cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7068395.v2
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.7068395.v1
title: Simulation code: nonspatial 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.
DOI: 10.6084/m9.figshare.7217039
title: Database for publication from A widespread thermodynamic effect, but maintenance of biological rates through space across life's major domains.

description: Database
DOI: 10.6084/m9.figshare.7218209
title: Supplementary raw data from Challenges and future prospects for developing Ca and Mg water quality guidelines: a meta-analysis.

description: This file contains all datasets used in the main article (background water hardness and Ca:Mg ratio, and R formatted data used in the article). This file also contains reference lists of all articles collected, preliminarily screened, successfully classified, and rejected.
DOI: 10.6084/m9.figshare.7241633
title: Supplementary data 2 from Colour pattern predicts outcome of female contest competition in a sexually monomorphic fish.

description: Model estimates obtained from permuted datasets, used in figure 2.
DOI: 10.6084/m9.figshare.7218209.v2
title: Supplementary raw data from Challenges and future prospects for developing Ca and Mg water quality guidelines: a meta-analysis.

description: This file contains all datasets used in the main article (background water hardness and Ca:Mg ratio, and R formatted data used in the article). This file also contains reference lists of all articles collected, preliminarily screened, successfully classified, and rejected.
DOI: 10.6084/m9.figshare.7217039.v2
title: Database for publication from A widespread thermodynamic effect, but maintenance of biological rates through space across life's major domains.

description: Database
DOI: 10.6084/m9.figshare.7241642
title: Supplementary data 1 from Colour pattern predicts outcome of female contest competition in a sexually monomorphic fish.

description: Data used for the analysis of the contest competition experiment (table1, 2 and 3 in the main text).
DOI: 10.6084/m9.figshare.7241636
title: Supplementary data 4 from Colour pattern predicts outcome of female contest competition in a sexually monomorphic fish.

description: R script for statistical analyses.
DOI: 10.6084/m9.figshare.7241633.v2
title: Supplementary data 2 from Colour pattern predicts outcome of female contest competition in a sexually monomorphic fish.

description: Model estimates obtained from permuted datasets, used in figure 2.
DOI: 10.6084/m9.figshare.7241636.v2
title: Supplementary data 4 from Colour pattern predicts outcome of female contest competition in a sexually monomorphic fish.

description: R script for statistical analyses.
DOI: 10.6084/m9.figshare.7241645
title: Supplementary data 3 from Colour pattern predicts outcome of female contest competition in a sexually monomorphic fish.

description: Measurements of bar width and SL, used in figure S3.
DOI: 10.6084/m9.figshare.7241633.v1
title: Supplementary data 2 from Colour pattern predicts outcome of female contest competition in a sexually monomorphic fish

description: Model estimates obtained from permuted datasets, used in figure 2.
DOI: 10.6084/m9.figshare.7241636.v1
title: Supplementary data 4 from Colour pattern predicts outcome of female contest competition in a sexually monomorphic fish

description: R script for statistical analyses.
DOI: 10.6084/m9.figshare.7241642.v2
title: Supplementary data 1 from Colour pattern predicts outcome of female contest competition in a sexually monomorphic fish.

description: Data used for the analysis of the contest competition experiment (table1, 2 and 3 in the main text).
DOI: 10.6084/m9.figshare.7241642.v1
title: Supplementary data 1 from Colour pattern predicts outcome of female contest competition in a sexually monomorphic fish

description: Data used for the analysis of the contest competition experiment (table1, 2 and 3 in the main text).
DOI: 10.6084/m9.figshare.7241645.v2
title: Supplementary data 3 from Colour pattern predicts outcome of female contest competition in a sexually monomorphic fish.

description: Measurements of bar width and SL, used in figure S3.
DOI: 10.6084/m9.figshare.7241645.v1
title: Supplementary data 3 from Colour pattern predicts outcome of female contest competition in a sexually monomorphic fish

description: Measurements of bar width and SL, used in figure S3.
DOI: 10.6084/m9.figshare.7308641
title: Database from Estimating the relative importance of demic and cultural diffusion in the spread of the Neolithic in Scandinavia.

description: Neolithic sites in Scandinavia, dates and distances
DOI: 10.6084/m9.figshare.7308641.v2
title: Database from Estimating the relative importance of demic and cultural diffusion in the spread of the Neolithic in Scandinavia.

description: Neolithic sites in Scandinavia, dates and distances
DOI: 10.6084/m9.figshare.7326476
title: File S3 from Intrinsic pre-zygotic reproductive isolation of distantly related pea aphid host races.

description: Number of crosses performed for each genotype, with the number of successful mating which occurred during the 90-min observation period shown in brackets.
DOI: 10.6084/m9.figshare.7308641.v1
title: Database from Estimating the relative importance of demic and cultural diffusion in the spread of the Neolithic in Scandinavia

description: Neolithic sites in Scandinavia, dates and distances
DOI: 10.6084/m9.figshare.7326479
title: File S2 from Intrinsic pre-zygotic reproductive isolation of distantly related pea aphid host races.

description: Names and sizes for microsatellite loci.
DOI: 10.6084/m9.figshare.7326476.v2
title: File S3 from Intrinsic pre-zygotic reproductive isolation of distantly related pea aphid host races.

description: Number of crosses performed for each genotype, with the number of successful mating which occurred during the 90-min observation period shown in brackets.
DOI: 10.6084/m9.figshare.7326479.v2
title: File S2 from Intrinsic pre-zygotic reproductive isolation of distantly related pea aphid host races.

description: Names and sizes for microsatellite loci.
DOI: 10.6084/m9.figshare.7326476.v1
title: File S3 from Intrinsic pre-zygotic reproductive isolation of distantly related pea aphid host races

description: Number of crosses performed for each genotype, with the number of successful mating which occurred during the 90-min observation period shown in brackets.
DOI: 10.6084/m9.figshare.7326479.v1
title: File S2 from Intrinsic pre-zygotic reproductive isolation of distantly related pea aphid host races

description: Names and sizes for microsatellite loci.
DOI: 10.6084/m9.figshare.7531385
title: Dataset from Host density predicts the probability of parasitism by avian brood parasites.

description: The spatial distribution of hosts can be a determining factor in the reproductive success of parasites. Highly aggregated hosts may offer more opportunities for reproduction but can have better defences than isolated hosts. Here we connect macro- and micro-evolutionary processes to understand the link between host density and parasitism, using avian brood parasites as a model system. We analyse data across more than 200 host species using phylogenetic comparative analyses and quantify parasitism rate and host reproductive success in relation to spatial distribution using field data collected on one host species over 6 years. Our comparative analysis reveals that hosts occurring at intermediate densities are more likely to be parasitized than colonial or widely dispersed hosts. Correspondingly, our intraspecific field data show that individuals living at moderate densities experience higher parasitism rates than individuals at either low or high densities. Moreover, we show for the first time that the effect of host density on host reproductive success varies according to the intensity of parasitism; hosts have greater reproductive success when living at high densities if parasitism rates are high, but fare better at low densities when parasitism rates are low. We provide the first evidence of the trade-off between host density and parasitism at both macro- and micro-evolutionary scales in brood parasites.This article is part of the theme issue ‘The coevolutionary biology of brood parasitism: from mechanism to pattern’.
DOI: 10.6084/m9.figshare.7564895
title: Supplementary Table 2 from Convergent evolution of reduced eggshell conductance in avian brood parasites.

description: Source of eggshell fragment conductance data for values taken from the literature
DOI: 10.6084/m9.figshare.7531385.v2
title: Dataset from Host density predicts the probability of parasitism by avian brood parasites.

description: The spatial distribution of hosts can be a determining factor in the reproductive success of parasites. Highly aggregated hosts may offer more opportunities for reproduction but can have better defences than isolated hosts. Here we connect macro- and micro-evolutionary processes to understand the link between host density and parasitism, using avian brood parasites as a model system. We analyse data across more than 200 host species using phylogenetic comparative analyses and quantify parasitism rate and host reproductive success in relation to spatial distribution using field data collected on one host species over 6 years. Our comparative analysis reveals that hosts occurring at intermediate densities are more likely to be parasitized than colonial or widely dispersed hosts. Correspondingly, our intraspecific field data show that individuals living at moderate densities experience higher parasitism rates than individuals at either low or high densities. Moreover, we show for the first time that the effect of host density on host reproductive success varies according to the intensity of parasitism; hosts have greater reproductive success when living at high densities if parasitism rates are high, but fare better at low densities when parasitism rates are low. We provide the first evidence of the trade-off between host density and parasitism at both macro- and micro-evolutionary scales in brood parasites.This article is part of the theme issue ‘The coevolutionary biology of brood parasitism: from mechanism to pattern’.
DOI: 10.6084/m9.figshare.7564895.v2
title: Supplementary Table 2 from Convergent evolution of reduced eggshell conductance in avian brood parasites.

description: Source of eggshell fragment conductance data for values taken from the literature
DOI: 10.6084/m9.figshare.7531385.v1
title: Dataset from Host density predicts the probability of parasitism by avian brood parasites

description: The spatial distribution of hosts can be a determining factor in the reproductive success of parasites. Highly aggregated hosts may offer more opportunities for reproduction but can have better defences than isolated hosts. Here we connect macro- and micro-evolutionary processes to understand the link between host density and parasitism, using avian brood parasites as a model system. We analyse data across more than 200 host species using phylogenetic comparative analyses and quantify parasitism rate and host reproductive success in relation to spatial distribution using field data collected on one host species over 6 years. Our comparative analysis reveals that hosts occurring at intermediate densities suffer higher rates of brood parasitism than colonial or widely dispersed hosts. Correspondingly, our intraspecific field data show that individuals living at moderate densities experience higher parasitism rates than individuals at either low or high densities. Moreover, we show for the first time that the effect of host density on host reproductive success varies according to the intensity of parasitism; hosts have greater reproductive success when living at high densities if parasitism rates are high, but fare better at low densities when parasitism rates are low. We provide the first evidence of the trade-off between host density and parasitism at both macro- and micro-evolutionary scales in brood parasites.This article is part of the theme issue ‘The coevolutionary biology of brood parasitism: from mechanism to pattern’.
DOI: 10.6084/m9.figshare.7564889.v2
title: Supplementary Table 1 from Convergent evolution of reduced eggshell conductance in avian brood parasites.

description: Source of whole egg conductance data for values taken from the literature
DOI: 10.6084/m9.figshare.7564889
title: Supplementary Table 1 from Convergent evolution of reduced eggshell conductance in avian brood parasites.

description: Source of whole egg conductance data for values taken from the literature
DOI: 10.6084/m9.figshare.7564895.v1
title: Supplementary Table 2 from Convergent evolution of reduced eggshell conductance in avian brood parasites

description: Source of eggshell fragment conductance data for values taken from the literature
DOI: 10.6084/m9.figshare.7564889.v1
title: Supplementary Table 1 from Convergent evolution of reduced eggshell conductance in avian brood parasites

description: Source of whole egg conductance data for values taken from the literature
DOI: 10.6084/m9.figshare.7745150
title: Supplementary figures S1-S5 from Narrow habitat breadth and late-summer emergence increases extinction vulnerability in Central European bees.

description: Evaluating intrinsic and extrinsic traits that predispose species to local extinction is important for targeting conservation efforts. Among the species of special concern in Europe are bees, which, along with butterflies, are the best monitored insects. Bees are most species-rich in Mediterranean-type climates with short winters, warm springs, and dry summers. In Central Europe, climate warming <i>per se</i> is, therefore, expected to benefit most bee species, while pesticides and the loss of habitats and plant diversity should constitute threats. Here, we use the bee fauna of Germany, which has been monitored for Red Lists for over 40 years, to analyse the effects of habitat breadth, pollen specialization, body size, nesting sites, sociality, duration of flight activity, and time of emergence during the season. We tested each factor's predictive power against changes in commonness and Red List status, using phylogenetically informed hierarchical Bayesian (HB) models. Extinction vulnerability is strongly increased in bees flying in late summer, with a statistical model that included flight time, habitat preference, and duration of activity correctly predicting the vulnerability status of 85% of the species. Conversely, spring emergence and occurrence in urban areas each reduce vulnerability, pointing to intensive land use especially harming summer-active bees, with the combination of these factors currently shifting Germany's bee diversity towards warm-adapted, spring-flying, city-dwelling species.
DOI: 10.6084/m9.figshare.7745147
title: Table S1 from Narrow habitat breadth and late-summer emergence increases extinction vulnerability in Central European bees.

description: The 17 traits and their states for all species coded
DOI: 10.6084/m9.figshare.7745150.v2
title: Supplementary figures S1-S5 from Narrow habitat breadth and late-summer emergence increases extinction vulnerability in Central European bees.

description: Evaluating intrinsic and extrinsic traits that predispose species to local extinction is important for targeting conservation efforts. Among the species of special concern in Europe are bees, which, along with butterflies, are the best monitored insects. Bees are most species-rich in Mediterranean-type climates with short winters, warm springs, and dry summers. In Central Europe, climate warming <i>per se</i> is, therefore, expected to benefit most bee species, while pesticides and the loss of habitats and plant diversity should constitute threats. Here, we use the bee fauna of Germany, which has been monitored for Red Lists for over 40 years, to analyse the effects of habitat breadth, pollen specialization, body size, nesting sites, sociality, duration of flight activity, and time of emergence during the season. We tested each factor's predictive power against changes in commonness and Red List status, using phylogenetically informed hierarchical Bayesian (HB) models. Extinction vulnerability is strongly increased in bees flying in late summer, with a statistical model that included flight time, habitat preference, and duration of activity correctly predicting the vulnerability status of 85% of the species. Conversely, spring emergence and occurrence in urban areas each reduce vulnerability, pointing to intensive land use especially harming summer-active bees, with the combination of these factors currently shifting Germany's bee diversity towards warm-adapted, spring-flying, city-dwelling species.
DOI: 10.6084/m9.figshare.7745147.v2
title: Table S1 from Narrow habitat breadth and late-summer emergence increases extinction vulnerability in Central European bees.

description: The 17 traits and their states for all species coded
DOI: 10.6084/m9.figshare.7745147.v1
title: Table S2 from Narrow habitat breadth and late-summer emergence increases extinction vulnerability in Central European bees

description: Flight times for all bee species coded in this study
DOI: 10.6084/m9.figshare.7745150.v1
title: Table S1 from Narrow habitat breadth and late-summer emergence increases extinction vulnerability in Central European bees

description: The 17 traits and their states for all species coded
DOI: 10.6084/m9.figshare.7867580
title: Coelho et al. DATA-ESM from Drivers of geographical patterns of North American language diversity.

description: The data used to run the analysis
DOI: 10.6084/m9.figshare.7867580.v2
title: Coelho et al. DATA-ESM from Drivers of geographical patterns of North American language diversity.

description: The data used to run the analysis
DOI: 10.6084/m9.figshare.7867580.v1
title: Coelho et al. DATA-ESM from Drivers of geographical patterns of North American language diversity

description: The data used to run the analysis
DOI: 10.6084/m9.figshare.7867583.v2
title: Coelho et al. Source code for statistical analysis-ESM from Drivers of geographical patterns of North American language diversity.

description: The code for statistical analysis that can be run in R
DOI: 10.6084/m9.figshare.7867583
title: Coelho et al. Source code for statistical analysis-ESM from Drivers of geographical patterns of North American language diversity.

description: The code for statistical analysis that can be run in R
DOI: 10.6084/m9.figshare.7867583.v1
title: Coelho et al. Source code for statistical analysis-ESM from Drivers of geographical patterns of North American language diversity

description: The code for statistical analysis that can be run in R
DOI: 10.6084/m9.figshare.7879985
title: Data and Code supporting manuscript from Quantifying the consequences of measles-induced immune modulation for whooping cough epidemiology.

description: Measles, an acute viral disease, continues to be an important cause of childhood mortality worldwide. Infection with the measles virus is thought to be associated with a transient but profound period of immune suppression. Recently, it has been claimed that measles-induced immune manipulation lasts for about 30 months and results in increased susceptibility to other co-circulating infectious diseases and more severe disease outcomes upon infection. We tested this hypothesis using model-based inference applied to parallel historical records of measles and whooping cough mortality and morbidity. Specifically, we used maximum likelihood to fit a mechanistic transmission model to incidence data from three different eras, spanning mortality records from 1904 to 1912 and 1922 to 1932 and morbidity records from 1946 to 1956. Our aim was to quantify the timing, severity and pathogenesis impacts of measles-induced immune modulation and their consequences for whooping cough epidemiology across a temporal gradient of measles transmission. We identified an increase in susceptibility to whooping cough following recent measles infection by approximately 85-, 10- and 36-fold for the three eras, respectively, although the duration of this effect was variable. Overall, while the immune impacts of measles may be strong and clearly evident at the individual level, their epidemiological signature in these data appears both modest and inconsistent.This article is part of the theme issue ‘Detection, forecasting and control of infectious disease epidemics: modelling outbreaks in humans, animals and plants Part 1’.