaneous calibration interval seems to be the method of choice to preserve the coverage at 95% under parametric and nonparametric conditions but is a conservative method. When samples came from a Poisson distribution, the ISO propagation of errors and Bayesian approaches seem to be the closest to the 95% coverage. <b>Conclusions:</b> The Modified Crow and Gardner method should be preferred over the Garwood method for Poisson exact confidence intervals. The unlimited simultaneous calibration interval did not lose its property to preserve the coverage at 95% applying a regression coverage factor of value 2.02 at the point of doses studied in the simulation.
DOI: 10.6084/m9.figshare.11734500
title: The modeling group

description: Samples with normalized mRNA expression data and integrated clinical data were included in the overall analysis, and total of 70% of the total number of samples was randomly selected as the modeling group.
DOI: 10.6084/m9.figshare.11734497
title: The validation group

description: Samples with normalized mRNA expression data and integrated clinical data were included in the overall analysis, and total of 30% of the total number of samples was randomly selected as the validation group.
DOI: 10.6084/m9.figshare.11734500.v1
title: The modeling group

description: Samples with normalized mRNA expression data and integrated clinical data were included in the overall analysis, and total of 70% of the total number of samples was randomly selected as the modeling group.
DOI: 10.6084/m9.figshare.11734467
title: esprit2_simulations.tar.gz

description: Results on simulated fragmentation.
DOI: 10.6084/m9.figshare.11734467.v1
title: esprit2_simulations.tar.gz

description: Results on simulated fragmentation.
DOI: 10.6084/m9.figshare.11734353
title: Extended data - Delphi Questions v1.0

description: IntelliSpace Portal (ISP) is an advanced visualization platform that offers a single integrated solution designed to help physicians work more efficiently. This study aimed to develop a consensus statement on the clinical and economic benefits of two Intellispace Portal (ISP) applications (computed tomography (CT) transcatheter aortic-valve implantation (TAVI) and Spectral CT) applications.<br>
DOI: 10.6084/m9.figshare.11734353.v1
title: Extended data - Delphi Questions v1.0

description: IntelliSpace Portal (ISP) is an advanced visualization platform that offers a single integrated solution designed to help physicians work more efficiently. This study aimed to develop a consensus statement on the clinical and economic benefits of two Intellispace Portal (ISP) applications (computed tomography (CT) transcatheter aortic-valve implantation (TAVI) and Spectral CT) applications.<br>
DOI: 10.6084/m9.figshare.11734341
title: esprit_cassava.tar.gz

description: Predictions by ESPRIT
DOI: 10.6084/m9.figshare.11734341.v1
title: esprit_cassava.tar.gz

description: Predictions by ESPRIT
DOI: 10.6084/m9.figshare.11734296
title: Supplementary tracks from Wind conditions influence breeding season movements in a nomadic polygynous shorebird

description: Shows the individual tracks with wind data
DOI: 10.6084/m9.figshare.11734296.v1
title: Supplementary tracks from Wind conditions influence breeding season movements in a nomadic polygynous shorebird

description: Shows the individual tracks with wind data
DOI: 10.6084/m9.figshare.11734293
title: esprit2_cassava.tar.gz

description: Predictions by ESPRIT 2
DOI: 10.6084/m9.figshare.11734293.v1
title: esprit2_cassava.tar.gz

description: Predictions by ESPRIT 2
DOI: 10.6084/m9.figshare.11734218
title: Survival genes expression analysis following ionizing radiation to LiCl treated KG1a cells

description: <b>Purpose:</b> Lithium chloride (LiCl) is clinically used for manic disorders. Its role has been shown in improving cell survival by decreasing Bax and p53 expression and increasing Bcl-2 concentration in the cell. This potential of LiCl is responsible for reducing irradiated cell death. In this study, we have explored the role of LiCl as a radioprotectant affecting survival genes. <b>Materials and methods:</b> To find out the cellular response upon LiCl pretreatment to radiation-exposed KG1a cells; viability, clonogenic assay and microarray studies were performed. This was followed by the detection of transcription factor binding motif in coregulated genes. These results were confirmed by reverse transcription-polymerase chain reaction (RT-PCR) and chromatin immunoprecipitation (CHIP). <b>Results:</b> LiCl improved irradiated KG1a cell survival and its clonogenicity at 2 mM concentration (clinically used). Microarray data analysis showed differential expression of cell-protecting genes playing an important role in apoptosis, cell cycle, adhesion and inflammation, etc. The coregulation analysis revealed genes involved in bile acid biosynthesis were also affected by LiCl treatment, these genes are likely to be responsible for radiation-induced gastrointestinal (GI) syndrome through bile production. <b>Conclusions:</b> This is the first study with respect to global genetic expression upon LiCl treatment to radiation-exposed cells. Our results suggest considering repurposing of LiCl as a protective agent for radiation injury.
DOI: 10.6084/m9.figshare.11734215
title: Morphological features of pulmonary fibrosis in workers occupationally exposed to alpha radiation

description: <b>Purpose:</b> The article reports on a comparative analysis of biological specimens of lung tissues collected from workers with pulmonary fibrosis induced by internal exposure to plutonium alpha-particles (plutonium-induced pulmonary fibrosis [PuPF]) and with etiologically different pulmonary fibrosis (non-PuPF) that developed as an outcome of a chronic obstructive pulmonary disease (COPD). <b>Materials and methods:</b> To perform histological examinations, lung tissues were sampled during autopsy. Six samples of various lung regions (the apical region, the lingula of the left lung and the inferior lobe) were collected from each donor. The resected tissue samples were fixed in 10% neutral-buffered formalin during 24 h and embedded into paraffin blocks (FFPE). FFPE blocks with lung tissue specimens collected from 56 workers with PuPF, 34 workers with non-PuPF and 35 workers without any lung disease were used in the study. To perform microscopic examination, lung tissue specimens were hematoxylin and eosin stained. To examine the connective-tissue scaffold of lung stroma and identify foci of pulmonary fibrosis, the cut sections of paraffin blocks were stained by Van Gizon’s method (to assess the total volume of fibrosis-affected tissues), Gomori’s technique (to define the reticular scaffold of lung stroma) and Weigert’s technique (to examine elastic fibers). Morphological patterns of all biological specimens were studied using immunohistochemistry. To fit the empirical data, the Weibull’s model was used. <b>Results and conclusions:</b> The study found qualitative and quantitative morphological features specific for PuPF compared to non-PuPF. The study demonstrated that hyper-production of collagen type V plays a key role in PuPF. The collagen type V content in fibrotic foci in lung tissue specimens from workers with PuPF was found to be increased.
DOI: 10.6084/m9.figshare.11734218.v1
title: Survival genes expression analysis following ionizing radiation to LiCl treated KG1a cells

description: <b>Purpose:</b> Lithium chloride (LiCl) is clinically used for manic disorders. Its role has been shown in improving cell survival by decreasing Bax and p53 expression and increasing Bcl-2 concentration in the cell. This potential of LiCl is responsible for reducing irradiated cell death. In this study, we have explored the role of LiCl as a radioprotectant affecting survival genes. <b>Materials and methods:</b> To find out the cellular response upon LiCl pretreatment to radiation-exposed KG1a cells; viability, clonogenic assay and microarray studies were performed. This was followed by the detection of transcription factor binding motif in coregulated genes. These results were confirmed by reverse transcription-polymerase chain reaction (RT-PCR) and chromatin immunoprecipitation (CHIP). <b>Results:</b> LiCl improved irradiated KG1a cell survival and its clonogenicity at 2 mM concentration (clinically used). Microarray data analysis showed differential expression of cell-protecting genes playing an important role in apoptosis, cell cycle, adhesion and inflammation, etc. The coregulation analysis revealed genes involved in bile acid biosynthesis were also affected by LiCl treatment, these genes are likely to be responsible for radiation-induced gastrointestinal (GI) syndrome through bile production. <b>Conclusions:</b> This is the first study with respect to global genetic expression upon LiCl treatment to radiation-exposed cells. Our results suggest considering repurposing of LiCl as a protective agent for radiation injury.
DOI: 10.6084/m9.figshare.11734215.v2
title: Morphological features of pulmonary fibrosis in workers occupationally exposed to alpha radiation

description: <b>Purpose:</b> The article reports on a comparative analysis of biological specimens of lung tissues collected from workers with pulmonary fibrosis induced by internal exposure to plutonium alpha-particles (plutonium-induced pulmonary fibrosis [PuPF]) and with etiologically different pulmonary fibrosis (non-PuPF) that developed as an outcome of a chronic obstructive pulmonary disease (COPD). <b>Materials and methods:</b> To perform histological examinations, lung tissues were sampled during autopsy. Six samples of various lung regions (the apical region, the lingula of the left lung and the inferior lobe) were collected from each donor. The resected tissue samples were fixed in 10% neutral-buffered formalin during 24 h and embedded into paraffin blocks (FFPE). FFPE blocks with lung tissue specimens collected from 56 workers with PuPF, 34 workers with non-PuPF and 35 workers without any lung disease were used in the study. To perform microscopic examination, lung tissue specimens were hematoxylin and eosin stained. To examine the connective-tissue scaffold of lung stroma and identify foci of pulmonary fibrosis, the cut sections of paraffin blocks were stained by Van Gizon’s method (to assess the total volume of fibrosis-affected tissues), Gomori’s technique (to define the reticular scaffold of lung stroma) and Weigert’s technique (to examine elastic fibers). Morphological patterns of all biological specimens were studied using immunohistochemistry. To fit the empirical data, the Weibull’s model was used. <b>Results and conclusions:</b> The study found qualitative and quantitative morphological features specific for PuPF compared to non-PuPF. The study demonstrated that hyper-production of collagen type V plays a key role in PuPF. The collagen type V content in fibrotic foci in lung tissue specimens from workers with PuPF was found to be increased.
DOI: 10.6084/m9.figshare.11734203
title: The mRNA expression data of DTC patients

description: The mRNA expression data of cancerous and paracancerous tissue were collected up to October 29, 2019 from the TCGA-THCA data set<br>
DOI: 10.6084/m9.figshare.11734215.v1
title: Morphological features of pulmonary fibrosis in workers occupationally exposed to alpha radiation

description: <b>Purpose</b>. The paper reports on a comparative analysis of biological specimens of lung tissues collected from workers with pulmonary fibrosis induced by internal exposure to plutonium alpha-particles (PuPF) and with etiologically different pulmonary fibrosis (non-PuPF) that developed as an outcome of a chronic obstructive pulmonary disease (COPD). <b>Materials and methods</b>. To perform histological examinations, lung tissues were sampled during autopsy. Six samples of various lung regions (the apical region, the lingula of the left lung, the inferior lobe) were collected from each donor. The resected tissue samples were fixed in 10% neutral-buffered formalin during 24 hours and embedded into paraffin blocks (FFPE). FFPE blocks with lung tissue specimens collected from 56 workers with PuPF, 34 workers with non-PuPF and 35 workers without any lung disease were used in the study. To perform microscopic examination, lung tissue specimens were hematoxylin and eosin stained. To examine the connective-tissue scaffold of lung stroma and identify foci of pulmonary fibrosis, the cut sections of paraffin blocks were stained by Van-Gizon’s method (to assess the total volume of fibrosis-affected tissues); by Gomori’s technique (to define the reticular scaffold of lung stroma), by Weigert’s technique (to examine elastic fibers). Morphological patterns of all biological specimens were studied using immunohistochemistry. To fit the empirical data, the Weibull’s model was used. <b>Results and Conclusions</b>. The study found qualitative and quantitative morphological features specific for PuPF compared to non-PuPF. The study demonstrated that hyper-production of collagen type V plays a key role in PuPF. The collagen type V content in fibrotic foci in lung tissue specimens from workers with PuPF was found to be increased.
DOI: 10.6084/m9.figshare.11734203.v1
title: The mRNA expression data of DTC patients

description: The mRNA expression data of cancerous and paracancerous tissue were collected up to October 29, 2019 from the TCGA-THCA data set<br>
DOI: 10.25376/hra.11734164
title: PAS RCT_BRION - ORAL 042919.pptx

description: Oral presentation (4/29/2019) of abstract submitted to Pediatric Academy Societies Meeting, Baltimore, MD 2019
DOI: 10.25376/hra.11734164.v1
title: PAS RCT_BRION - ORAL 042919.pptx

description: Oral presentation (4/29/2019) of abstract submitted to Pediatric Academy Societies Meeting, Baltimore, MD 2019
DOI: 10.6084/m9.figshare.11734011
title: Supplementary Table 8

description: The top 10 up- and down-regulated differentially expressed mRNAs both in stearic and palmitic acid-induced β-TC 6 cells compared with control group.
DOI: 10.6084/m9.figshare.11733996
title: Supplementary Table 7

description: The log2FoldChange of differentially expressed mRNAs in palmitic acid-induced β-TC 6 cells compared both with stearic acid and control group.
DOI: 10.6084/m9.figshare.11734011.v1
title: Supplementary Table 8

description: The top 10 up- and down-regulated differentially expressed mRNAs both in stearic and palmitic acid-induced β-TC 6 cells compared with control group.
DOI: 10.6084/m9.figshare.11733990
title: Supplementary Table 6

description: The log2FoldChange of differentially expressed mRNAs in stearic acid-induced β-TC 6 cells compared both with palmitic acid and control group.
DOI: 10.6084/m9.figshare.11733996.v1
title: Supplementary Table 7

description: The log2FoldChange of differentially expressed mRNAs in palmitic acid-induced β-TC 6 cells compared both with stearic acid and control group.
DOI: 10.6084/m9.figshare.11733987
title: Supplementary Table 5

description: The differentially expressed miRNAs both in stearic and palmitic acid-induced β-TC 6 cells compared with control group.
DOI: 10.6084/m9.figshare.11733987.v1
title: Supplementary Table 5

description: The differentially expressed miRNAs both in stearic and palmitic acid-induced β-TC 6 cells compared with control group.
DOI: 10.6084/m9.figshare.11733990.v1
title: Supplementary Table 6

description: The log2FoldChange of differentially expressed mRNAs in stearic acid-induced β-TC 6 cells compared both with palmitic acid and control group.
DOI: 10.6084/m9.figshare.11733981
title: Supplementary Table 4

description: The differentially expressed miRNA in palmitic acid-induced β-TC 6 cells compared both with stearic acid and control group.
DOI: 10.6084/m9.figshare.11733975
title: esprit2_distribution_investigation.tar.gz

description: Preliminary investigation of empirical distributions of the likelihood ratio value—files with values for selected cases.
DOI: 10.6084/m9.figshare.11733981.v1
title: Supplementary Table 4

description: The differentially expressed miRNA in palmitic acid-induced β-TC 6 cells compared both with stearic acid and control group.
DOI: 10.6084/m9.figshare.11733975.v1
title: esprit2_distribution_investigation.tar.gz

description: Preliminary investigation of empirical distributions of the likelihood ratio value—files with values for selected cases.
DOI: 10.6084/m9.figshare.11733969
title: Supplementary Table 3

description: Body weight and serum analysis in normal and HSD mice at 16 weeks.
DOI: 10.6084/m9.figshare.11733969.v1
title: Supplementary Table 3

description: Body weight and serum analysis in normal and HSD mice at 16 weeks.
DOI: 10.6084/m9.figshare.11733957
title: Supplementary Table 2

description: The composition of fasting serum NEFAs profile in normal and HSD mice at 16 weeks
DOI: 10.6084/m9.figshare.11733957.v1
title: Supplementary Table 2

description: The composition of fasting serum NEFAs profile in normal and HSD mice at 16 weeks
DOI: 10.6084/m9.figshare.11733927
title: Supplementary Table 1

description: The composition of the diet for mice
DOI: 10.6084/m9.figshare.11733927.v1
title: Supplementary Table 1

description: The composition of the diet for mice
DOI: 10.6084/m9.figshare.11733894
title: Metadata

description: Metadata file.
DOI: 10.6084/m9.figshare.11733897
title: Nematode_abundance_dataset

description: Soil nematoda abundance data. This dataset includes 6,825 georeferenced soil samples from all continents and biomes.
DOI: 10.6084/m9.figshare.11733894.v1
title: Metadata

description: Metadata file.
DOI: 10.6084/m9.figshare.11733897.v1
title: Nematode_abundance_dataset

description: Soil nematoda abundance data. This dataset includes 6,825 georeferenced soil samples from all continents and biomes.
DOI: 10.6084/m9.figshare.11733891
title: Nematode_abundance_aggregated_wCovar

description: Soil nematode abundance data, aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers.
DOI: 10.6084/m9.figshare.11733891.v1
title: Nematode_abundance_aggregated_wCovar

description: Soil nematode abundance data, aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers.
DOI: 10.6084/m9.figshare.11733831
title: Planar trend model coefficients

description: Planar trend model coefficients for the representation of the midlatitude ionosphere, estimated in the least square sense for 2011 using JPL-GIMTEC every two hours and UHR-GIMTEC at every hour. Dataset contains coefficients for 48 different midlatitude regions. Each mat file contains estimated model coefficients at a specific local time as indicated in the file name. The table in the document lists geographic and geomagnetic coordinates of each region considered in the study.<br>
DOI: 10.6084/m9.figshare.11733831.v1
title: Planar trend model coefficients

description: Planar trend model coefficients for the representation of the midlatitude ionosphere, estimated in the least square sense for 2011 using JPL-GIMTEC every two hours and UHR-GIMTEC at every hour. Dataset contains coefficients for 48 different midlatitude regions. Each mat file contains estimated model coefficients at a specific local time as indicated in the file name. The table in the document lists geographic and geomagnetic coordinates of each region considered in the study.<br>