cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10029245.v1
title: Datasets of hippocampal subsection and brain area dimorphism plus the phylogenetic tree used from Primate hippocampus size and organization are predicted by sociality but not diet

description: The hippocampus is well known for its roles in spatial navigation and memory, but it is organized into regions that have different connections and functional specializations. Notably, the region CA2 has a role in social and not spatial cognition, as is the case for the regions CA1 and CA3 that surround it. Here, we investigated the evolution of the hippocampus in terms of its size and organization in relation to the evolution of social and ecological variables in primates, namely home range, diet and different measures of group size. We found that the volumes within the whole cornu ammonis coevolve with group size, while only the volume of CA1 and subiculum can also be predicted by home range. On the other hand, diet, expressed as a shift from folivory towards frugivory, was shown to not be related to hippocampal volume. Interestingly, CA2 was shown to exhibit phylogenetic signal only against certain measures of group size but not with ecological factors. We also found that sex differences in the hippocampus are related to body size sex dimorphism. This is in line with reports of sex differences in hippocampal volume in non-primates that are related to social structure and sex differences in behaviour. Our findings support the notion that in primates, the hippocampus is a mosaic structure evolving in line with social pressures, where certain subsections evolve in line with spatial ability too.
DOI: 10.6084/m9.figshare.10029236.v1
title: Results from all the PGSL analysis in separate txt files with ANOVA tables from Primate hippocampus size and organization are predicted by sociality but not diet

description: The hippocampus is well known for its roles in spatial navigation and memory, but it is organized into regions that have different connections and functional specializations. Notably, the region CA2 has a role in social and not spatial cognition, as is the case for the regions CA1 and CA3 that surround it. Here, we investigated the evolution of the hippocampus in terms of its size and organization in relation to the evolution of social and ecological variables in primates, namely home range, diet and different measures of group size. We found that the volumes within the whole cornu ammonis coevolve with group size, while only the volume of CA1 and subiculum can also be predicted by home range. On the other hand, diet, expressed as a shift from folivory towards frugivory, was shown to not be related to hippocampal volume. Interestingly, CA2 was shown to exhibit phylogenetic signal only against certain measures of group size but not with ecological factors. We also found that sex differences in the hippocampus are related to body size sex dimorphism. This is in line with reports of sex differences in hippocampal volume in non-primates that are related to social structure and sex differences in behaviour. Our findings support the notion that in primates, the hippocampus is a mosaic structure evolving in line with social pressures, where certain subsections evolve in line with spatial ability too.
DOI: 10.6084/m9.figshare.10029242.v1
title: R code for all the analysis included from Primate hippocampus size and organization are predicted by sociality but not diet

description: The hippocampus is well known for its roles in spatial navigation and memory, but it is organized into regions that have different connections and functional specializations. Notably, the region CA2 has a role in social and not spatial cognition, as is the case for the regions CA1 and CA3 that surround it. Here, we investigated the evolution of the hippocampus in terms of its size and organization in relation to the evolution of social and ecological variables in primates, namely home range, diet and different measures of group size. We found that the volumes within the whole cornu ammonis coevolve with group size, while only the volume of CA1 and subiculum can also be predicted by home range. On the other hand, diet, expressed as a shift from folivory towards frugivory, was shown to not be related to hippocampal volume. Interestingly, CA2 was shown to exhibit phylogenetic signal only against certain measures of group size but not with ecological factors. We also found that sex differences in the hippocampus are related to body size sex dimorphism. This is in line with reports of sex differences in hippocampal volume in non-primates that are related to social structure and sex differences in behaviour. Our findings support the notion that in primates, the hippocampus is a mosaic structure evolving in line with social pressures, where certain subsections evolve in line with spatial ability too.
DOI: 10.6084/m9.figshare.10247615
title: Electronic supplementary data from A regional-scale assessment of using metabolic scaling theory to predict ecosystem properties.

description: The metabolic scaling theory (MST) is one of ecology's most high-profile general models and can be used to link size distributions and productivity in forest systems. Much of MST's foundation is based on size distributions following a power law function with a scaling exponent of −2, a property assumed to be consistent in steady-state ecosystems. We tested the theory's generality by comparing actual size distributions with those predicted using MST parameters assumed to be general. We then used environmental variables and functional traits to explain deviation from theoretical expectations. Finally, we compared values of relative productivity predicted using the MST with a remote-sensed measure of productivity. We found that fire-prone heath communities deviated from MST-predicted size distributions, whereas fire-sensitive rainforests largely agreed with the theory. Scaling exponents ranged from −1.4 to −5.3. Deviation from the power law assumption was best explained by the specific leaf area which varies along fire frequency and moisture gradients. While the MST may hold in low-disturbance systems, we show that it cannot be applied under many environmental contexts. The theory should remain general, but understanding the factors driving deviation from the MST and subsequent refinements are required if it is to be applied robustly across larger scales.
DOI: 10.6084/m9.figshare.10247615.v1
title: Electronic supplementary data from A regional-scale assessment of using the metabolic scaling theory to predict ecosystem properties

description: The metabolic scaling theory (MST) is one of ecology's most high-profile general models and can be used to link size distributions and productivity in forest systems. Much of MST's foundation is based on size distributions following a power law function with a scaling exponent of −2, a property assumed to be consistent in steady-state ecosystems. We tested the theory's generality by comparing actual size distributions with those predicted using MST parameters assumed to be general. We then used environmental variables and functional traits to explain deviation from theoretical expectations. Finally, we compared values of relative productivity predicted using the MST with a remote-sensed measure of productivity. We found that fire-prone heath communities deviated from MST-predicted size distributions, whereas fire-sensitive rainforests largely agreed with the theory. Scaling exponents ranged from −1.4 to −5.3. Deviation from the power law assumption was best explained by the specific leaf area which varies along fire frequency and moisture gradients. While the MST may hold in low-disturbance systems, we show that it cannot be applied under many environmental contexts. The theory should remain general, but understanding the factors driving deviation from the MST and subsequent refinements are required if it is to be applied robustly across larger scales.
DOI: 10.6084/m9.figshare.10264748
title: Diagnostic Test Code from Posterior-based proposals for speeding up Markov chain Monte Carlo.

description: c++ code used in Section 5.1
DOI: 10.6084/m9.figshare.10264736
title: Stochastic Volatility Code from Posterior-based proposals for speeding up Markov chain Monte Carlo.

description: c++ code used in Section 5.2
DOI: 10.6084/m9.figshare.10264748.v2
title: Diagnostic Test Code from Posterior-based proposals for speeding up Markov chain Monte Carlo.

description: c++ code used in Section 5.1
DOI: 10.6084/m9.figshare.10264736.v2
title: Stochastic Volatility Code from Posterior-based proposals for speeding up Markov chain Monte Carlo.

description: c++ code used in Section 5.2
DOI: 10.6084/m9.figshare.10264748.v1
title: Diagnostic Test Code from Posterior-based proposals for speeding up Markov chain Monte Carlo

description: c++ code used in Section 5.1
DOI: 10.6084/m9.figshare.10264745
title: Mixed Model Code from Posterior-based proposals for speeding up Markov chain Monte Carlo.

description: c++ code used in Section 5.3
DOI: 10.6084/m9.figshare.10264736.v1
title: Stochastic Volatility Code from Posterior-based proposals for speeding up Markov chain Monte Carlo

description: c++ code used in Section 5.2
DOI: 10.6084/m9.figshare.10264739
title: Logistic Population Model Code from Posterior-based proposals for speeding up Markov chain Monte Carlo.

description: c++ code used in Section 5.4
DOI: 10.6084/m9.figshare.10264745.v2
title: Mixed Model Code from Posterior-based proposals for speeding up Markov chain Monte Carlo.

description: c++ code used in Section 5.3
DOI: 10.6084/m9.figshare.10264739.v2
title: Logistic Population Model Code from Posterior-based proposals for speeding up Markov chain Monte Carlo.

description: c++ code used in Section 5.4
DOI: 10.6084/m9.figshare.10264745.v1
title: Mixed Model Code from Posterior-based proposals for speeding up Markov chain Monte Carlo

description: c++ code used in Section 5.3
DOI: 10.6084/m9.figshare.10272065
title: Supplementary Code S1 from Repeated sex chromosome evolution in vertebrates supported by expanded avian sex chromosomes.

description: Code for extracting gametologous gene pairs
DOI: 10.6084/m9.figshare.10264739.v1
title: Logistic Population Model Code from Posterior-based proposals for speeding up Markov chain Monte Carlo

description: c++ code used in Section 5.4
DOI: 10.6084/m9.figshare.10272068
title: Document S1 from Repeated sex chromosome evolution in vertebrates supported by expanded avian sex chromosomes.

description: List of Gene Ontology terms associated with sex-linked genes
DOI: 10.6084/m9.figshare.10272065.v2
title: Supplementary Code S1 from Repeated sex chromosome evolution in vertebrates supported by expanded avian sex chromosomes.

description: Code for extracting gametologous gene pairs
DOI: 10.6084/m9.figshare.10272065.v1
title: Supplementary Code S1 from Repeated sex chromosome evolution in vertebrates supported by expanded avian sex chromosomes

description: Code for extracting gametologous gene pairs
DOI: 10.6084/m9.figshare.10272068.v2
title: Document S1 from Repeated sex chromosome evolution in vertebrates supported by expanded avian sex chromosomes.

description: List of Gene Ontology terms associated with sex-linked genes
DOI: 10.6084/m9.figshare.10272068.v1
title: Document S1 from Repeated sex chromosome evolution in vertebrates supported by expanded avian sex chromosomes

description: List of Gene Ontology terms associated with sex-linked genes
DOI: 10.6084/m9.figshare.10289387
title: Supplementary Tables from Social modularity: conserved genes and regulatory elements underlie caste-antecedent behavioural states in an incipiently social bee.

description: The evolutionary origins of advanced eusociality, one of the most complex forms of phenotypic plasticity in nature, have long been a focus within the field of sociobiology. Although eusocial insects are known to have evolved from solitary ancestors, sociogenomic research among incipiently social taxa has only recently provided empirical evidence supporting theories that modular regulation and deeply conserved genes may play important roles in both the evolutionary emergence and elaboration of insect sociality. There remains, however, a paucity of data to further test the biological reality of these and other evolutionary theories among taxa in the earliest stages of social evolution. Here, we present brain transcriptomic data from the incipiently social small carpenter bee, <i>Ceratina calcarata</i>, which captures patterns of <i>cis</i>-regulation and gene expression associated with female maturation, and underlying two well-defined behavioural states, foraging and guarding, concurrently demonstrated by mothers and daughters during early autumn. We find that an incipiently social nest environment may dramatically affect gene expression. We further reveal foraging and guarding behaviours to be putatively caste-antecedent states in <i>C. calcarata</i>, and offer strong empirical support for the operation of modular regulation, involving deeply conserved and differentially expressed genes in the expression of early social forms.
DOI: 10.6084/m9.figshare.10289387.v2
title: Supplementary Tables from Social modularity: conserved genes and regulatory elements underlie caste-antecedent behavioural states in an incipiently social bee.

description: The evolutionary origins of advanced eusociality, one of the most complex forms of phenotypic plasticity in nature, have long been a focus within the field of sociobiology. Although eusocial insects are known to have evolved from solitary ancestors, sociogenomic research among incipiently social taxa has only recently provided empirical evidence supporting theories that modular regulation and deeply conserved genes may play important roles in both the evolutionary emergence and elaboration of insect sociality. There remains, however, a paucity of data to further test the biological reality of these and other evolutionary theories among taxa in the earliest stages of social evolution. Here, we present brain transcriptomic data from the incipiently social small carpenter bee, <i>Ceratina calcarata</i>, which captures patterns of <i>cis</i>-regulation and gene expression associated with female maturation, and underlying two well-defined behavioural states, foraging and guarding, concurrently demonstrated by mothers and daughters during early autumn. We find that an incipiently social nest environment may dramatically affect gene expression. We further reveal foraging and guarding behaviours to be putatively caste-antecedent states in <i>C. calcarata</i>, and offer strong empirical support for the operation of modular regulation, involving deeply conserved and differentially expressed genes in the expression of early social forms.
DOI: 10.6084/m9.figshare.10289387.v1
title: Supplementary Tables from Social modularity: conserved genes and regulatory elements underlie caste-antecedent behavioural states in an incipiently social bee

description: The evolutionary origins of advanced eusociality, one of the most complex forms of phenotypic plasticity in nature, have long been a focus within the field of sociobiology. Although eusocial insects are known to have evolved from solitary ancestors, sociogenomic research among incipiently social taxa has only recently provided empirical evidence supporting theories that modular regulation and deeply conserved genes may play important roles in both the evolutionary emergence and elaboration of insect sociality. There remains, however, a paucity of data to further test the biological reality of these and other evolutionary theories among taxa in the earliest stages of social evolution. Here, we present brain transcriptomic data from the incipiently social small carpenter bee, <i>Ceratina calcarata</i>, which captures patterns of <i>cis</i>-regulation and gene expression associated with female maturation, and underlying two well-defined behavioural states, foraging and guarding, concurrently demonstrated by mothers and daughters during early autumn. We find that an incipiently social nest environment may dramatically affect gene expression. We further reveal foraging and guarding behaviours to be putatively caste-antecedent states in <i>C. calcarata</i>, and offer strong empirical support for the operation of modular regulation, involving deeply conserved and differentially expressed genes in the expression of early social forms.
DOI: 10.6084/m9.figshare.10320230
title: NMRT2 spectrum data from Microscopic characterization and strength characteristics of cemented backfill under different humidity curing conditions.

description: This document indicates that the data used in the paper was tested by the instrument.
DOI: 10.6084/m9.figshare.10320233
title: Uniaxial compressive strength data from Microscopic characterization and strength characteristics of cemented backfill under different humidity curing conditions.

description: This document indicates that the data used in the paper was tested by the instrument.
DOI: 10.6084/m9.figshare.10320230.v2
title: NMRT2 spectrum data from Microscopic characterization and strength characteristics of cemented backfill under different humidity curing conditions.

description: This document indicates that the data used in the paper was tested by the instrument.
DOI: 10.6084/m9.figshare.10320230.v1
title: Particle size distribution data from Microscopic characterization and strength characteristics of cemented backfill under different humidity curing conditions

description: This document indicates that the data used in the paper was tested by the instrument.
DOI: 10.6084/m9.figshare.10320233.v2
title: Uniaxial compressive strength data from Microscopic characterization and strength characteristics of cemented backfill under different humidity curing conditions.

description: This document indicates that the data used in the paper was tested by the instrument.
DOI: 10.6084/m9.figshare.10320233.v1
title: NMRT2 spectrum data from Microscopic characterization and strength characteristics of cemented backfill under different humidity curing conditions

description: This document indicates that the data used in the paper was tested by the instrument.
DOI: 10.6084/m9.figshare.10345157
title: Data files from Testing the role of intraflagellar transport in flagellar length control using length-altering mutants of <i>Chlamydomonas</i>.

description: Cilia and flagella are ideal model organelles in which to study the general question of organelle size control. Flagellar microtubules are steady-state structures whose size is set by the balance of assembly and disassembly. Assembly requires intraflagellar transport (IFT), and measurements of IFT have shown that the rate of entry of IFT particles into the flagellum is a decreasing function of length. It has been proposed that this length dependence of IFT may be the basis for flagellar length control. Here, we test this idea by showing that three different long-flagella mutations in <i>Chlamydomonas</i> all cause increased IFT injection, thus confirming that IFT can influence length control. However, quantitative comparisons with mathematical models suggest that the increase in injection is not sufficient to explain the full increase in length seen in these mutants; hence, some other mechanism may be at work. One alternative mechanism that has been proposed is length-regulated binding of tubulin to the IFT particles. However, we find that the apparent length dependence of tubulin loading that has previously been reported may actually reflect length-dependent organization of IFT trains.This article is part of the Theo Murphy meeting ‘Unity and diversity of ciliary systems in locomotion and transport’.
DOI: 10.6084/m9.figshare.10345157.v2
title: Data files from Testing the role of intraflagellar transport in flagellar length control using length-altering mutants of <i>Chlamydomonas</i>.

description: Cilia and flagella are ideal model organelles in which to study the general question of organelle size control. Flagellar microtubules are steady-state structures whose size is set by the balance of assembly and disassembly. Assembly requires intraflagellar transport (IFT), and measurements of IFT have shown that the rate of entry of IFT particles into the flagellum is a decreasing function of length. It has been proposed that this length dependence of IFT may be the basis for flagellar length control. Here, we test this idea by showing that three different long-flagella mutations in <i>Chlamydomonas</i> all cause increased IFT injection, thus confirming that IFT can influence length control. However, quantitative comparisons with mathematical models suggest that the increase in injection is not sufficient to explain the full increase in length seen in these mutants; hence, some other mechanism may be at work. One alternative mechanism that has been proposed is length-regulated binding of tubulin to the IFT particles. However, we find that the apparent length dependence of tubulin loading that has previously been reported may actually reflect length-dependent organization of IFT trains.This article is part of the Theo Murphy meeting ‘Unity and diversity of ciliary systems in locomotion and transport’.
DOI: 10.6084/m9.figshare.10345157.v1
title: Data files from Testing the role of intraflagellar transport in flagellar length control using length-altering mutants of Chlamydomonas

description: Cilia and flagella are ideal model organelles in which to study the general question of organelle size control. Flagellar microtubules are steady-state structures whose size is set by the balance of assembly and disassembly. Assembly requires intraflagellar transport (IFT), and measurements of IFT have shown that the rate of entry of IFT particles into the flagellum is a decreasing function of length. It has been proposed that this length dependence of IFT may be the basis for flagellar length control. Here, we test this idea by showing that three different long-flagella mutations in <i>Chlamydomonas</i> all cause increased IFT injection, thus confirming that IFT can influence length control. However, quantitative comparisons with mathematical models suggest that the increase in injection is not sufficient to explain the full increase in length seen in these mutants; hence, some other mechanism may be at work. One alternative mechanism that has been proposed is length-regulated binding of tubulin to the IFT particles. However, we find that the apparent length dependence of tubulin loading that has previously been reported may actually reflect length-dependent organization of IFT trains.This article is part of the Theo Murphy meeting ‘Unity and diversity of ciliary systems in locomotion and transport’.
DOI: 10.6084/m9.figshare.10659665
title: Table S1 from Behavioural analysis of single-cell aneural ciliate, <i>Stentor roeseli,</i> using machine learning approaches.

description: Links to all videos available to download from Mendeley
DOI: 10.6084/m9.figshare.10659665.v2
title: Table S1 from Behavioural analysis of single-cell aneural ciliate, <i>Stentor roeseli,</i> using machine learning approaches.

description: Links to all videos available to download from Mendeley
DOI: 10.5281/zenodo.4090384
title: PADRe Study Interviews

description: <em>A data set containing 12 anonymised survey interviews conducted as part of a funded study. See journal article, '</em><em> Nobody ever questions – polypharmacy in care homes: a mixed methods evaluation of a multidisciplinary medicines optimisation initiative’</em>
DOI: 10.6084/m9.figshare.10659665.v1
title: Table S1 from Behavioural analysis of single-cell aneural ciliate, <i>Stentor roeseli,</i> using machine learning approaches

description: Links to all videos available to download from Mendeley
DOI: 10.5281/zenodo.4090383
title: PADRe Study Interviews

description: <em>A data set containing 12 anonymised survey interviews conducted as part of a funded study. See journal article, '</em><em> Nobody ever questions – polypharmacy in care homes: a mixed methods evaluation of a multidisciplinary medicines optimisation initiative’</em>