cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6063032.v1
title: Data from Gopko M, Chowdhury M, Taskinen J (2018) Interactions between two common parasites in brown trout (Salmo trutta): consequences of pre-infection.

description: Two data files (csv) and one text file with the description of the variables.<br>In brief, our research concerned the influence of pre-infection with one parasitic species on the success of subsequent infections. We infected brown trout with glochidia of the freshwater pearl mussel and then with <i>D. pseudospathaceum</i> cercariae under controlled laboratory conditions and vice versa in the reverse order.
DOI: 10.6084/m9.figshare.6063026
title: Linear Hypothesis Testing With Functional Data

description: In real data analysis, it is often interesting to consider a general linear hypothesis testing (GLHT) problem for functional data, which includes the one-way ANOVA, post hoc, or contrast analysis as special cases. Existing tests for this GLHT problem include an <i>L</i><sup>2</sup>-norm-based test and an <i>F</i>-type test but their theoretical properties have not been investigated. In addition, for functional one-way ANOVA, simulation studies in the literature indicate that they are less powerful than the globalizing pointwise <i>F</i> (GPF) test and the <i>F</i><sub>max </sub>-test. The GPF and <i>F</i><sub>max </sub>-test enjoy several other good properties. They are scale-invariant in the sense that their test statistics do not change if we multiply each of functional curves with a nonzero function of the observed locations. In this article, the GPF and <i>F</i><sub>max </sub>-test are adapted to the above GLHT problem. Their theoretical properties, for example, root-<i>n</i> consistency as well as those of the <i>L</i><sup>2</sup>-norm-based and <i>F</i>-type tests are established. Intensive simulation studies are carried out to compare the finite-sample behavior of the tests under consideration in scenarios reflecting various practical characteristics of functional data. Simulation results indicate that the GPF test has higher power than other tests when the functional data are less correlated, and the <i>F</i><sub>max </sub>-test has higher power than other tests when the functional data are moderately or highly correlated. These results are also confirmed by application of the GPF and <i>F</i><sub>max </sub> tests to the corneal surface data coming from medical industry. This application suggests the new methods may help to make more clear and sure decisions in practice. For a convenient application of the considered testing procedures, their implementation is developed in the R programming language. Supplementary materials for the article are available online.
DOI: 10.6084/m9.figshare.6063026.v2
title: Linear Hypothesis Testing With Functional Data

description: In real data analysis, it is often interesting to consider a general linear hypothesis testing (GLHT) problem for functional data, which includes the one-way ANOVA, post hoc, or contrast analysis as special cases. Existing tests for this GLHT problem include an <i>L</i><sup>2</sup>-norm-based test and an <i>F</i>-type test but their theoretical properties have not been investigated. In addition, for functional one-way ANOVA, simulation studies in the literature indicate that they are less powerful than the globalizing pointwise <i>F</i> (GPF) test and the <i>F</i><sub>max </sub>-test. The GPF and <i>F</i><sub>max </sub>-test enjoy several other good properties. They are scale-invariant in the sense that their test statistics do not change if we multiply each of functional curves with a nonzero function of the observed locations. In this article, the GPF and <i>F</i><sub>max </sub>-test are adapted to the above GLHT problem. Their theoretical properties, for example, root-<i>n</i> consistency as well as those of the <i>L</i><sup>2</sup>-norm-based and <i>F</i>-type tests are established. Intensive simulation studies are carried out to compare the finite-sample behavior of the tests under consideration in scenarios reflecting various practical characteristics of functional data. Simulation results indicate that the GPF test has higher power than other tests when the functional data are less correlated, and the <i>F</i><sub>max </sub>-test has higher power than other tests when the functional data are moderately or highly correlated. These results are also confirmed by application of the GPF and <i>F</i><sub>max </sub> tests to the corneal surface data coming from medical industry. This application suggests the new methods may help to make more clear and sure decisions in practice. For a convenient application of the considered testing procedures, their implementation is developed in the R programming language. Supplementary materials for the article are available online.
DOI: 10.6084/m9.figshare.6063026.v1
title: Linear hypothesis testing with functional data

description: In real data analysis, it is often interesting to consider a general linear hypothesis testing (GLHT) problem for functional data, which includes the one-way ANOVA, post hoc or contrast analysis as special cases. Existing tests for this GLHT problem include a <i>L</i><sup>2</sup>-norm-based test and an <i>F</i>-type test but their theoretical properties have not been investigated. In addition, for functional one-way ANOVA, simulation studies in the literature indicate that they are less powerful than the globalizing pointwise <i>F</i> (GPF) test and the <i>F</i><sub>max</sub>-test. The GPF and <i>F</i><sub>max</sub>-test enjoy several other good properties. They are scale-invariant in the sense that their test statistics do not change if we multiply each of functional curves with a non-zero function of the observed locations. In this paper, the GPF and <i>F</i><sub>max</sub>-test are adapted to the above GLHT problem. Their theoretical properties, for example root-<i>n</i> consistency as well as those of the <i>L</i><sup>2</sup>-norm-based and <i>F</i>-type tests are established. Intensive simulation studies are carried out to compare the finite-sample behavior of the tests under consideration in scenarios reflecting various practical characteristics of functional data. Simulation results indicate that the GPF test has higher power than other tests when the functional data are less correlated, and the <i>F</i><sub>max</sub>-test has higher power than other tests when the functional data are moderately or highly correlated. These results are also confirmed by application of the GPF and <i>F</i><sub>max</sub> tests to the corneal surface data coming from medical industry. This application suggests the new methods may help to make more clear and sure decisions in practice. For a convenient application of the considered testing procedures, their implementation is developed in the R programming language.
DOI: 10.6084/m9.figshare.6063017
title: Generalized Additive Models for Pair-Copula Constructions

description: Pair-copula constructions are flexible dependence models that use bivariate copulas as building blocks. In this article, we extend them with generalized additive models to allow covariates effects. Borrowing ideas from a traditionally univariate context, we let each pair-copula parameter depend directly on the covariates in a parametric, semiparametric, or nonparametric way. We propose a sequential estimation method that we study by simulation, and apply it to investigate the time-varying dependence structure between the intraday returns on four major foreign exchange rates. An R package, scripts reproducing the results in this article, and additional simulation results are provided as supplementary material.
DOI: 10.6084/m9.figshare.6063017.v1
title: Generalized Additive Models for Pair-Copula Constructions

description: Pair-copula constructions are flexible dependence models that use bivariate copulas as building blocks. In this article, we extend them with generalized additive models to allow covariates effects. Borrowing ideas from a traditionally univariate context, we let each pair-copula parameter depend directly on the covariates in a parametric, semiparametric, or nonparametric way. We propose a sequential estimation method that we study by simulation, and apply it to investigate the time-varying dependence structure between the intraday returns on four major foreign exchange rates. An R package, scripts reproducing the results in this article, and additional simulation results are provided as supplementary material.
DOI: 10.6084/m9.figshare.6062987
title: A proteomic approach reveals the variation in human platelet protein composition after storage at different temperatures

description: Cryopreservation can slow down the metabolism and decrease the risk of bacterial contamination. But, chilled platelets (PLTs) show a reduced period in circulation due to the rapid clearance by hepatic cells or spleen macrophages after transfusion. The deleterious changes that PLTs undergo are mainly considered the result of PLT protein variation. However, the basis for proteomic variation of stored PLTs remains poorly understood. Besides count, activation markers (CD62P and Annexin V), and aggregation, we used quantitative mass spectrometry to create the first comprehensive and quantitative human PLT proteome of samples stored at different temperatures (22°C, 10°C and −80°C). We found different conditions caused different platelet storage lesion (PSL). PLT count was decreased no matter at what temperature stored. PLTs viability at low temperature dropped by 21.78% and 11.21%, respectively, as compared 10.26% at room temperature, there were no significant differences between the storage methods. Membrane expression of CD62P gradually increased in all groups especially stored at 22°C up to 40% and 10°C up to 30%. However, exposure of PS on the PLT membrane was below 1% in every group. The PLT proteome showed there were 575 and 454 potential proteins identified by general iTRAQ analysis and phosphorylation iTRAQ a nalysis, respectively, among them, 33 common differentially expressed proteins caused by storage time and 44 caused by storage temperature Especially, membrane-bound proteins (such as FERMT3, STX4, MYL9 and TAGLN2) played key roles in PLT storage lesion. The pathways “Endocytosis”, “Fc gamma R-mediated phagocytosis” and “Regulation of actin cytoskeleton” were affected predominantly by storage time. And the pathways “SNARE interactions in vesicular transport” and “Vasopressin-regulated water reabsorption” were affected by cold storage in our study. Proteomic results can help us to understand PLT biochemistry and physiology and thus unravel the mechanisms of PSL in time and space for more successful PLT transfusion therapy.
DOI: 10.6084/m9.figshare.6062987.v2
title: A proteomic approach reveals the variation in human platelet protein composition after storage at different temperatures

description: Cryopreservation can slow down the metabolism and decrease the risk of bacterial contamination. But, chilled platelets (PLTs) show a reduced period in circulation due to the rapid clearance by hepatic cells or spleen macrophages after transfusion. The deleterious changes that PLTs undergo are mainly considered the result of PLT protein variation. However, the basis for proteomic variation of stored PLTs remains poorly understood. Besides count, activation markers (CD62P and Annexin V), and aggregation, we used quantitative mass spectrometry to create the first comprehensive and quantitative human PLT proteome of samples stored at different temperatures (22°C, 10°C and −80°C). We found different conditions caused different platelet storage lesion (PSL). PLT count was decreased no matter at what temperature stored. PLTs viability at low temperature dropped by 21.78% and 11.21%, respectively, as compared 10.26% at room temperature, there were no significant differences between the storage methods. Membrane expression of CD62P gradually increased in all groups especially stored at 22°C up to 40% and 10°C up to 30%. However, exposure of PS on the PLT membrane was below 1% in every group. The PLT proteome showed there were 575 and 454 potential proteins identified by general iTRAQ analysis and phosphorylation iTRAQ a nalysis, respectively, among them, 33 common differentially expressed proteins caused by storage time and 44 caused by storage temperature Especially, membrane-bound proteins (such as FERMT3, STX4, MYL9 and TAGLN2) played key roles in PLT storage lesion. The pathways “Endocytosis”, “Fc gamma R-mediated phagocytosis” and “Regulation of actin cytoskeleton” were affected predominantly by storage time. And the pathways “SNARE interactions in vesicular transport” and “Vasopressin-regulated water reabsorption” were affected by cold storage in our study. Proteomic results can help us to understand PLT biochemistry and physiology and thus unravel the mechanisms of PSL in time and space for more successful PLT transfusion therapy.
DOI: 10.6084/m9.figshare.6062987.v1
title: A proteomic approach reveals the variation in human platelet protein composition after storage at different temperatures

description: Cryopreservation can slow down the metabolism and decrease the risk of bacterial contamination. But, chilled platelets (PLTs) show a reduced period in circulation due to the rapid clearance by hepatic cells or spleen macrophages after transfusion. The deleterious changes that PLTs undergo are mainly considered the result of PLT protein variation. However, the basis for proteomic variation of stored PLTs remains poorly understood. Besides count, activation markers (CD62P and Annexin V), and aggregation, we used quantitative mass spectrometry to create the first comprehensive and quantitative human PLT proteome of samples stored at different temperatures (22°C, 10°C and −80°C). We found different conditions caused different platelet storage lesion (PSL). PLT count was decreased no matter at what temperature stored. PLTs viability at low temperature dropped by 21.78% and 11.21%, respectively, as compared 10.26% at room temperature, there were no significant differences between the storage methods. Membrane expression of CD62P gradually increased in all groups especially stored at 22°C up to 40% and 10°C up to 30%. However, exposure of PS on the PLT membrane was below 1% in every group. The PLT proteome showed there were 575 and 454 potential proteins identified by general iTRAQ analysis and phosphorylation iTRAQ a nalysis, respectively, among them, 33 common differentially expressed proteins caused by storage time and 44 caused by storage temperature Especially, membrane-bound proteins (such as FERMT3, STX4, MYL9 and TAGLN2) played key roles in PLT storage lesion. The pathways “Endocytosis”, “Fc gamma R-mediated phagocytosis” and “Regulation of actin cytoskeleton” were affected predominantly by storage time. And the pathways “SNARE interactions in vesicular transport” and “Vasopressin-regulated water reabsorption” were affected by cold storage in our study. Proteomic results can help us to understand PLT biochemistry and physiology and thus unravel the mechanisms of PSL in time and space for more successful PLT transfusion therapy.
DOI: 10.6084/m9.figshare.6062954
title: real E.coli data results

description: Results of BacTag analysis for 189 real E.coli datasets. Datasets are grouped per expected ST. Sequencing reads are publicly available and not included to this fileset
DOI: 10.6084/m9.figshare.6062954.v1
title: real E.coli data results

description: Results of BacTag analysis for 189 real E.coli datasets. Datasets are grouped per expected ST. Sequencing reads are publicly available and not included to this fileset
DOI: 10.6084/m9.figshare.6062951
title: Preprocessed database

description: Results of Achtman 7 gene MLST database preprocessing
DOI: 10.6084/m9.figshare.6062951.v1
title: Preprocessed database

description: Results of Achtman 7 gene MLST database preprocessing
DOI: 10.6084/m9.figshare.6062945
title: E.coli artificial reads BacTag results

description: Results for 7 artificial <i>E.coli </i>datasets. Artificial paired reads are also included.
DOI: 10.6084/m9.figshare.6062945.v1
title: E.coli artificial reads BacTag results

description: Results for 7 artificial <i>E.coli </i>datasets. Artificial paired reads are also included.
DOI: 10.6084/m9.figshare.6062936
title: Palaeomagnetic data. Magnetostratigraphy of the Toarcian Stage (Lower Jurassic) of the Llanbedr (Mochras Farm) Borehole, Wales: basis for a global standard and implications for volcanic forcing of palaeoenvironmental change

description: Palaeomagnetic data
DOI: 10.6084/m9.figshare.6062936.v1
title: Palaeomagnetic data. Magnetostratigraphy of the Toarcian Stage (Lower Jurassic) of the Llanbedr (Mochras Farm) Borehole, Wales: basis for a global standard and implications for volcanic forcing of palaeoenvironmental change

description: Palaeomagnetic data
DOI: 10.6084/m9.figshare.6062822
title: Emotion identification across adulthood using the Dynamic FACES database of emotional expressions in younger, middle aged, and older adults

description: Facial stimuli are widely used in behavioural and brain science research to investigate emotional facial processing. However, some studies have demonstrated that dynamic expressions elicit stronger emotional responses compared to static images. To address the need for more ecologically valid and powerful facial emotional stimuli, we created Dynamic FACES, a database of morphed videos <i>(n = 1026)</i> from younger, middle-aged, and older adults displaying naturalistic emotional facial expressions (neutrality, sadness, disgust, fear, anger, happiness). To assess adult age differences in emotion identification of dynamic stimuli and to provide normative ratings for this modified set of stimuli, healthy adults (<i>n</i> = 1822, age range 18–86 years) categorised for each video the emotional expression displayed, rated the expression distinctiveness, estimated the age of the face model, and rated the naturalness of the expression. We found few age differences in emotion identification when using dynamic stimuli. Only for angry faces did older adults show lower levels of identification accuracy than younger adults. Further, older adults outperformed middle-aged adults’ in identification of sadness. The use of dynamic facial emotional stimuli has previously been limited, but Dynamic FACES provides a large database of high-resolution naturalistic, dynamic expressions across adulthood. Information on using Dynamic FACES for research purposes can be found at http://faces.mpib-berlin.mpg.de.
DOI: 10.6084/m9.figshare.6062822.v1
title: Emotion identification across adulthood using the Dynamic FACES database of emotional expressions in younger, middle aged, and older adults

description: Facial stimuli are widely used in behavioural and brain science research to investigate emotional facial processing. However, some studies have demonstrated that dynamic expressions elicit stronger emotional responses compared to static images. To address the need for more ecologically valid and powerful facial emotional stimuli, we created Dynamic FACES, a database of morphed videos <i>(n = 1026)</i> from younger, middle-aged, and older adults displaying naturalistic emotional facial expressions (neutrality, sadness, disgust, fear, anger, happiness). To assess adult age differences in emotion identification of dynamic stimuli and to provide normative ratings for this modified set of stimuli, healthy adults (<i>n</i> = 1822, age range 18–86 years) categorised for each video the emotional expression displayed, rated the expression distinctiveness, estimated the age of the face model, and rated the naturalness of the expression. We found few age differences in emotion identification when using dynamic stimuli. Only for angry faces did older adults show lower levels of identification accuracy than younger adults. Further, older adults outperformed middle-aged adults’ in identification of sadness. The use of dynamic facial emotional stimuli has previously been limited, but Dynamic FACES provides a large database of high-resolution naturalistic, dynamic expressions across adulthood. Information on using Dynamic FACES for research purposes can be found at http://faces.mpib-berlin.mpg.de.
DOI: 10.6084/m9.figshare.6062804
title: Dhaka_household_cholera

description: Data for Domman et al., Nature Genetics (2018).
DOI: 10.6084/m9.figshare.6062804.v1
title: Dhaka_household_cholera

description: Data for Domman et al., Nature Genetics (2018).
DOI: 10.23645/epacomptox.6062785
title: ToxCast Data Pipeline Overview

description: The tcpl package was developed to process high-throughput and high-content screening data generated by the ToxCast program. ToxCast is screening thousands of chemicals with hundreds of assays coming from numerous and diverse biochemical and cell-based technology platforms. The diverse data, received in heterogeneous formats from numerous vendors, are transformed to a standard computable format and loaded into the tcpl database by vendor-specific R scripts. Once data is loaded into the database, ToxCast utilizes the generalized processing functions provided in this package to process, normalize, model, qualify, flag, inspect, and visualize the data. While developed primarily for ToxCast, we have attempted to make the tcpl package generally applicable to chemical-screening community.
DOI: 10.23645/epacomptox.6062773
title: EPA Literature Database Cleft Palate Chemical Data

description: Literature Database Cleft Palate chemical data
DOI: 10.23645/epacomptox.6062773.v1
title: EPA Literature Database Cleft Palate Chemical Data

description: Literature Database Cleft Palate chemical data
DOI: 10.23645/epacomptox.6062755
title: Chemical Products Database Exposure Relevant Data in Consumer Products: Data Associated with (Forthcoming) Publication

description: Data associated with forthcoming publication on Chemical Products Database Exposure Relevant Data in Consumer Products.
DOI: 10.23645/epacomptox.6062737
title: Application of IATA- A case study in evaluating the global and local performance of a Bayesian network model for skin sensitization: Data Associated with Publication

description: Data associated with publication on Application of IATA- A case study in evaluating the global and local performance of a Bayesian network model for skin sensitization. Publication DOI: https://doi.org/10.1080/1062936X.2017.1311941
DOI: 10.23645/epacomptox.6062734
title: A Comparison of Three Liquid Chromatography (LC) Retention Time Prediction Models: Data Associated with Publication

description: Data associated with publication on A Comparison of Three Liquid Chromatography (LC) Retention Time Prediction Models. Publication DOI: https://doi.org/10.1016/j.talanta.2018.01.022
DOI: 10.23645/epacomptox.6062728
title: High-Throughput Screening of Chemical Effects on Steroidogenesis Using H295R Human Adrenocortical Carcinoma Cells: Data Associated with Publication

description: Data associated with publication on High-Throughput Screening of Chemical Effects on Steroidogenesis Using H295R Human Adrenocortical Carcinoma Cells. Publication DOI: https://doi.org/10.1093/toxsci/kfw002
DOI: 10.23645/epacomptox.6062725
title: Predicting In Vivo Effect Levels for Repeat-Dose Systemic Toxicity Using Chemical, Biological, Kinetic and Study Covariates: Data Associated with Publication

description: Data associated with publication on Predicting In Vivo Effect Levels for Repeat-Dose Systemic Toxicity Using Chemical, Biological, Kinetic and Study Covariates. Publication DOI: https://doi.org/10.1007/s00204-017-2067-x
DOI: 10.23645/epacomptox.6062719
title: Computational Modeling and Simulation of Genital Tubercle Development: Data Associated with Publication

description: Data associated with publication on Computational Modeling and Simulation of Genital Tubercle Development. Publication DOI: https://doi.org/10.1016/j.reprotox.2016.05.005