cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4309289
title: Phylogeny and origins of chemosynthetic vesicomyid clams

description: Large vesicomyid clams (Veneroida: Vesicomyidae: Pliocardiinae) are prominent members of the communities associated with sulphide-rich deep-sea habitats. Taxonomic uncertainties within the Pliocardiinae result from both plasticity in shell morphologies and the common occurrence of cryptic species. Molecular taxonomic studies have now clarified many species-level assignments and provided DNA-barcodes for more than 50 species worldwide. Nonetheless, genus-level assignments remain uncertain, because the existing <i>COI</i> barcode sequences are not sufficient for identifying higher-level groupings. To construct a robust phylogeny for this subfamily, we conducted a combined Bayesian analysis of the <i>COI</i> mitochondrial fragment and five additional independent nuclear gene segments. The phylogenetic results provide a better foundation for assessing genus-level assignments within the subfamily and reveal goals for future taxonomic research. Furthermore, morphological examinations helped to clarify and solidify generic classifications. Calibration of molecular clocks with recently verified fossil data permitted realistic estimates for the origins and evolutionary age of pliocardiins during the Cenozoic Era from a deep-dwelling ancestor. http://zoobank.org/urn:lsid:zoobank.org:pub:2554122D-96D4-4CBF-BC70-B017998AF64D
DOI: 10.6084/m9.figshare.4309289.v1
title: Phylogeny and origins of chemosynthetic vesicomyid clams

description: Large vesicomyid clams (Veneroida: Vesicomyidae: Pliocardiinae) are prominent members of the communities associated with sulphide-rich deep-sea habitats. Taxonomic uncertainties within the Pliocardiinae result from both plasticity in shell morphologies and the common occurrence of cryptic species. Molecular taxonomic studies have now clarified many species-level assignments and provided DNA-barcodes for more than 50 species worldwide. Nonetheless, genus-level assignments remain uncertain, because the existing <i>COI</i> barcode sequences are not sufficient for identifying higher-level groupings. To construct a robust phylogeny for this subfamily, we conducted a combined Bayesian analysis of the <i>COI</i> mitochondrial fragment and five additional independent nuclear gene segments. The phylogenetic results provide a better foundation for assessing genus-level assignments within the subfamily and reveal goals for future taxonomic research. Furthermore, morphological examinations helped to clarify and solidify generic classifications. Calibration of molecular clocks with recently verified fossil data permitted realistic estimates for the origins and evolutionary age of pliocardiins during the Cenozoic Era from a deep-dwelling ancestor. http://zoobank.org/urn:lsid:zoobank.org:pub:2554122D-96D4-4CBF-BC70-B017998AF64D
DOI: 10.6084/m9.figshare.4309268
title: Face-like inversion effects with cars

description: Car inversion effects reported in Rezlescu, Chapman, Susilo, & Caramazza (submitted). One sample of web participants (n=63, MTurks), and one sample of lab participants (n=57, undergraduate students from Victoria University of Wellington).
DOI: 10.6084/m9.figshare.4309283
title: Phylogeny of the nominotypical subgenus of <i>Culex</i> (Diptera: Culicidae): insights from analyses of anatomical data into interspecific relationships and species groups in an unresolved tree

description: The aim of this study was to produce the first objective and comprehensive phylogenetic analysis of the speciose subgenus <i>Culex</i> based on morphological data. We used implied and equally weighted parsimony methods to analyse a dataset comprised of 286 characters of the larval, pupal, and adult stages of 150 species of the subgenus and an outgroup of 17 species. We determined the optimal support by summing the GC supports for each MPC, selecting the cladograms with the highest supports to generate a strict consensus tree. We then collapsed the branches with GC support &lt; 1 to obtain the ‘best’ topography of relationships. The analyses largely failed to resolve relationships among the species and the informal groups in which they are currently placed based on morphological similarities and differences. All analyses, however, support the monophyly of genus <i>Culex</i>. With the exception of the Atriceps Group, the analyses failed to find positive support for any of the informal species groups (monophyly of the Duttoni Group could not be established because only one of the two species of the group was included in the analyses). Since the analyses would seem to include sufficient data for phylogenetic reconstruction, lack of resolution appears to be the result of inadequate or conflicting character data, and perhaps incorrect homology assessments. Molecular and other biological data are needed to gain insights into the evolution of subgenus <i>Culex</i>. Nevertheless, we discuss the placement of several taxa in the current morphology-based classification of the subgenus based on insights realized during the study.
DOI: 10.6084/m9.figshare.4309268.v2
title: Face-like inversion effects with cars

description: Car inversion effects reported in Rezlescu, Chapman, Susilo, & Caramazza (submitted). One sample of web participants (n=63, MTurks), and one sample of lab participants (n=57, undergraduate students from Victoria University of Wellington).
DOI: 10.6084/m9.figshare.4309283.v1
title: Phylogeny of the nominotypical subgenus of <i>Culex</i> (Diptera: Culicidae): insights from analyses of anatomical data into interspecific relationships and species groups in an unresolved tree

description: The aim of this study was to produce the first objective and comprehensive phylogenetic analysis of the speciose subgenus <i>Culex</i> based on morphological data. We used implied and equally weighted parsimony methods to analyse a dataset comprised of 286 characters of the larval, pupal, and adult stages of 150 species of the subgenus and an outgroup of 17 species. We determined the optimal support by summing the GC supports for each MPC, selecting the cladograms with the highest supports to generate a strict consensus tree. We then collapsed the branches with GC support &lt; 1 to obtain the ‘best’ topography of relationships. The analyses largely failed to resolve relationships among the species and the informal groups in which they are currently placed based on morphological similarities and differences. All analyses, however, support the monophyly of genus <i>Culex</i>. With the exception of the Atriceps Group, the analyses failed to find positive support for any of the informal species groups (monophyly of the Duttoni Group could not be established because only one of the two species of the group was included in the analyses). Since the analyses would seem to include sufficient data for phylogenetic reconstruction, lack of resolution appears to be the result of inadequate or conflicting character data, and perhaps incorrect homology assessments. Molecular and other biological data are needed to gain insights into the evolution of subgenus <i>Culex</i>. Nevertheless, we discuss the placement of several taxa in the current morphology-based classification of the subgenus based on insights realized during the study.
DOI: 10.6084/m9.figshare.4309268.v1
title: Results car inversion effects

description: Car inversion effects reported in Rezlescu, Chapman, Susilo, & Caramazza (submitted). One sample of web participants (n=63, MTurks), and one sample of lab participants (n=57, undergraduate students from Victoria University of Wellington).
DOI: 10.6084/m9.figshare.4309217
title: New draft Habitat Use and Spatial Variability of Hawkfishes with a Focus on Colour Polymorphism in Paracirrhites forsteri

description: Identifying relationships between fishes and their environment is an integral part of understanding coral reef ecosystems. However, this information is lacking for many species, particularly in understudied and remote regions. With coral reefs continuing to face environmental pressures, insight into abundance and distribution patterns along with resource use of fish communities will aid in advancing our ecological understanding and management processes. Based on ecological surveys of hawkfish assemblages (Family: Cirrhitidae) in the Red Sea, we reveal distinct patterns in the distribution and abundance across the continental shelf, wave exposure, and with depth, particularly in the four colour morphs of <i>Paracirrhites forsteri</i>. Distinct patterns were observed among hawkfishes, with higher abundance of all species recorded on reefs farther from shore and on wave exposed reef zones. <i>Cirrhitus spilotoceps</i> was only recorded on the exposed crest, but unlike the other species, did not associate with live coral colonies. Overall, the most abundant species was <i>P. forsteri. </i>This species exploited a variety of habitats but showed an affinity for complex habitats provided by live and dead coral colonies. No difference in habitat use was observed among the four colour morphs, but distinct patterns were apparent in distribution and abundance with depth. This study suggests that in addition to <i>P. forsteri</i> exhibiting diverse colour morphologies, these various morphotypes appear to have corresponding ecological differences in the Red Sea. To better understand this, further studies are needed to identify what these differences extend to and the mechanisms involved.
DOI: 10.6084/m9.figshare.4309232
title: Promethazine improves antibiotic efficacy and disrupts biofilms of <i>Burkholderia pseudomallei</i>

description: Efflux pumps are important defense mechanisms against antimicrobial drugs and maintenance of <i>Burkholderia pseudomallei</i> biofilms. This study evaluated the effect of the efflux pump inhibitor promethazine on the structure and antimicrobial susceptibility of <i>B</i>. <i>pseudomallei</i> biofilms. Susceptibility of planktonic cells and biofilms to promethazine alone and combined with antimicrobials was assessed by the broth microdilution test and biofilm metabolic activity was determined with resazurin. The effect of promethazine on 48 h-grown biofilms was also evaluated through confocal and electronic microscopy. The minimum inhibitory concentration (MIC) of promethazine was 780 mg l<sup>−1</sup>, while the minimum biofilm elimination concentration (MBEC) was 780–3,120 mg l<sup>−1</sup>. Promethazine reduced the MIC values for erythromycin, trimethoprim/sulfamethoxazole, gentamicin and ciprofloxacin and reduced the MBEC values for all tested drugs (<i>p</i>&lt;0.05). Microscopic analyses demonstrated that promethazine altered the biofilm structure of <i>B</i>. <i>pseudomallei</i>, even at subinhibitory concentrations, possibly facilitating antibiotic penetration. Promethazine improves antibiotics efficacy against <i>B. pseudomallei</i> biofilms, by disrupting biofilm structure.
DOI: 10.6084/m9.figshare.4309217.v1
title: New draft Habitat Use and Spatial Variability of Hawkfishes with a Focus on Colour Polymorphism in Paracirrhites forsteri

description: Identifying relationships between fishes and their environment is an integral part of understanding coral reef ecosystems. However, this information is lacking for many species, particularly in understudied and remote regions. With coral reefs continuing to face environmental pressures, insight into abundance and distribution patterns along with resource use of fish communities will aid in advancing our ecological understanding and management processes. Based on ecological surveys of hawkfish assemblages (Family: Cirrhitidae) in the Red Sea, we reveal distinct patterns in the distribution and abundance across the continental shelf, wave exposure, and with depth, particularly in the four colour morphs of <i>Paracirrhites forsteri</i>. Distinct patterns were observed among hawkfishes, with higher abundance of all species recorded on reefs farther from shore and on wave exposed reef zones. <i>Cirrhitus spilotoceps</i> was only recorded on the exposed crest, but unlike the other species, did not associate with live coral colonies. Overall, the most abundant species was <i>P. forsteri. </i>This species exploited a variety of habitats but showed an affinity for complex habitats provided by live and dead coral colonies. No difference in habitat use was observed among the four colour morphs, but distinct patterns were apparent in distribution and abundance with depth. This study suggests that in addition to <i>P. forsteri</i> exhibiting diverse colour morphologies, these various morphotypes appear to have corresponding ecological differences in the Red Sea. To better understand this, further studies are needed to identify what these differences extend to and the mechanisms involved.
DOI: 10.6084/m9.figshare.4309232.v1
title: Promethazine improves antibiotic efficacy and disrupts biofilms of <i>Burkholderia pseudomallei</i>

description: Efflux pumps are important defense mechanisms against antimicrobial drugs and maintenance of <i>Burkholderia pseudomallei</i> biofilms. This study evaluated the effect of the efflux pump inhibitor promethazine on the structure and antimicrobial susceptibility of <i>B</i>. <i>pseudomallei</i> biofilms. Susceptibility of planktonic cells and biofilms to promethazine alone and combined with antimicrobials was assessed by the broth microdilution test and biofilm metabolic activity was determined with resazurin. The effect of promethazine on 48 h-grown biofilms was also evaluated through confocal and electronic microscopy. The minimum inhibitory concentration (MIC) of promethazine was 780 mg l<sup>−1</sup>, while the minimum biofilm elimination concentration (MBEC) was 780–3,120 mg l<sup>−1</sup>. Promethazine reduced the MIC values for erythromycin, trimethoprim/sulfamethoxazole, gentamicin and ciprofloxacin and reduced the MBEC values for all tested drugs (<i>p</i>&lt;0.05). Microscopic analyses demonstrated that promethazine altered the biofilm structure of <i>B</i>. <i>pseudomallei</i>, even at subinhibitory concentrations, possibly facilitating antibiotic penetration. Promethazine improves antibiotics efficacy against <i>B. pseudomallei</i> biofilms, by disrupting biofilm structure.
DOI: 10.6084/m9.figshare.4309124
title: Xenopus laevis head movement kinematics: Dataset

description: Datasets underlying the following paper: Hänzi, Sara, and Straka, Hans: "Developmental changes in head movement kinematics during swimming in Xenopus laevis tadpoles." <i>Journal of Experimental Biology</i> (2016): doi:10.1242/jeb.146449.<br> <br> For permissions and methods please see the paper.<br> <br> The mat file entitled kinematicsDataShare contains two variables; the kinematics data struct contains the main data from the videos. There are fields specifying the filename (fn), the developmental stage (stage), the temperature at which the behavior was recorded (temp), left and right eye positions (leftEye and rightEye, each has a subfield for the x and y coordinate), the timestamp of each frame (ts), the head angle relative to some arbitrary external reference (angleEye, already corrected for jumps between quadrants), the index of the animal (animalIndex), and a struct for converting pixels to mm (sizeCalibration), and comments.<br> <br> There is an additional variable, called anatomicalMeasures, which is also a struct containing filenames, the animal's index (which is the same as in the kinematics), and measurements of the different anatomical parameters indicated as pixel. As described in the methods of the paper, every measure was repeated in 4 different frames of the same animal, and the mean was taken as the final value.<br> <br> The second file is called fictiveSwimmingDataShare.mat and contains a struct called fictiveSwimming with fields of filename, developmental stage, length of the animal, and the frequency data (i.e. the frequency of fictive swimming calculated from electrophysiological recordings of a ventral root).
DOI: 10.6084/m9.figshare.4309124.v1
title: Xenopus laevis head movement kinematics: Dataset

description: Datasets underlying the following paper: Hänzi, Sara, and Straka, Hans: "Developmental changes in head movement kinematics during swimming in Xenopus laevis tadpoles." <i>Journal of Experimental Biology</i> (2016): doi:10.1242/jeb.146449.<br> <br> For permissions and methods please see the paper.<br> <br> The mat file entitled kinematicsDataShare contains two variables; the kinematics data struct contains the main data from the videos. There are fields specifying the filename (fn), the developmental stage (stage), the temperature at which the behavior was recorded (temp), left and right eye positions (leftEye and rightEye, each has a subfield for the x and y coordinate), the timestamp of each frame (ts), the head angle relative to some arbitrary external reference (angleEye, already corrected for jumps between quadrants), the index of the animal (animalIndex), and a struct for converting pixels to mm (sizeCalibration), and comments.<br> <br> There is an additional variable, called anatomicalMeasures, which is also a struct containing filenames, the animal's index (which is the same as in the kinematics), and measurements of the different anatomical parameters indicated as pixel. As described in the methods of the paper, every measure was repeated in 4 different frames of the same animal, and the mean was taken as the final value.<br> <br> The second file is called fictiveSwimmingDataShare.mat and contains a struct called fictiveSwimming with fields of filename, developmental stage, length of the animal, and the frequency data (i.e. the frequency of fictive swimming calculated from electrophysiological recordings of a ventral root).
DOI: 10.6084/m9.figshare.4309010
title: Supplementary Data File 1 from Antibody responses to avian influenza viruses in wild birds broaden with age

description: Raw data files
DOI: 10.6084/m9.figshare.4308983
title: Supplementary sequence file II from Phylogenomics-guided discovery of a novel conserved cassette of short linear motifs in BubR1 essential for the spindle checkpoint

description: FastA file containing conserved MadBub sequence features classified for all homologs in this study
DOI: 10.6084/m9.figshare.4308983.v1
title: Supplementary sequence file II from Phylogenomics-guided discovery of a novel conserved cassette of short linear motifs in BubR1 essential for the spindle checkpoint

description: FastA file containing conserved MadBub sequence features classified for all homologs in this study
DOI: 10.6084/m9.figshare.4308953
title: Supplementary sequence file I from Phylogenomics-guided discovery of a novel conserved cassette of short linear motifs in BubR1 essential for the spindle checkpoint

description: FastA file containing all sequences used in this study
DOI: 10.6084/m9.figshare.4308953.v1
title: Supplementary sequence file I from Phylogenomics-guided discovery of a novel conserved cassette of short linear motifs in BubR1 essential for the spindle checkpoint

description: FastA file containing all sequences used in this study
DOI: 10.6084/m9.figshare.4308941
title: Quantifying spatial variation in the size and structure of ecologically stratified communities

description: Data used in the application of the multi-region community model (MRCM) to detection non-detection data collected from bird communities in R=8 geographically distinct regions in northern Italy. We augmented the data for all regions such that M = M_r = 200, i.e., by 200-n_r species for each region. The data file contains the following objects: (i) dataREG: region-specific covariates; (ii) guild: species-by-region matrix indicating the functional group to which each species belongs; (iii) K_tot: number of sampling occasions for each site in each region; (iv) M: total number of species in the augmented data set; (v) mass: body mass (in grams) for each species in each region; (vi) nsites: total number of sites per region; (vii) nspecies: total number of observed species for each region; (viii) species: scientific name of each species observed in each region; (ix) Yaug_tot: augmented species-by-sites-by-region detection frequency matrix.
DOI: 10.6084/m9.figshare.4308941.v1
title: Quantifying spatial variation in the size and structure of ecologically stratified communities

description: Data used in the application of the multi-region community model (MRCM) to detection non-detection data collected from bird communities in R=8 geographically distinct regions in northern Italy. We augmented the data for all regions such that M = M_r = 200, i.e., by 200-n_r species for each region. The data file contains the following objects: (i) dataREG: region-specific covariates; (ii) guild: species-by-region matrix indicating the functional group to which each species belongs; (iii) K_tot: number of sampling occasions for each site in each region; (iv) M: total number of species in the augmented data set; (v) mass: body mass (in grams) for each species in each region; (vi) nsites: total number of sites per region; (vii) nspecies: total number of observed species for each region; (viii) species: scientific name of each species observed in each region; (ix) Yaug_tot: augmented species-by-sites-by-region detection frequency matrix.
DOI: 10.6084/m9.figshare.4308926
title: microCT scans of bone and cement-bone microstructures

description: Repeated scans of:VOI1 - the largest possible area that could be inscribed in all vertebrae (300x300x432 voxels);VOI2 - regions of fully cement-augmented trabecular bone (152x152x432 voxels);VOI3 - regions of interface between augmented and non-augmented trabecular bone (152x152x432 voxels);VOI4 - regions containing both trabecular and cortical bone (152x152x432 voxels);VOI5 - regions containing both trabecular and cortical bone with surrounding saline solution (152x152x432 voxels).<br>The spatial resolution of each scan is of 39 micrometers.
DOI: 10.6084/m9.figshare.4308917
title: Paranoia and the social representation of others: a large-scale game theory approach

description: The .csv file comprises the raw data necessary to reproduce the analyses in Raihani & Bell: Paranoia and the social representation of others: a large-scale game theory approach. The R code file contains the code to produce the key analyses and plots from these data. <br> <br>
DOI: 10.6084/m9.figshare.4308926.v1
title: microCT scans of bone and cement-bone microstructures

description: Repeated scans of:VOI1 - the largest possible area that could be inscribed in all vertebrae (300x300x432 voxels);VOI2 - regions of fully cement-augmented trabecular bone (152x152x432 voxels);VOI3 - regions of interface between augmented and non-augmented trabecular bone (152x152x432 voxels);VOI4 - regions containing both trabecular and cortical bone (152x152x432 voxels);VOI5 - regions containing both trabecular and cortical bone with surrounding saline solution (152x152x432 voxels).<br>The spatial resolution of each scan is of 39 micrometers.
DOI: 10.6084/m9.figshare.4308914
title: A positive effect of flowers rather than eye images in a large-scale, cross-cultural dictator game." Proc. R. Soc. B. The Royal Society, 2012.

description: Datasets to accompany <br>Raihani, Nichola J., and Redouan Bshary. "A positive effect of flowers rather than eye images in a large-scale, cross-cultural dictator game." <i>Proc. R. Soc. B</i>. The Royal Society, 2012.
DOI: 10.6084/m9.figshare.4308917.v1
title: Paranoid Attributions of Harmful Intent in Experienced and Observed Economic Loss

description: The .csv file comprises the raw data necessary to reproduce the analyses in Raihani & Bell: Paranoid Attributions of Harmful Intent in Experienced and Observed Economic Loss . The R code file contains the code to produce the key analyses and plots from these data. <br> <br>
DOI: 10.6084/m9.figshare.4308914.v2
title: A positive effect of flowers rather than eye images in a large-scale, cross-cultural dictator game." Proc. R. Soc. B. The Royal Society, 2012.

description: Datasets to accompany <br>Raihani, Nichola J., and Redouan Bshary. "A positive effect of flowers rather than eye images in a large-scale, cross-cultural dictator game." <i>Proc. R. Soc. B</i>. The Royal Society, 2012.