cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4496735
title: Components of the SNARE-containing regulon are co-regulated in root cells undergoing defense

description: The term regulon has been coined in the genetic model plant <i>Arabidopsis thaliana</i>, denoting a structural and physiological defense apparatus defined genetically through the identification of the <i>penetration</i> (<i>pen</i>) mutants. The regulon is composed partially by the soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor (SNARE) syntaxin PEN1. PEN1 has homology to a <i>Saccharomyces cerevisae</i> gene that regulates a Secretion (Sec) protein, Suppressor of Sec 1 (Sso1p). The regulon is also composed of the β-glucosidase (PEN2) and an ATP binding cassette (ABC) transporter (PEN3). While important in inhibiting pathogen infection, limited observations have been made regarding the transcriptional regulation of regulon genes until now. Experiments made using the model agricultural <i>Glycine max</i> (soybean) have identified co-regulated gene expression of regulon components. The results explain the observation of hundreds of genes expressed specifically in the root cells undergoing the natural process of defense. Data regarding additional <i>G. max</i> genes functioning within the context of the regulon are presented here, including Sec 14, Sec 4 and Sec 23. Other examined <i>G. max</i> homologs of membrane fusion genes include an endosomal bromo domain-containing protein1 (Bro1), syntaxin6 (SYP6), SYP131, SYP71, SYP8, Bet1, coatomer epsilon (ϵ-COP), a coatomer zeta (ζ-COP) paralog and an ER to Golgi component (ERGIC) protein. Furthermore, the effectiveness of biochemical pathways that would function within the context of the regulon ave been examined, including xyloglucan xylosyltransferase (XXT), reticuline oxidase (RO) and galactinol synthase (GS). The experiments have unveiled the importance of the regulon during defense in the root and show how the deposition of callose relates to the process.
DOI: 10.6084/m9.figshare.4496729
title: Self-regulation and social pressure reduce prejudiced responding and increase the motivation to be non-prejudiced

description: Self-regulation constrains the expression of prejudice, but when self-regulation falters, the immediate environment can act as an external source of prejudice regulation. This hypothesis derives from work demonstrating that external controls and internal self-regulation can prompt goal pursuit in the absence of self-imposed controls. Across four studies, we found support for this complementary model of prejudice regulation. In Study 1, self-regulatory fatigue resulted in less motivation to be non-prejudiced, compared to a non-fatigued control. In Study 2, strong (vs. weak) perceived social pressure was related to greater motivation to be non-prejudiced. In Study 3, dispositional self-regulation predicted non-prejudice motivation when perceived social pressure was weak or moderate, but not when it was strong. Finally, in Study 4 self-regulatory fatigue increased prejudice when social pressure was weak but not when it was strong.
DOI: 10.6084/m9.figshare.4496735.v1
title: Components of the SNARE-containing regulon are co-regulated in root cells undergoing defense

description: The term regulon has been coined in the genetic model plant <i>Arabidopsis thaliana</i>, denoting a structural and physiological defense apparatus defined genetically through the identification of the <i>penetration</i> (<i>pen</i>) mutants. The regulon is composed partially by the soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor (SNARE) syntaxin PEN1. PEN1 has homology to a <i>Saccharomyces cerevisae</i> gene that regulates a Secretion (Sec) protein, Suppressor of Sec 1 (Sso1p). The regulon is also composed of the β-glucosidase (PEN2) and an ATP binding cassette (ABC) transporter (PEN3). While important in inhibiting pathogen infection, limited observations have been made regarding the transcriptional regulation of regulon genes until now. Experiments made using the model agricultural <i>Glycine max</i> (soybean) have identified co-regulated gene expression of regulon components. The results explain the observation of hundreds of genes expressed specifically in the root cells undergoing the natural process of defense. Data regarding additional <i>G. max</i> genes functioning within the context of the regulon are presented here, including Sec 14, Sec 4 and Sec 23. Other examined <i>G. max</i> homologs of membrane fusion genes include an endosomal bromo domain-containing protein1 (Bro1), syntaxin6 (SYP6), SYP131, SYP71, SYP8, Bet1, coatomer epsilon (ϵ-COP), a coatomer zeta (ζ-COP) paralog and an ER to Golgi component (ERGIC) protein. Furthermore, the effectiveness of biochemical pathways that would function within the context of the regulon ave been examined, including xyloglucan xylosyltransferase (XXT), reticuline oxidase (RO) and galactinol synthase (GS). The experiments have unveiled the importance of the regulon during defense in the root and show how the deposition of callose relates to the process.
DOI: 10.6084/m9.figshare.4496729.v1
title: Self-regulation and social pressure reduce prejudiced responding and increase the motivation to be non-prejudiced

description: Self-regulation constrains the expression of prejudice, but when self-regulation falters, the immediate environment can act as an external source of prejudice regulation. This hypothesis derives from work demonstrating that external controls and internal self-regulation can prompt goal pursuit in the absence of self-imposed controls. Across four studies, we found support for this complementary model of prejudice regulation. In Study 1, self-regulatory fatigue resulted in less motivation to be non-prejudiced, compared to a non-fatigued control. In Study 2, strong (vs. weak) perceived social pressure was related to greater motivation to be non-prejudiced. In Study 3, dispositional self-regulation predicted non-prejudice motivation when perceived social pressure was weak or moderate, but not when it was strong. Finally, in Study 4 self-regulatory fatigue increased prejudice when social pressure was weak but not when it was strong.
DOI: 10.6084/m9.figshare.4496483
title: Image cuantification on ROIs

description: Microsoft Excell files generated during image quantification
DOI: 10.6084/m9.figshare.4496483.v1
title: Image cuantification on ROIs

description: Microsoft Excell files generated during image quantification
DOI: 10.6084/m9.figshare.4496456
title: pH-taxis by the dispersal stage of choanoflagellates.

description: We used video microscopy to study the response to gradients of pH of choanoflagellate Salpingoeca rosetta. This choanoflagellates presents a life history that includes fast- and slow-swimming unicellular forms and multicellular colonies. In the associated data we show and quantify the presence of both types of unicellular swimmers.The data shows that unicellular fast swimmers exhibited taxis into patches of attractant. When this type of choanoflagellates is exposed to patches with different pH, we observed accumulation of cells in regions where pH is in the range of 6 to 7. In contrast, a repulsive response is observed at lower pH.
DOI: 10.6084/m9.figshare.4496090
title: Lerback-Hanson Blinded Data Nature 2017.xlsx

description: The excel sheet provides anonymized data used in Lerback and Hanson, Nature (2017). Identifiers are anonymized across each tab to prevent identification.
DOI: 10.6084/m9.figshare.4496054
title: Photogrammetric model + photos of quadrupedal squirrel trace

description: Really nice squirrel impressions including fur/skin marks behind the footprints. Dataset includes model (FBX) and photos.
DOI: 10.6084/m9.figshare.4496090.v1
title: Lerback-Hanson Blinded Data Nature 2017.xlsx

description: The excel sheet provides anonymized data used in Lerback and Hanson, Nature (2017). Identifiers are anonymized across each tab to prevent identification.
DOI: 10.6084/m9.figshare.4496054.v2
title: Photogrammetric model + photos of quadrupedal squirrel trace

description: Really nice squirrel impressions including fur/skin marks behind the footprints. Dataset includes model (FBX) and photos.
DOI: 10.6084/m9.figshare.4496054.v1
title: Squirrel - 4 feet

description: Really nice squirrel impressions including fur/skin marks behind the footprints. Dataset includes model (FBX) and photos.
DOI: 10.6084/m9.figshare.4496015.v1
title: RITMARE_Linea Dati_Webinar 1

description: L'obiettivo del primo webinar erogato dalla Linea Dati del progetto RITMARE è informare tutte le Linee di ricerca circa le modalità con cui poter prendere parte attivamente al popolamento dell’infrastruttura Dati RITMARE. <br>Durante il webinar saranno presentate le iniziative di supporto tecnologico e formativo messe a disposizione dalla Linea Dati.<br>
DOI: 10.6084/m9.figshare.4495919
title: facs raw data (fcs) for microRNA-mediated mRNA competition

description: 17 zip files. Each file.zip contains multiple fcs raw data. <br>The file_matlab.zip contains the matlab scripts used to read and analyze data as well as a read_me.txt file. <br>
DOI: 10.6084/m9.figshare.4495919.v1
title: facs raw data (fcs) for microRNA-mediated mRNA competition

description: 17 zip files. Each file.zip contains multiple fcs raw data. <br>The file_matlab.zip contains the matlab scripts used to read and analyze data as well as a read_me.txt file. <br>
DOI: 10.6084/m9.figshare.4495832
title: 454 data used in the paper 'On the importance of the microbiome and pathobiome in coral health and disease'

description: Examples of visualisations of microbial networks associated with <i>Acorpora muricata</i> collected at four different locations (Australia, Fiji, Maldives and Solomon Islands). Networks with vertices representing individual OTUs, and edges representing absolute values of correlation coefficients of greater than 0.6, were derived from OTU abundances in a) healthy corals and b) diseased corals. Edges shown in green show positive correlations, whereas those shown in red represent negative correlations. Networks were derived using the qgraph function in the qgraph package (Epskamp et al., 2012). c) shows the network derived from the healthy coral arranged according to a community clustering algorithm (fastgreedy.community from the igraph package; (Csardi and Nepusz, 2006)). The algorithm tries to identify clusters of OTUs which show similar patterns of abundance across samples. d) Shows the relationship between the cut-off correlation value (x-axis) determining which of the correlations between OTU abundances should be included and the proportion of all the pair wise edges included in the network. All network analysis was done using the R statistical programming language (R Core Team, 2016). Methods: <i>Acropora muricata</i> samples were collected and preserved in 100% molecular grade ethanol (Sweet and Séré, 2016). All samples were extracted using the Qiagen DNeasy Extraction kit, amplified with primers 357 and 518 and sequenced on the 454 platform. All samples were pooled on the same run with barcodes for a complete list of methods including downstream processing of the sequencing run please refer to Sweet and Bythell, (2015).
DOI: 10.6084/m9.figshare.4495832.v2
title: 454 data used in the paper 'On the importance of the microbiome and pathobiome in coral health and disease'

description: Examples of visualisations of microbial networks associated with <i>Acorpora muricata</i> collected at four different locations (Australia, Fiji, Maldives and Solomon Islands). Networks with vertices representing individual OTUs, and edges representing absolute values of correlation coefficients of greater than 0.6, were derived from OTU abundances in a) healthy corals and b) diseased corals. Edges shown in green show positive correlations, whereas those shown in red represent negative correlations. Networks were derived using the qgraph function in the qgraph package (Epskamp et al., 2012). c) shows the network derived from the healthy coral arranged according to a community clustering algorithm (fastgreedy.community from the igraph package; (Csardi and Nepusz, 2006)). The algorithm tries to identify clusters of OTUs which show similar patterns of abundance across samples. d) Shows the relationship between the cut-off correlation value (x-axis) determining which of the correlations between OTU abundances should be included and the proportion of all the pair wise edges included in the network. All network analysis was done using the R statistical programming language (R Core Team, 2016). Methods: <i>Acropora muricata</i> samples were collected and preserved in 100% molecular grade ethanol (Sweet and Séré, 2016). All samples were extracted using the Qiagen DNeasy Extraction kit, amplified with primers 357 and 518 and sequenced on the 454 platform. All samples were pooled on the same run with barcodes for a complete list of methods including downstream processing of the sequencing run please refer to Sweet and Bythell, (2015).
DOI: 10.6084/m9.figshare.4495832.v1
title: 454 data for Microbiome paper

description: Examples of visualisations of microbial networks associated with <i>Acorpora muricata</i> collected at four different locations (Australia, Fiji, Maldives and Solomon Islands). Networks with vertices representing individual OTUs, and edges representing absolute values of correlation coefficients of greater than 0.6, were derived from OTU abundances in a) healthy corals and b) diseased corals. Edges shown in green show positive correlations, whereas those shown in red represent negative correlations. Networks were derived using the qgraph function in the qgraph package (Epskamp et al., 2012). c) shows the network derived from the healthy coral arranged according to a community clustering algorithm (fastgreedy.community from the igraph package; (Csardi and Nepusz, 2006)). The algorithm tries to identify clusters of OTUs which show similar patterns of abundance across samples. d) Shows the relationship between the cut-off correlation value (x-axis) determining which of the correlations between OTU abundances should be included and the proportion of all the pair wise edges included in the network. All network analysis was done using the R statistical programming language (R Core Team, 2016). Methods: <i>Acropora muricata</i> samples were collected and preserved in 100% molecular grade ethanol (Sweet and Séré, 2016). All samples were extracted using the Qiagen DNeasy Extraction kit, amplified with primers 357 and 518 and sequenced on the 454 platform. All samples were pooled on the same run with barcodes for a complete list of methods including downstream processing of the sequencing run please refer to Sweet and Bythell, (2015).
DOI: 10.6084/m9.figshare.4495766
title: Supplementary Table 2 from Structure and dynamics of bacterial ribosome biogenesis

description: Table of LSU rRNA residues and helix assignments
DOI: 10.6084/m9.figshare.4495766.v1
title: Supplementary Table 2 from Structure and dynamics of bacterial ribosome biogenesis

description: Table of LSU rRNA residues and helix assignments
DOI: 10.6084/m9.figshare.4495751
title: The code used is included as a separate file ‘supplementary_code.zip’, which contains two files suitable for building with a C++ compiler:• main.cpp, which is the main model code• mersenne_twister.h, which contains the Mersenne twister functionThe latter is an amended version of a library distributed under a GNU Library General Public License - please see the file header for details. from Leaving safety to visit a feeding site: is it optimal to hesitate while exposed?

description: Animals living in complex environments experience differing risks of predation depending upon their location within the landscape. An animal could reduce the risk it experiences by remaining in a refuge site, but it may need to emerge from its refuge and enter more dangerous sites for feeding and other activities. Here, I consider the actions of an animal choosing to travel a short distance between a safe refuge and a dangerous foraging site, such as a bird leaving cover to visit a feeder. Although much work has been conducted examining the choice between a refuge and a foraging site when faced with a trade-off between starvation and predation risk, the work presented here is the first to consider the travel behaviour between these locations. Using state-dependent stochastic dynamic programming, I illustrate that there are several forms of optimal behaviour that can emerge. In some situations, the animal should choose to travel without stopping between sites, but in other cases, it is optimal for the animal to travel hesitantly towards the food, and to stop its travel at a point before it reaches the refuge. I discuss how this hesitant ‘dawdling’ behaviour may be optimal, and suggest further work to test these predictions.
DOI: 10.6084/m9.figshare.4495748
title: Supplementary Table 1 from Structure and dynamics of bacterial ribosome biogenesis

description: Table of SSU rRNA residues and helix assignments
DOI: 10.6084/m9.figshare.4495748.v1
title: Supplementary Table 1 from Structure and dynamics of bacterial ribosome biogenesis

description: Table of SSU rRNA residues and helix assignments
DOI: 10.6084/m9.figshare.4495751.v1
title: The code used is included as a separate file ‘supplementary_code.zip’, which contains two files suitable for building with a C++ compiler:• main.cpp, which is the main model code• mersenne_twister.h, which contains the Mersenne twister functionThe latter is an amended version of a library distributed under a GNU Library General Public License - please see the file header for details. from Leaving safety to visit a feeding site: is it optimal to hesitate while exposed?

description: Animals living in complex environments experience differing risks of predation depending upon their location within the landscape. An animal could reduce the risk it experiences by remaining in a refuge site, but it may need to emerge from its refuge and enter more dangerous sites for feeding and other activities. Here, I consider the actions of an animal choosing to travel a short distance between a safe refuge and a dangerous foraging site, such as a bird leaving cover to visit a feeder. Although much work has been conducted examining the choice between a refuge and a foraging site when faced with a trade-off between starvation and predation risk, the work presented here is the first to consider the travel behaviour between these locations. Using state-dependent stochastic dynamic programming, I illustrate that there are several forms of optimal behaviour that can emerge. In some situations, the animal should choose to travel without stopping between sites, but in other cases, it is optimal for the animal to travel hesitantly towards the food, and to stop its travel at a point before it reaches the refuge. I discuss how this hesitant ‘dawdling’ behaviour may be optimal, and suggest further work to test these predictions.
DOI: 10.6084/m9.figshare.4495745
title: Chromatic variability data from Conspicuous plumage colours are highly variable

description: Data required for the analyses.
DOI: 10.6084/m9.figshare.4495724
title: Leaf water potentials at turgor loss point of lianas within a tropical forest of French Guiana from Stronger seasonal adjustment in leaf turgor loss point in lianas than trees in an Amazonian forest

description: Dataset of estimated leaf water potentials at turgor loss point (in MPa) of lianas within a tropical forest of French Guiana
DOI: 10.6084/m9.figshare.4495709
title: Supplementary Material for: Why Almost Always Animals? Ranking Fluency Tasks for the Detection of Dementia Based on Receiver Operating Characteristic (ROC) and Quality ROC Analyses

description: <b><i>Background/Aims:</i></b> Category fluency tasks have been widely used to assess cognitive functioning in both clinical and experimental environments as an index of cognitive and psycholinguistic dysfunctions in dementia. Typically, a reduced group of semantic categories has been selected for neuropsychological assessment (e.g., <i>animals</i>, <i>fruits</i> or <i>vegetables</i>), although empirical support for the prevalence of one category among others is absent in the literature. <b><i>Methods:</i></b> We provide an empirical evaluation of the ability of 14 category fluency tasks to discriminate between subjects with dementia of the Alzheimer type and healthy elderly participants. As a novelty, we used both receiver operating characteristic (ROC) curves and quality ROC calibrated analyses to characterize the interplay of sensitivity and specificity of every category fluency task performance as a screening tool. The use of calibrated measures provided us with a useful tool for comparing the diagnostic ability of the different categories, as well as making rankings of categories based on the quality indices of efficiency, sensitivity, and specificity. <b><i>Results:</i></b> The habitually used category of <i>animals</i> is far from being the most efficient one in terms of its diagnostic power to evaluate dementia. <b><i>Conclusion:</i></b> Our study might guide the selection of suitable category fluency tasks according to the diagnostic purposes in dementia.
DOI: 10.25345/c5rx79
title: MassIVE MSV000086060 - CARA - Human skin multi-omics study - GC-MS
title: CARA study for a human skin multi-omics cohort. GC-MS data were collected with three different extraction protocols.
DOI: 10.6084/m9.figshare.4495691
title: Multivariate morphometric analysis and taxa delimitation in two narrow Greek endemics: <b><i>Astragalus maniaticus</i></b> and <b><i>Aethionema saxatile</i></b> subsp. <b><i>corinthiacum</i></b>

description: <i>Astragalus maniaticus</i> and <i>Aethionema saxatile</i> subsp. <i>corinthiacum</i> have vague taxonomic relationships. <i>Astragalus maniaticus</i> was placed in sect. <i>Hypoglottis</i> but shows affinities to <i>A. suberosus</i> subsp. <i>haarbachii</i> of sect. <i>Platyglottis</i>. The <i>Aethionema saxatile</i> complex is an intriguing group due to the wide distribution and morphological variability of its taxa. In order to elucidate the variation patterns of these two taxa and to test their morphological identity, we carried out several multivariate morphometric (stepwise canonical and classificatory) analyses. They revealed that <i>Astragalus maniaticus</i> cannot be distinguished from <i>A. suberosus</i> subsp. <i>haarbachii</i> on morphological grounds. Therefore, it is transferred to sect. <i>Platyglottis</i> and regarded a heterotypic synonym of <i>A. suberosus</i> subsp. <i>haarbachii</i>. The taxonomic interpretation of <i>Aethionema saxatile</i> subsp. <i>corinthiacum</i> necessitated a broad revision of the <i>Ae. saxatile</i> group in Greece and detection of its relations with <i>Ae. rhodopaeum</i>, a Bulgarian endemic. The analyses showed that <i>Ae</i>. <i>saxatile</i> subsp. <i>corinthiacum</i> represents a distinct taxon; likewise, three additional subspecies receive support of similar strength: subsp. <i>creticum</i>, subsp. <i>graecum</i> and subsp. <i>oreophilum</i>. Intermediate forms between subsp. <i>oreophilum</i> and subsp. <i>saxatile</i> were detected in NW Greece. <i>Ae</i>. <i>rhodopaeum</i> is more variable than its original circumscription and is considered as another subspecies of <i>Ae. saxatile.</i>