cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1311513
title: The dynamic balance of import and export of zinc in Escherichia coli suggests a heterogeneous population response to stress

description: Data from: Hiroki Takahashi, Taku Oshima, Jon L. Hobman, Neil Doherty, Selina R. Clayton , Mudassar Iqbal, Philip J. Hill, Toru Tobe, Naotake Ogasawara, Shigehiko Kanaya and Dov J. Stekel. 2015. Journal of the Royal Society Interface DOI 10.1098/rsif.2015.0069 The dynamic balance of import and export of zinc in Escherichia coli suggests a heterogeneous population response to stress.
DOI: 10.6084/m9.figshare.1311513.v2
title: The dynamic balance of import and export of zinc in Escherichia coli suggests a heterogeneous population response to stress

description: Data from: Hiroki Takahashi, Taku Oshima, Jon L. Hobman, Neil Doherty, Selina R. Clayton , Mudassar Iqbal, Philip J. Hill, Toru Tobe, Naotake Ogasawara, Shigehiko Kanaya and Dov J. Stekel. 2015. Journal of the Royal Society Interface DOI 10.1098/rsif.2015.0069 The dynamic balance of import and export of zinc in Escherichia coli suggests a heterogeneous population response to stress.
DOI: 10.6084/m9.figshare.1311513.v1
title: The dynamic balance of import and export of zinc in Escherichia coli suggests a heterogeneous population response to stress

description: Data from: Hiroki Takahashi, Taku Oshima, Neil Doherty, Selina R. Clayton , Mudassar Iqbal, Philip J. Hill, Jon L. Hobman, Toru Tobe, Naotake Ogasawara, Shigehiko Kanaya and Dov J. Stekel. 2015. Journal of the Royal Society Interface vol. TBC pp TBC. DOI TBC. The dynamic balance of import and export of zinc in Escherichia coli suggests a heterogeneous population response to stress.
DOI: 10.6084/m9.figshare.1311468
title: Direction of Effects in Multiple Linear Regression Models

description: Previous studies analyzed asymmetric properties of the Pearson correlation coefficient using higher than second order moments. These asymmetric properties can be used to determine the direction of dependence in a linear regression setting (i.e., establish which of two variables is more likely to be on the outcome side) within the framework of cross-sectional observational data. Extant approaches are restricted to the bivariate regression case. The present contribution extends the direction of dependence methodology to a multiple linear regression setting by analyzing distributional properties of residuals of competing multiple regression models. It is shown that, under certain conditions, the third central moments of estimated regression residuals can be used to decide upon direction of effects. In addition, three different approaches for statistical inference are discussed: a combined D’Agostino normality test, a skewness difference test, and a bootstrap difference test. Type I error and power of the procedures are assessed using Monte Carlo simulations, and an empirical example is provided for illustrative purposes. In the discussion, issues concerning the quality of psychological data, possible extensions of the proposed methods to the fourth central moment of regression residuals, and potential applications are addressed.
DOI: 10.6084/m9.figshare.1311468.v1
title: Direction of Effects in Multiple Linear Regression Models

description: Previous studies analyzed asymmetric properties of the Pearson correlation coefficient using higher than second order moments. These asymmetric properties can be used to determine the direction of dependence in a linear regression setting (i.e., establish which of two variables is more likely to be on the outcome side) within the framework of cross-sectional observational data. Extant approaches are restricted to the bivariate regression case. The present contribution extends the direction of dependence methodology to a multiple linear regression setting by analyzing distributional properties of residuals of competing multiple regression models. It is shown that, under certain conditions, the third central moments of estimated regression residuals can be used to decide upon direction of effects. In addition, three different approaches for statistical inference are discussed: a combined D’Agostino normality test, a skewness difference test, and a bootstrap difference test. Type I error and power of the procedures are assessed using Monte Carlo simulations, and an empirical example is provided for illustrative purposes. In the discussion, issues concerning the quality of psychological data, possible extensions of the proposed methods to the fourth central moment of regression residuals, and potential applications are addressed.
DOI: 10.6084/m9.figshare.1311640.v3
title: 2014 08 13 Field Notes

description: 2016 following the increase in allowed file size by figshare.Field notes including image and/or video records. Original versions of all videos are available as of 20 Jan 2016 following the increase in allowed file size by figshare.
DOI: 10.6084/m9.figshare.1310598
title: Dataset for the Paper Anchoring Heuristic and Inflation Targerting

description: Dataset for the paper Anchoring Heuristic and Inflation Targeting
DOI: 10.6084/m9.figshare.1310598.v1
title: Dataset for the Paper Anchoring Heuristic and Inflation Targerting

description: Dataset for the paper Anchoring Heuristic and Inflation Targeting
DOI: 10.6084/m9.figshare.1310590
title: Temporal patterns of ant diversity across a mountain with climatically contrasting aspects in the tropics of Africa

description: Factors that drive species richness over space and time are still poorly understood and are often context specific. Identifying these drivers for ant diversity has become particularly relevant within the context of contemporary global change events. We report on a long-term bi-annual (wet and dry seasons), standardized sampling of epigeal ants over a five year period on the mesic and arid aspects of an inselberg (Soutpansberg Mountain Range) in the tropics of Africa. We detail seasonal, annual and long-term trends of species density, test the relative contribution of geometric constraints, energy, available area, climate, local environmental variables, time, and space in explaining ant species density patterns through Generalized Linear Mixed Models (GLMM) where replicates were included as random factors to account for temporal pseudo20 replication. Seasonal patterns were very variable and we found evidence of decreased seasonal variation in species density with increased elevation. The extent and significance of a decrease in species density with increased elevation varied with season. Annual patterns point to an increase in ant diversity over time. Ant density patterns were positively correlated with mean monthly temperature but geometric constraints dominated model performance while soil characteristics were minor correlates. These drivers and correlates accounted for all the spatio-temporal variability in the database. Ant diversity was therefore mainly determined by geometric constraints and temperature while soil characteristics (clay and carbon content) accounted for smaller but significant amounts of variation. This study documents the role of season, elevation and their interaction in affecting ant species densities while highlighting the importance of neutral processes and temperature in driving these patterns.
DOI: 10.6084/m9.figshare.1310609.v3
title: 29 July 2014 Field Notes

description: Field notes including image and/or video records.
DOI: 10.6084/m9.figshare.1310551
title: Abnormalities in automatic processing of illness-related stimuli in self-rated alexithymia

description: Data set corresponding to the paper "Abnormalities in automatic processing of illness-related stimuli in self-rated alexithymia" Authors: Laura Brandt 1, 2, Nina M. Pintzinger 2, Ulrich S. Tran2 1 Center for Public Health, Medical University of Vienna, Kinderspitalgasse 15, 1090 Vienna, Austria 2 Faculty of Psychology, University of Vienna, Liebiggasse 5, 1010 Vienna, Austria
DOI: 10.6084/m9.figshare.1310590.v2
title: Temporal patterns of ant diversity across a mountain with climatically contrasting aspects in the tropics of Africa

description: Factors that drive species richness over space and time are still poorly understood and are often context specific. Identifying these drivers for ant diversity has become particularly relevant within the context of contemporary global change events. We report on a long-term bi-annual (wet and dry seasons), standardized sampling of epigeal ants over a five year period on the mesic and arid aspects of an inselberg (Soutpansberg Mountain Range) in the tropics of Africa. We detail seasonal, annual and long-term trends of species density, test the relative contribution of geometric constraints, energy, available area, climate, local environmental variables, time, and space in explaining ant species density patterns through Generalized Linear Mixed Models (GLMM) where replicates were included as random factors to account for temporal pseudo20 replication. Seasonal patterns were very variable and we found evidence of decreased seasonal variation in species density with increased elevation. The extent and significance of a decrease in species density with increased elevation varied with season. Annual patterns point to an increase in ant diversity over time. Ant density patterns were positively correlated with mean monthly temperature but geometric constraints dominated model performance while soil characteristics were minor correlates. These drivers and correlates accounted for all the spatio-temporal variability in the database. Ant diversity was therefore mainly determined by geometric constraints and temperature while soil characteristics (clay and carbon content) accounted for smaller but significant amounts of variation. This study documents the role of season, elevation and their interaction in affecting ant species densities while highlighting the importance of neutral processes and temperature in driving these patterns.
DOI: 10.6084/m9.figshare.1310590.v1
title: Temporal patterns of ant diversity 1 across a mountain with climatically contrasting aspects in the tropics of Africa

description: Factors that drive species richness over space and time are still poorly understood and are often context specific. Identifying these drivers for ant diversity has become particularly relevant within the context of contemporary global change events. We report on a long-term bi-annual (wet and dry seasons), standardized sampling of epigeal ants over a five year period on the mesic and arid aspects of an inselberg (Soutpansberg Mountain Range) in the tropics of Africa. We detail seasonal, annual and long-term trends of species density, test the relative contribution of geometric constraints, energy, available area, climate, local environmental variables, time, and space in explaining ant species density patterns through Generalized Linear Mixed Models (GLMM) where replicates were included as random factors to account for temporal pseudo20 replication. Seasonal patterns were very variable and we found evidence of decreased seasonal variation in species density with increased elevation. The extent and significance of a decrease in species density with increased elevation varied with season. Annual patterns point to an increase in ant diversity over time. Ant density patterns were positively correlated with mean monthly temperature but geometric constraints dominated model performance while soil characteristics were minor correlates. These drivers and correlates accounted for all the spatio-temporal variability in the database. Ant diversity was therefore mainly determined by geometric constraints and temperature while soil characteristics (clay and carbon content) accounted for smaller but significant amounts of variation. This study documents the role of season, elevation and their interaction in affecting ant species densities while highlighting the importance of neutral processes and temperature in driving these patterns.
DOI: 10.6084/m9.figshare.1310561.v2
title: 22 July 2014 Field Notes

description: Field notes including images and/or video records.
DOI: 10.6084/m9.figshare.1310606.v3
title: 2014 07 28 Field Notes

description: Field notes including image and/or video records. Original versions of all videos are available as of 21 Jan 2016 following the increase in allowed file size by figshare.
DOI: 10.6084/m9.figshare.1310609.v6
title: 2014 07 29 Field Notes

description: Field notes including image and/or video records. Original versions of all videos are available as of 21 Jan 2016 following the increase in allowed file size by figshare.
DOI: 10.6084/m9.figshare.1310498
title: Simulation: Syntax

description: Mplus automation input files and R code to run the script
DOI: 10.6084/m9.figshare.1310498.v1
title: Simulation: Syntax

description: Mplus automation input files and R code to run the script
DOI: 10.6084/m9.figshare.1310561.v5
title: 2014 07 22 Field Notes

description: Field notes including images and/or video records. Original versions of all videos are available as of 21 Jan 2016 following the increase in allowed file size by figshare.
DOI: 10.6084/m9.figshare.1310469
title: Association of heterotrophic bacteria with aggregated <i>Arthrospira platensis</i> exopolysaccharides: implications in the induction of axenic cultures

description: Inducing an axenic culture of the edible cyanobacterium <i>Arthrospira</i> (<i>Spirulina</i>) <i>platensis</i> using differential filtration alone is never successful; thus, it has been thought that, in non-axenic cultures, a portion of contaminating bacteria is strongly associated with <i>Arthrospira</i> cells. However, examination of the behavior of these bacteria during filtration revealed that they were not associated with <i>Arthrospira</i> cells but with aggregates of exopolysaccharides present in the medium away from the <i>Arthrospira</i> cells. Based on this finding, a rapid and reliable method for preparing axenic trichomes of <i>A. platensis</i> was established. After verifying the axenicity of the resulting trichomes on enriched agar plates, they were individually transferred to fresh sterile medium using a handmade tool, a microtrowel, to produce axenic cultures. With this technique, axenic cultures of various <i>A. platensis</i> strains were successfully produced. The technique described in this study is potentially applicable to a wider range of filamentous cyanobacteria.
DOI: 10.6084/m9.figshare.1310467
title: Protein kinase C regulates the expression of cell wall-related genes in RlmA-dependent and independent manners in <i>Aspergillus nidulans</i>

description: A protein kinase C of <i>Aspergillus nidulans</i>, PkcA, is required for cell wall integrity (CWI) and is considered a major component of the regulating pathway. To investigate whether PkcA regulates the transcription of cell wall-related genes, we constructed strains expressing <i>pkcA</i>(R429A) that encodes an activated form of PkcA. The mRNA levels of most chitin synthase genes and an α-glucan synthase gene, <i>agsB</i>, were increased when <i>pkcA</i>(R429A) expression was induced. These mRNA increases were not observed or were only partially observed, in a deletion mutant of <i>rlmA</i>, an ortholog of <i>RLM1</i> that encodes a transcription factor in the CWI pathway in <i>Saccharomyces cerevisiae</i>. In addition, in a <i>pkcA</i> temperature-sensitive mutant under heat stress, the mRNA levels of some chitin synthase genes and <i>agsB</i> did not increase. These results suggest that PkcA is involved in CWI maintenance through the transcriptional regulation of cell wall-related genes.
DOI: 10.6084/m9.figshare.1310468
title: Adhesion properties of <i>Lactobacillus rhamnosus</i> mucus-binding factor to mucin and extracellular matrix proteins

description: We previously described potential probiotic <i>Lactobacillus rhamnosus</i> strains, isolated from fermented mare milk produced in Sumbawa Island, Indonesia, which showed high adhesion to porcine colonic mucin (PCM) and extracellular matrix (ECM) proteins. Recently, mucus-binding factor (MBF) was found in the GG strain of <i>L. rhamnosus</i> as a mucin-binding protein. In this study, we assessed the ability of recombinant MBF protein from the FSMM22 strain, one of the isolates of <i>L. rhamnosus</i> from fermented Sumbawa mare milk, to adhere to PCM and ECM proteins by overlay dot blot and Biacore assays. MBF bound to PCM, laminin, collagen IV, and fibronectin with submicromolar dissociation constants. Adhesion of the FSMM22 <i>mbf</i> mutant strain to PCM and ECM proteins was significantly less than that of the wild-type strain. Collectively, these results suggested that MBF contribute to <i>L. rhamnosus</i> host colonization via mucin and ECM protein binding.
DOI: 10.6084/m9.figshare.1310466
title: Identification of genes encoding photoconvertible (Class I) water-soluble chlorophyll-binding proteins from <i>Chenopodium ficifolium</i>

description: Photoconvertible water-soluble chlorophyll-binding proteins, called Class I WSCPs, have been detected in Chenopodiaceae, Amaranthaceae and Polygonaceae plant species. To date, <i>Chenopodium album WSCP</i> (<i>CaWSCP</i>) is the only cloned gene encoding a Class I WSCP. In this study, we identified two cDNAs encoding <i>Chenopodium ficifolium</i> Class I WSCPs, <i>CfWSCP1</i>, and <i>CfWSCP2</i>. Sequence analyses revealed that the open reading frames of <i>CfWSCP1</i> and <i>CfWSCP2</i> were 585 and 588 bp, respectively. Furthermore, both CfWSCPs contain cystein2 and cystein30, which are essential for the chlorophyll-binding ability of CaWSCP. Recombinant CfWSCP1 and CfWSCP2, expressed in <i>Escherichia coli</i> as hexa-histidine fusion proteins (CfWSCP1-His and CfWSCP2-His), formed inclusion bodies; however, we were able to solubilize these using a buffer containing 8 M urea and then refold them by dialysis. The refolded CfWSCP1-His and CfWSCP2-His could bind chlorophylls and exhibited photoconvertibility, confirming that the cloned CfWSCPs are further examples of Class I WSCPs.
DOI: 10.6084/m9.figshare.1310468.v1
title: Adhesion properties of <i>Lactobacillus rhamnosus</i> mucus-binding factor to mucin and extracellular matrix proteins

description: We previously described potential probiotic <i>Lactobacillus rhamnosus</i> strains, isolated from fermented mare milk produced in Sumbawa Island, Indonesia, which showed high adhesion to porcine colonic mucin (PCM) and extracellular matrix (ECM) proteins. Recently, mucus-binding factor (MBF) was found in the GG strain of <i>L. rhamnosus</i> as a mucin-binding protein. In this study, we assessed the ability of recombinant MBF protein from the FSMM22 strain, one of the isolates of <i>L. rhamnosus</i> from fermented Sumbawa mare milk, to adhere to PCM and ECM proteins by overlay dot blot and Biacore assays. MBF bound to PCM, laminin, collagen IV, and fibronectin with submicromolar dissociation constants. Adhesion of the FSMM22 <i>mbf</i> mutant strain to PCM and ECM proteins was significantly less than that of the wild-type strain. Collectively, these results suggested that MBF contribute to <i>L. rhamnosus</i> host colonization via mucin and ECM protein binding.
DOI: 10.6084/m9.figshare.1310469.v1
title: Association of heterotrophic bacteria with aggregated <i>Arthrospira platensis</i> exopolysaccharides: implications in the induction of axenic cultures

description: Inducing an axenic culture of the edible cyanobacterium <i>Arthrospira</i> (<i>Spirulina</i>) <i>platensis</i> using differential filtration alone is never successful; thus, it has been thought that, in non-axenic cultures, a portion of contaminating bacteria is strongly associated with <i>Arthrospira</i> cells. However, examination of the behavior of these bacteria during filtration revealed that they were not associated with <i>Arthrospira</i> cells but with aggregates of exopolysaccharides present in the medium away from the <i>Arthrospira</i> cells. Based on this finding, a rapid and reliable method for preparing axenic trichomes of <i>A. platensis</i> was established. After verifying the axenicity of the resulting trichomes on enriched agar plates, they were individually transferred to fresh sterile medium using a handmade tool, a microtrowel, to produce axenic cultures. With this technique, axenic cultures of various <i>A. platensis</i> strains were successfully produced. The technique described in this study is potentially applicable to a wider range of filamentous cyanobacteria.
DOI: 10.6084/m9.figshare.1310466.v1
title: Identification of genes encoding photoconvertible (Class I) water-soluble chlorophyll-binding proteins from <i>Chenopodium ficifolium</i>

description: Photoconvertible water-soluble chlorophyll-binding proteins, called Class I WSCPs, have been detected in Chenopodiaceae, Amaranthaceae and Polygonaceae plant species. To date, <i>Chenopodium album WSCP</i> (<i>CaWSCP</i>) is the only cloned gene encoding a Class I WSCP. In this study, we identified two cDNAs encoding <i>Chenopodium ficifolium</i> Class I WSCPs, <i>CfWSCP1</i>, and <i>CfWSCP2</i>. Sequence analyses revealed that the open reading frames of <i>CfWSCP1</i> and <i>CfWSCP2</i> were 585 and 588 bp, respectively. Furthermore, both CfWSCPs contain cystein2 and cystein30, which are essential for the chlorophyll-binding ability of CaWSCP. Recombinant CfWSCP1 and CfWSCP2, expressed in <i>Escherichia coli</i> as hexa-histidine fusion proteins (CfWSCP1-His and CfWSCP2-His), formed inclusion bodies; however, we were able to solubilize these using a buffer containing 8 M urea and then refold them by dialysis. The refolded CfWSCP1-His and CfWSCP2-His could bind chlorophylls and exhibited photoconvertibility, confirming that the cloned CfWSCPs are further examples of Class I WSCPs.
DOI: 10.6084/m9.figshare.1310469.v3
title: Association of heterotrophic bacteria with aggregated <i>Arthrospira platensis</i> exopolysaccharides: implications in the induction of axenic cultures

description: Inducing an axenic culture of the edible cyanobacterium <i>Arthrospira</i> (<i>Spirulina</i>) <i>platensis</i> using differential filtration alone is never successful; thus, it has been thought that, in non-axenic cultures, a portion of contaminating bacteria is strongly associated with <i>Arthrospira</i> cells. However, examination of the behavior of these bacteria during filtration revealed that they were not associated with <i>Arthrospira</i> cells but with aggregates of exopolysaccharides present in the medium away from the <i>Arthrospira</i> cells. Based on this finding, a rapid and reliable method for preparing axenic trichomes of <i>A. platensis</i> was established. After verifying the axenicity of the resulting trichomes on enriched agar plates, they were individually transferred to fresh sterile medium using a handmade tool, a microtrowel, to produce axenic cultures. With this technique, axenic cultures of various <i>A. platensis</i> strains were successfully produced. The technique described in this study is potentially applicable to a wider range of filamentous cyanobacteria.
DOI: 10.6084/m9.figshare.1310467.v1
title: Protein kinase C regulates the expression of cell wall-related genes in RlmA-dependent and independent manners in <i>Aspergillus nidulans</i>

description: A protein kinase C of <i>Aspergillus nidulans</i>, PkcA, is required for cell wall integrity (CWI) and is considered a major component of the regulating pathway. To investigate whether PkcA regulates the transcription of cell wall-related genes, we constructed strains expressing <i>pkcA</i>(R429A) that encodes an activated form of PkcA. The mRNA levels of most chitin synthase genes and an α-glucan synthase gene, <i>agsB</i>, were increased when <i>pkcA</i>(R429A) expression was induced. These mRNA increases were not observed or were only partially observed, in a deletion mutant of <i>rlmA</i>, an ortholog of <i>RLM1</i> that encodes a transcription factor in the CWI pathway in <i>Saccharomyces cerevisiae</i>. In addition, in a <i>pkcA</i> temperature-sensitive mutant under heat stress, the mRNA levels of some chitin synthase genes and <i>agsB</i> did not increase. These results suggest that PkcA is involved in CWI maintenance through the transcriptional regulation of cell wall-related genes.