cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5822577
title: Model of the circuit in Figure 2A from Realizing ‘integral control’ in living cells: how to overcome leaky integration due to dilution?.

description: Matlab ODE model of the phosphorylation-based controller.
DOI: 10.6084/m9.figshare.5822580
title: Matlab code to generate Figure 2B from Realizing ‘integral control’ in living cells: how to overcome leaky integration due to dilution?.

description: Matlab code that generates Figure 2B.
DOI: 10.6084/m9.figshare.5822580.v2
title: Matlab code to generate Figure 2B from Realizing ‘integral control’ in living cells: how to overcome leaky integration due to dilution?.

description: Matlab code that generates Figure 2B.
DOI: 10.6084/m9.figshare.5822577.v2
title: Model of the circuit in Figure 2A from Realizing ‘integral control’ in living cells: how to overcome leaky integration due to dilution?.

description: Matlab ODE model of the phosphorylation-based controller.
DOI: 10.6084/m9.figshare.5822580.v1
title: Matlab code to generate Figure 2B from Realizing ‘integral control’ in living cells: how to overcome leaky integration due to dilution?

description: Matlab code that generates Figure 2B.
DOI: 10.6084/m9.figshare.5822574.v2
title: Matlab code to generate Figure 2D from Realizing ‘integral control’ in living cells: how to overcome leaky integration due to dilution?.

description: Matlab code that generates Figure 2D.
DOI: 10.6084/m9.figshare.5822577.v1
title: Model of the circuit in Figure 2A from Realizing ‘integral control’ in living cells: how to overcome leaky integration due to dilution?

description: Matlab ODE model of the phosphorylation-based controller.
DOI: 10.6084/m9.figshare.5822553
title: Matlab code to generate Figure 1D from Realizing ‘integral control’ in living cells: how to overcome leaky integration due to dilution?.

description: Matlab code that generates Figure 1D.
DOI: 10.6084/m9.figshare.5822574.v1
title: Matlab code to generate Figure 2D from Realizing ‘integral control’ in living cells: how to overcome leaky integration due to dilution?

description: Matlab code that generates Figure 2D.
DOI: 10.6084/m9.figshare.5822571
title: Model of the type 1 ICM in Figure 1 from Realizing ‘integral control’ in living cells: how to overcome leaky integration due to dilution?.

description: Matlab ODE model of the type 1 ICMs in Figure 1A-C.
DOI: 10.6084/m9.figshare.5822553.v2
title: Matlab code to generate Figure 1D from Realizing ‘integral control’ in living cells: how to overcome leaky integration due to dilution?.

description: Matlab code that generates Figure 1D.
DOI: 10.6084/m9.figshare.5822553.v1
title: Matlab code to generate Figure 1D from Realizing ‘integral control’ in living cells: how to overcome leaky integration due to dilution?

description: Matlab code that generates Figure 1D.
DOI: 10.6084/m9.figshare.5822571.v2
title: Model of the type 1 ICM in Figure 1 from Realizing ‘integral control’ in living cells: how to overcome leaky integration due to dilution?.

description: Matlab ODE model of the type 1 ICMs in Figure 1A-C.
DOI: 10.6084/m9.figshare.5822571.v1
title: Model of the type 1 ICM in Figure 1 from Realizing ‘integral control’ in living cells: how to overcome leaky integration due to dilution?

description: Matlab ODE model of the type 1 ICMs in Figure 1A-C.
DOI: 10.6084/m9.figshare.5956729
title: drav_cov_est_ucln_yule.xml from A Bayesian phylogenetic study of the Dravidian language family.

description: BEAST 2 xml file that was used for the best-supported analysis, relaxed covarion model with relative mutation rates estimated.
DOI: 10.6084/m9.figshare.5956729.v2
title: drav_cov_est_ucln_yule.xml from A Bayesian phylogenetic study of the Dravidian language family.

description: BEAST 2 xml file that was used for the best-supported analysis, relaxed covarion model with relative mutation rates estimated.
DOI: 10.6084/m9.figshare.5956729.v1
title: drav_cov_est_ucln_yule.xml from A Bayesian phylogenetic study of the Dravidian language family

description: BEAST 2 xml file that was used for the best-supported analysis, relaxed covarion model with relative mutation rates estimated.
DOI: 10.6084/m9.figshare.5999741
title: Data from Modelling cointegration and Granger causality network to detect long-term equilibrium and diffusion paths in the financial system.

description: The stock prices time series
DOI: 10.6084/m9.figshare.5999741.v2
title: Data from Modelling cointegration and Granger causality network to detect long-term equilibrium and diffusion paths in the financial system.

description: The stock prices time series
DOI: 10.6084/m9.figshare.5999741.v1
title: Data from Modelling cointegration and Granger causality network to detect long-term equilibrium and diffusion paths in financial system

description: The stock prices time series
DOI: 10.6084/m9.figshare.6204878
title: Source codes and data files from Application of low-order potential solutions to higher-order vertical traction boundary problems in an elastic half-space.

description: New solutions of potential functions for the bilinear vertical traction boundary condition are derived and presented. The discretization and interpolation of higher-order tractions and the superposition of the bilinear solutions provide a method of forming approximate and continuous solutions for the equilibrium state of a homogeneous and isotropic elastic half-space subjected to arbitrary normal surface tractions. Past experimental measurements of contact pressure distributions in granular media are reviewed in conjunction with the application of the proposed solution method to analysis of elastic settlement in shallow foundations. A numerical example is presented for an empirical ‘saddle-shaped’ traction distribution at the contact interface between a rigid square footing and a supporting soil medium. Non-dimensional soil resistance is computed as the reciprocal of normalized surface displacements under this empirical traction boundary condition, and the resulting internal stresses are compared to classical solutions to uniform traction boundary conditions.
DOI: 10.6084/m9.figshare.6287723
title: ESM S21 from <i>Waptia fieldensis</i> Walcott, a mandibulate arthropod from the middle Cambrian Burgess Shale.

description: S21. Waptia fieldensis, matrix of characters used in the present cladistic analysis.
DOI: 10.6084/m9.figshare.6204878.v1
title: Source codes and data files from Application of low-order potential solutions to higher-order vertical traction boundary problems in an elastic half-space

description: New solutions of potential functions for the bilinear vertical traction boundary condition are derived and presented. The discretization and interpolation of higher-order tractions and the superposition of the bilinear solutions provide a method of forming approximate and continuous solutions for the equilibrium state of a homogeneous and isotropic elastic half-space subjected to arbitrary normal surface tractions. Past experimental measurements of contact pressure distributions in granular media are reviewed in conjunction with the application of the proposed solution method to analysis of elastic settlement in shallow foundations. A numerical example is presented for an empirical ‘saddle-shaped’ traction distribution at the contact interface between a rigid square footing and a supporting soil medium. Non-dimensional soil resistance is computed as the reciprocal of normalized surface displacements under this empirical traction boundary condition, and the resulting internal stresses are compared to classical solutions to uniform traction boundary conditions.
DOI: 10.6084/m9.figshare.6287723.v2
title: ESM S21 from <i>Waptia fieldensis</i> Walcott, a mandibulate arthropod from the middle Cambrian Burgess Shale.

description: S21. Waptia fieldensis, matrix of characters used in the present cladistic analysis.
DOI: 10.6084/m9.figshare.6287723.v1
title: ESM S21 from <i>Waptia fieldensis</i> Walcott, a mandibulate arthropod from the middle Cambrian Burgess Shale

description: S21. Waptia fieldensis, matrix of characters used in the present cladistic analysis.
DOI: 10.6084/m9.figshare.6866777
title: SAS Code from Cows are highly motivated to access a grooming substrate.

description: Code used for statistical analysis (Kaplan-Meier Survival Analysis). Requires SAS.
DOI: 10.6084/m9.figshare.6866774.v2
title: Experimental Data from Cows are highly motivated to access a grooming substrate.

description: Excel sheet of the data used in statistical analysis. Data was collected by watching video footage of cows in the experimental pen. This is the input for the SAS Code (ESM2).
DOI: 10.6084/m9.figshare.6866774
title: Experimental Data from Cows are highly motivated to access a grooming substrate.

description: Excel sheet of the data used in statistical analysis. Data was collected by watching video footage of cows in the experimental pen. This is the input for the SAS Code (ESM2).
DOI: 10.6084/m9.figshare.6866777.v1
title: SAS Code from Cows are highly motivated to access a grooming substrate

description: Code used for statistical analysis (Kaplan-Meier Survival Analysis). Requires SAS.
DOI: 10.6084/m9.figshare.6866774.v1
title: Experimental Data from Cows are highly motivated to access a grooming substrate

description: Excel sheet of the data used in statistical analysis. Data was collected by watching video footage of cows in the experimental pen. This is the input for the SAS Code (ESM2).
DOI: 10.6084/m9.figshare.6931427
title: Supplementary figures from The interaction between sex-specific selection and local adaptation in species without separate sexes.

description: Higher resolution versions of the figures in Appendix A
DOI: 10.6084/m9.figshare.6931427.v2
title: Supplementary figures from The interaction between sex-specific selection and local adaptation in species without separate sexes.

description: Higher resolution versions of the figures in Appendix A
DOI: 10.6084/m9.figshare.6931427.v1
title: Supplementary figures from The interaction between sex-specific selection and local adaptation in species without separate sexes

description: Higher resolution versions of the figures in Appendix A
DOI: 10.6084/m9.figshare.13102538.v1
title: Database iZEWATA 0203 analysis.zip

description: The dataset accompanies the zero-waste multi-criteria decision-support model for the iron and steel industry in developing countries in Southern Africa. <br>
DOI: 10.6084/m9.figshare.6931433.v2
title: Appendix B - Model Analytic Results from The interaction between sex-specific selection and local adaptation in species without separate sexes.

description: Mathematica code to reproduce key analytical results
DOI: 10.6084/m9.figshare.13102538
title: Database iZEWATA 0203 analysis.zip

description: The dataset accompanies the zero-waste multi-criteria decision-support model for the iron and steel industry in developing countries in Southern Africa. <br>
DOI: 10.6084/m9.figshare.6931433
title: Appendix B - Model Analytic Results from The interaction between sex-specific selection and local adaptation in species without separate sexes.

description: Mathematica code to reproduce key analytical results
DOI: 10.6084/m9.figshare.6931433.v1
title: Appendix B - Model Analytic Results from The interaction between sex-specific selection and local adaptation in species without separate sexes

description: Mathematica code to reproduce key analytical results
DOI: 10.6084/m9.figshare.6960929
title: Complete_data_healthhui.xlsx from A liver health hui: hepatitis C knowledge and associated risk factors in New Zealand gang members and their families.

description: Hepatitis C virus (HCV) and B virus (HBV) infections are highly prevalent, with a high percentage of undiagnosed cases. Knowledge of HCV and its modes of transmission are essential for disease prevention and management. We studied a high-risk New Zealand gang population on viral hepatitis prevalence, their level of knowledge and the liver health risk factors in a community setting. Participants completed demographic, risk factor and knowledge questionnaires in three health meetings in New Zealand. Participants' blood samples were tested for HBV, HCV, biochemical indicators of liver disease. Liver fibrosis levels were assessed using a Fibroscan<sup>®</sup> device. We studied 52 adult Mongrel Mob members, affiliates and whānau (extended family) throughout New Zealand. We identified no HCV and two HBV cases, confirmed high-risk factors levels and poor associated knowledge, with a significant association between lack of knowledge and presence of specific risk factors. We successfully conducted a community-focused, high-risk, hard-to-reach gang population study, and found a link between lack of knowledge and risk factors for HCV infection. This study provided first-of-its-kind data on viral hepatitis in a gang population and demonstrated the need for educational screening programmes to aid early HCV detection, prevention and treatment.
DOI: 10.6084/m9.figshare.6960929.v2
title: Complete_data_healthhui.xlsx from A liver health hui: hepatitis C knowledge and associated risk factors in New Zealand gang members and their families.

description: Hepatitis C virus (HCV) and B virus (HBV) infections are highly prevalent, with a high percentage of undiagnosed cases. Knowledge of HCV and its modes of transmission are essential for disease prevention and management. We studied a high-risk New Zealand gang population on viral hepatitis prevalence, their level of knowledge and the liver health risk factors in a community setting. Participants completed demographic, risk factor and knowledge questionnaires in three health meetings in New Zealand. Participants' blood samples were tested for HBV, HCV, biochemical indicators of liver disease. Liver fibrosis levels were assessed using a Fibroscan<sup>®</sup> device. We studied 52 adult Mongrel Mob members, affiliates and whānau (extended family) throughout New Zealand. We identified no HCV and two HBV cases, confirmed high-risk factors levels and poor associated knowledge, with a significant association between lack of knowledge and presence of specific risk factors. We successfully conducted a community-focused, high-risk, hard-to-reach gang population study, and found a link between lack of knowledge and risk factors for HCV infection. This study provided first-of-its-kind data on viral hepatitis in a gang population and demonstrated the need for educational screening programmes to aid early HCV detection, prevention and treatment.
DOI: 10.6084/m9.figshare.6960929.v1
title: Complete_data_healthhui.xlsx from A liver health hui: hepatitis C knowledge and associated risk factors in New Zealand gang members and their families

description: Hepatitis C virus (HCV) and B virus (HBV) infections are highly prevalent, with a high percentage of undiagnosed cases. Knowledge of HCV and its modes of transmission are essential for disease prevention and management. We studied a high-risk New Zealand gang population on viral hepatitis prevalence, their level of knowledge and the liver health risk factors in a community setting. Participants completed demographic, risk factor and knowledge questionnaires in three health meetings in New Zealand. Participants' blood samples were tested for HBV, HCV, biochemical indicators of liver disease. Liver fibrosis levels were assessed using a Fibroscan<sup>®</sup> device. We studied 52 adult Mongrel Mob members, affiliates and whānau (extended family) throughout New Zealand. We identified no HCV and two HBV cases, confirmed high-risk factors levels and poor associated knowledge, with a significant association between lack of knowledge and presence of specific risk factors. We successfully conducted a community-focused, high-risk, hard-to-reach gang population study, and found a link between lack of knowledge and risk factors for HCV infection. This study provided first-of-its-kind data on viral hepatitis in a gang population; demonstrated the need for educational screening programmes to aid early HCV detection, prevention and treatment.
DOI: 10.6084/m9.figshare.7068389
title: Simulation code: spatial model from A spatio-temporal model reveals self-limiting Fc<i>ɛ</i>RI cross-linking by multivalent antigens.

description: Aggregation of cell surface receptor proteins by multivalent antigens is an essential early step for immune cell signalling. A number of experimental and modelling studies in the past have investigated multivalent ligand-mediated aggregation of IgE receptors (Fc<i>ɛ</i>RI) in the plasma membrane of mast cells. However, understanding of the mechanisms of Fc<i>ɛ</i>RI aggregation remains incomplete. Experimental reports indicate that Fc<i>ɛ</i>RI forms relatively small and finite-sized clusters when stimulated by a multivalent ligand. By contrast, modelling studies have shown that receptor cross-linking by a trivalent ligand may lead to the formation of large receptor superaggregates that may potentially give rise to hyperactive cellular responses. In this work, we have developed a Brownian dynamics-based spatio-temporal model to analyse Fc<i>ɛ</i>RI aggregation by a trivalent antigen. Unlike the existing models, which implemented non-spatial simulation approaches, our model explicitly accounts for the coarse-grained site-specific features of the multivalent species (molecules and complexes). The model incorporates membrane diffusion, steric collisions and sub-nanometre-scale site-specific interaction of the time-evolving species of arbitrary structures. Using the model, we investigated temporal evolution of the species and their diffusivities. Consistent with a recent experimental report, our model predicted sharp decay in species mobility in the plasma membrane in response receptor cross-linking by a multivalent antigen. We show that, due to such decay in the species mobility, post-stimulation receptor aggregation may become self-limiting. Our analysis reveals a potential regulatory mechanism suppressing hyperactivation of immune cells in response to multivalent antigens.
DOI: 10.6084/m9.figshare.7068395
title: Simulation code: nonspatial model from A spatio-temporal model reveals self-limiting Fc<i>ɛ</i>RI cross-linking by multivalent antigens.

description: Aggregation of cell surface receptor proteins by multivalent antigens is an essential early step for immune cell signalling. A number of experimental and modelling studies in the past have investigated multivalent ligand-mediated aggregation of IgE receptors (Fc<i>ɛ</i>RI) in the plasma membrane of mast cells. However, understanding of the mechanisms of Fc<i>ɛ</i>RI aggregation remains incomplete. Experimental reports indicate that Fc<i>ɛ</i>RI forms relatively small and finite-sized clusters when stimulated by a multivalent ligand. By contrast, modelling studies have shown that receptor cross-linking by a trivalent ligand may lead to the formation of large receptor superaggregates that may potentially give rise to hyperactive cellular responses. In this work, we have developed a Brownian dynamics-based spatio-temporal model to analyse Fc<i>ɛ</i>RI aggregation by a trivalent antigen. Unlike the existing models, which implemented non-spatial simulation approaches, our model explicitly accounts for the coarse-grained site-specific features of the multivalent species (molecules and complexes). The model incorporates membrane diffusion, steric collisions and sub-nanometre-scale site-specific interaction of the time-evolving species of arbitrary structures. Using the model, we investigated temporal evolution of the species and their diffusivities. Consistent with a recent experimental report, our model predicted sharp decay in species mobility in the plasma membrane in response receptor cross-linking by a multivalent antigen. We show that, due to such decay in the species mobility, post-stimulation receptor aggregation may become self-limiting. Our analysis reveals a potential regulatory mechanism suppressing hyperactivation of immune cells in response to multivalent antigens.
DOI: 10.6084/m9.figshare.7068389.v2
title: Simulation code: spatial model from A spatio-temporal model reveals self-limiting Fc<i>ɛ</i>RI cross-linking by multivalent antigens.

description: Aggregation of cell surface receptor proteins by multivalent antigens is an essential early step for immune cell signalling. A number of experimental and modelling studies in the past have investigated multivalent ligand-mediated aggregation of IgE receptors (Fc<i>ɛ</i>RI) in the plasma membrane of mast cells. However, understanding of the mechanisms of Fc<i>ɛ</i>RI aggregation remains incomplete. Experimental reports indicate that Fc<i>ɛ</i>RI forms relatively small and finite-sized clusters when stimulated by a multivalent ligand. By contrast, modelling studies have shown that receptor cross-linking by a trivalent ligand may lead to the formation of large receptor superaggregates that may potentially give rise to hyperactive cellular responses. In this work, we have developed a Brownian dynamics-based spatio-temporal model to analyse Fc<i>ɛ</i>RI aggregation by a trivalent antigen. Unlike the existing models, which implemented non-spatial simulation approaches, our model explicitly accounts for the coarse-grained site-specific features of the multivalent species (molecules and complexes). The model incorporates membrane diffusion, steric collisions and sub-nanometre-scale site-specific interaction of the time-evolving species of arbitrary structures. Using the model, we investigated temporal evolution of the species and their diffusivities. Consistent with a recent experimental report, our model predicted sharp decay in species mobility in the plasma membrane in response receptor cross-linking by a multivalent antigen. We show that, due to such decay in the species mobility, post-stimulation receptor aggregation may become self-limiting. Our analysis reveals a potential regulatory mechanism suppressing hyperactivation of immune cells in response to multivalent antigens.
DOI: 10.6084/m9.figshare.7068389.v1
title: Simulation code: spatial model from A spatio-temporal model reveals self-limiting Fc<i>ɛ</i>RI crosslinking by multivalent antigens

description: Aggregation of cell surface receptor proteins by multivalent antigens is an essential early step for immune cell signaling. A number of experimental and modelling studies in the past have investigated multivalent ligand-mediated aggregation of IgE receptors (Fc<i>ɛ</i>RI) in the plasma membrane of mast cells. However, understanding of the mechanisms of Fc<i>ɛ</i>RI aggregation remains incomplete. Experimental reports indicate that Fc<i>ɛ</i>RI forms relatively small and finite-sized clusters when stimulated by a multivalent ligand. By contrast, modelling studies have shown that receptor crosslinking by a trivalent ligand may lead to the formation of large receptor superaggregates that may potentially give rise to hyperactive cellular responses. In this work, we have developed a Brownian dynamics-based spatio-temporal model to analyse Fc<i>ɛ</i>RI aggregation by a trivalent antigen. Unlike the existing models, which implemented non-spatial simulation approaches, our model explicitly accounts for the coarse-grained site-specific features of the multivalent species (molecules and complexes). The model incorporates membrane diffusion, steric collisions and sub-nanometre-scale site-specific interaction of the time-evolving species of arbitrary structures. Using the model, we investigated temporal evolution of the species and their diffusivities. Consistent with a recent experimental report, our model-predicted sharp decay in species mobility in the plasma membrane in response receptor crosslinking by a multivalent antigen. We show that, due to such decay in the species mobility, post-stimulation receptor aggregation may become self-limiting. Our analysis reveals a potential regulatory mechanism suppressing hyperactivation of immune cells in response to multivalent antigens.