cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1597710.v1
title: A genome-scale investigation of how sequence-, function-, and tree-based gene properties influence phylogenetic inference

description: Molecular phylogenetic inference is inherently dependent on choices in both methodology and data. Many insightful studies have shown how choices in methodology, such as the model of sequence evolution or optimality criterion used, can strongly influence inference. In contrast, much less is known about the impact of choices in the properties of the data, typically genes, on phylogenetic inference. We investigated the relationships between 52 gene properties (24 sequence-based, 19 function-based, and 9 tree-based) with each other and with three measures of phylogenetic signal in two assembled data sets of 2,832 yeast and 2,002 mammalian genes. We found that most gene properties, such as evolutionary rate (measured through the percent average of pairwise identity across taxa) and total tree length, were highly correlated with each other. Similarly, several gene properties, such as gene alignment length, GC content, and the proportion of tree distance on internal branches divided by relative composition variability (treeness/RCV), were strongly correlated with phylogenetic signal. Analysis of partial correlations between gene properties and phylogenetic signal in which gene evolutionary rate and alignment length were simultaneously controlled, showed similar patterns of correlations, albeit weaker in strength. Examination of the relative importance of each gene property on phylogenetic signal identified gene alignment length, alongside with number of parsimony-informative sites and variable sites, as the most important predictors. Interestingly, the subsets of gene properties that optimally predicted phylogenetic signal differed considerably across our three phylogenetic measures and two data sets; however, gene alignment length and RCV were consistently included as predictors of all three phylogenetic measures in both yeasts and mammals. These results suggest that a handful of sequence-based gene properties are reliable predictors of phylogenetic signal and could be useful in guiding the choice of phylogenetic markers.
DOI: 10.6084/m9.figshare.1597701.v1
title: Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus

description: In <i>Staphylococcus aureus</i>, hundreds of small regulatory or small RNAs (sRNAs) have been identified, yet this class of molecule remains poorly understood and severely understudied. sRNA genes are typically absent from genome annotation files, and as a consequence, their existence is often overlooked, particularly in global transcriptomic studies. To facilitate improved detection and analysis of sRNAs in <i>S. aureus</i>, we generated updated GenBank files for three commonly used <i>S. aureus </i>strains (MRSA252, NCTC 8325, and USA300), in which we added annotations for &gt;260 previously identified sRNAs. These files, the first to include genome-wide annotation of sRNAs in <i>S. aureus</i>, were then used as a foundation to identify novel sRNAs in the community-associated methicillin-resistant strain USA300. This analysis led to the discovery of 39 previously unidentified sRNAs. Investigating the genomic loci of the newly identified sRNAs revealed a surprising degree of inconsistency in genome anno- tation in <i>S. aureus</i>, which may be hindering the analysis and functional exploration of these elements. Finally, using our newly created annotation files as a reference, we perform a global analysis of sRNA gene expression in <i>S. aureus </i>and demonstrate that the newly identified <i>tsr25 </i>is the most highly upregulated sRNA in human serum. This study provides an invaluable resource to the <i>S. aureus </i>research community in the form of our newly generated annotation files, while at the same time presenting the first examination of differential sRNA expression in pathophysiologically relevant conditions. <br>
DOI: 10.6084/m9.figshare.1597710.v2
title: A genome-scale investigation of how sequence-, function-, and tree-based gene properties influence phylogenetic inference

description: Molecular phylogenetic inference is inherently dependent on choices in both methodology and data. Many insightful studies have shown how choices in methodology, such as the model of sequence evolution or optimality criterion used, can strongly influence inference. In contrast, much less is known about the impact of choices in the properties of the data, typically genes, on phylogenetic inference. We investigated the relationships between 52 gene properties (24 sequence-based, 19 function-based, and 9 tree-based) with each other and with three measures of phylogenetic signal in two assembled data sets of 2,832 yeast and 2,002 mammalian genes. We found that most gene properties, such as evolutionary rate (measured through the percent average of pairwise identity across taxa) and total tree length, were highly correlated with each other. Similarly, several gene properties, such as gene alignment length, GC content, and the proportion of tree distance on internal branches divided by relative composition variability (treeness/RCV), were strongly correlated with phylogenetic signal. Analysis of partial correlations between gene properties and phylogenetic signal in which gene evolutionary rate and alignment length were simultaneously controlled, showed similar patterns of correlations, albeit weaker in strength. Examination of the relative importance of each gene property on phylogenetic signal identified gene alignment length, alongside with number of parsimony-informative sites and variable sites, as the most important predictors. Interestingly, the subsets of gene properties that optimally predicted phylogenetic signal differed considerably across our three phylogenetic measures and two data sets; however, gene alignment length and RCV were consistently included as predictors of all three phylogenetic measures in both yeasts and mammals. These results suggest that a handful of sequence-based gene properties are reliable predictors of phylogenetic signal and could be useful in guiding the choice of phylogenetic markers.
DOI: 10.6084/m9.figshare.1597679
title: Rhabditis sp. SB347 male, female and hermaphrodite attraction to ascr#1 and ascr#9

description: Data from figure S1. To quantify the degree of attraction of worms to conditioned medium produced by different sexes, we used chemotaxis assays. Conditioned medium (henceforth referred to as ‘supernatant’) was generated by placing 5-10 worms in 100 µL of M9 buffer for 12 h at room temperature. The supernatant was stored in 10 µL aliquots at -20 °C until required. The assay was performed either on a microscope slide with a layer of 1.5% agar placed on top of an empty plate, or on a 6 cm NGM plate. 3 µL of supernatant was added on one side of the slide and 3 cm apart from the control drop that just contained M9. 15 young-adults were placed on the midline between the spots. After 30 min, worms were scored on the basis of their location. To calculate the CI, the number of worms attracted to the test spot were subtracted by the number of worms in the control spot, and divided by the total number of males assayed. A CI of one indicates that all worms are attracted to the chemical in the test spot, whereas a CI close to zero indicates no attraction.
DOI: 10.6084/m9.figshare.1597680
title: Plant species richness, abundance, functional group composition and invasive species richness in woodlots and grasslands at York University, Keele Campus

description: Boyer, Boynton and Danby woodlots and Stong, Boynton and Danby grasslands at York University were randomly sampled to collect data over three days on October 1st, 8th and 15th. Each of the six sites was plotted by 50x50m area and was divided into 100 numbered quadrat grid cells of 5x5m from which samples for the experiment were randomly generated using a random number table. Transect tapes were used to locate the quadrat numbers generated and to create the 5x5m quadrat sample for data collection. The number of species within a quadrat, their abundance and their names were recorded to classify them into their functional groups that were identified to be trees, forbs, shrubs, vines and grasses. Wildflower guidebook and tree species identification manual were used to identify the species for initial data records.
DOI: 10.6084/m9.figshare.1597680.v1
title: Plant species richness, abundance, functional group composition and invasive species richness in woodlots and grasslands at York University, Keele Campus

description: Boyer, Boynton and Danby woodlots and Stong, Boynton and Danby grasslands at York University were randomly sampled to collect data over three days on October 1st, 8th and 15th. Each of the six sites was plotted by 50x50m area and was divided into 100 numbered quadrat grid cells of 5x5m from which samples for the experiment were randomly generated using a random number table. Transect tapes were used to locate the quadrat numbers generated and to create the 5x5m quadrat sample for data collection. The number of species within a quadrat, their abundance and their names were recorded to classify them into their functional groups that were identified to be trees, forbs, shrubs, vines and grasses. Wildflower guidebook and tree species identification manual were used to identify the species for initial data records.
DOI: 10.6084/m9.figshare.1597679.v1
title: Rhabditis sp. SB347 male, female and hermaphrodite attraction to ascr#1 and ascr#9

description: Data from figure S1. To quantify the degree of attraction of worms to conditioned medium produced by different sexes, we used chemotaxis assays. Conditioned medium (henceforth referred to as ‘supernatant’) was generated by placing 5-10 worms in 100 µL of M9 buffer for 12 h at room temperature. The supernatant was stored in 10 µL aliquots at -20 °C until required. The assay was performed either on a microscope slide with a layer of 1.5% agar placed on top of an empty plate, or on a 6 cm NGM plate. 3 µL of supernatant was added on one side of the slide and 3 cm apart from the control drop that just contained M9. 15 young-adults were placed on the midline between the spots. After 30 min, worms were scored on the basis of their location. To calculate the CI, the number of worms attracted to the test spot were subtracted by the number of worms in the control spot, and divided by the total number of males assayed. A CI of one indicates that all worms are attracted to the chemical in the test spot, whereas a CI close to zero indicates no attraction.
DOI: 10.6084/m9.figshare.1597662
title: Social Influences in Sequential Decision Making_Raw_Data

description: Raw Data from PlosOne Paper: <br>Social Influences in Sequential Decision Making<br>
DOI: 10.6084/m9.figshare.1597661
title: FRM4STS Laboratory calibration of ISAR @ Univ. Miami (Credit: C Donlon)

description: Laboratory calibration of ISAR @ Univ. Miami
DOI: 10.6084/m9.figshare.1597659
title: FRM4STS - CASOTS-2 Reference Radiance Source (Credit C. Donlon)

description: CASOTS-2 Reference Radiance Source
DOI: 10.6084/m9.figshare.1597657
title: FRM4STS - Prototype FICE comparison of ISAR and M-AERI aboard the Explorer of the Seas (Credit P. Minnett)

description: Prototype Field Inter Compasrison of ISAR and M-AERI aboard the Explorer of the Seas.
DOI: 10.6084/m9.figshare.1597661.v1
title: Laboratory calibration of ISAR @ Univ. Miami (Credit: C Donlon)

description: Laboratory calibration of ISAR @ Univ. Miami
DOI: 10.6084/m9.figshare.1597656
title: FRM4STS - At Sea Comparison of 3 radioameters (R/V Walton Smith, University of Miami) (Credit: P. Minnett)

description: At Sea Comparison of 3 radioameters (R/V Walton Smith, University of Miami) (Credit: P. Minnett)
DOI: 10.6084/m9.figshare.1597659.v1
title: CASOTS-2 Reference Radiance Source (Credit C. Donlon)

description: CASOTS-2 Reference Radiance Source
DOI: 10.6084/m9.figshare.1597661.v3
title: FRM4STS Laboratory calibration of ISAR @ Univ. Miami (Credit: C Donlon)

description: Laboratory calibration of ISAR @ Univ. Miami
DOI: 10.6084/m9.figshare.1597655
title: Soporific behavior of Rhabditis sp. SB347

description: In nematodes, males attempting to mate may induce soporific behavior, which results in the reduction of locomotory behavior of the opposite sex. Soporific behavior was quantified by placing 4-5 males in a twelve-well plate seeded with bacteria with either one hermaphrodite or female. Time was recorded for how long the hermaphrodite or female stopped moving as the male started mating. 21 females and 15 hermaphrodites were tested in total.
DOI: 10.6084/m9.figshare.1597656.v1
title: At Sea Comparison of 3 radioameters (R/V Walton Smith, University of Miami) (Credit: P. Minnett)

description: At Sea Comparison of 3 radioameters (R/V Walton Smith, University of Miami) (Credit: P. Minnett)
DOI: 10.6084/m9.figshare.1597659.v3
title: FRM4STS - CASOTS-2 Reference Radiance Source (Credit C. Donlon)

description: CASOTS-2 Reference Radiance Source
DOI: 10.6084/m9.figshare.1597661.v2
title: Laboratory calibration of ISAR @ Univ. Miami (Credit: C Donlon)

description: Laboratory calibration of ISAR @ Univ. Miami
DOI: 10.6084/m9.figshare.1597657.v1
title: Prototype FICE comparison of ISAR and M-AERI aboard the Explorer of the Seas (Credit P. Minnett)

description: Prototype Field Inter Compasrison of ISAR and M-AERI aboard the Explorer of the Seas.
DOI: 10.6084/m9.figshare.1597659.v2
title: CASOTS-2 Reference Radiance Source (Credit C. Donlon)

description: CASOTS-2 Reference Radiance Source
DOI: 10.6084/m9.figshare.1597653
title: Rhabditis sp. SB347 male attraction towards synthetic ascr#1 and ascr#9

description: Data from figure 4d. To quantify the degree of attraction of worms to conditioned medium produced by different sexes, we used chemotaxis assays. Conditioned medium (henceforth referred to as ‘supernatant’) was generated by placing 5-10 worms in 100 µL of M9 buffer for 12 h at room temperature. The supernatant was stored in 10 µL aliquots at -20 °C until required. The assay was performed either on a microscope slide with a layer of 1.5% agar placed on top of an empty plate, or on a 6 cm NGM plate. 3 µL of supernatant was added on one side of the slide and 3 cm apart from the control drop that just contained M9. 15 young-adults were placed on the midline between the spots. After 30 min, worms were scored on the basis of their location. To calculate the CI, the number of worms attracted to the test spot were subtracted by the number of worms in the control spot, and divided by the total number of males assayed. A CI of one indicates that all worms are attracted to the chemical in the test spot, whereas a CI close to zero indicates no attraction.
DOI: 10.6084/m9.figshare.1597654
title: Rhabditis sp. SB347 sperm size

description: To release the sperm and measure their size, ten animals of each sex were cut using a 22 gauge needle in the presence of 5-10 µL drop of sperm buffer (90 mM NaCl, 50 mM KCl, 2 mM MgCl2, 10 mM CaCl2, 100 mM HEPES, and 20 mM dextrose to pH 7.8 for a 2X solution). Males were cut at the level of the vas deferens and hermaphrodites at the level of the spermatheca. Immediately following the dissections, the slides were examined using DIC optics on a Carl Zeiss 510 confocal microscope. To improve the adhesion of the sperm cells to the slide, slides were pre-treated with Poly-L-Lysine. A 4-5 µL drop of 100% Poly-L-Lysine was placed at the center of the charged surface of a ColorFrost Plus slide. A second slide was placed on top of it in such a way that both charged surfaces were facing each other and a thin film of liquid formed between them. Once the film was formed, slides were separated by sliding them over each other. Subsequently, slides were baked at 60 °C for 1-2 h. To identify the sperm, which were often very small, we added Hoechst 33342 (Sigma-Aldrich) to the sperm media at a final concentration of 100 μg/mL. Hoechst helped to visualize and identify the characteristic condensed shape of the sperm nucleus. Sperm size was measured as the cross sectional area of the spermatid using the Carl Zeiss confocal software.
DOI: 10.6084/m9.figshare.1597655.v2
title: Soporific behavior of Rhabditis sp. SB347

description: In nematodes, males attempting to mate may induce soporific behavior, which results in the reduction of locomotory behavior of the opposite sex. Soporific behavior was quantified by placing 4-5 males in a twelve-well plate seeded with bacteria with either one hermaphrodite or female. Time was recorded for how long the hermaphrodite or female stopped moving as the male started mating. 21 females and 15 hermaphrodites were tested in total.
DOI: 10.6084/m9.figshare.1597657.v3
title: FRM4STS - Prototype FICE comparison of ISAR and M-AERI aboard the Explorer of the Seas (Credit P. Minnett)

description: Prototype Field Inter Compasrison of ISAR and M-AERI aboard the Explorer of the Seas.
DOI: 10.6084/m9.figshare.1597651
title: Rhabditis sp. SB347 males attracted to unablated animals (wild type), and ablated animals for precursors of germline (Z2 & Z3), vulva precursor cells (VPC) and precursors of somatic gonad (Z1 & Z4)

description: Data from figure 3e. To quantify the degree of attraction of worms to conditioned medium produced by different sexes, we used chemotaxis assays. Conditioned medium (henceforth referred to as ‘supernatant’) was generated by placing 5-10 worms in 100 µL of M9 buffer for 12 h at room temperature. The supernatant was stored in 10 µL aliquots at -20 °C until required. The assay was performed either on a microscope slide with a layer of 1.5% agar placed on top of an empty plate, or on a 6 cm NGM plate. 3 µL of supernatant was added on one side of the slide and 3 cm apart from the control drop that just contained M9. 15 young-adults were placed on the midline between the spots. After 30 min, worms were scored on the basis of their location. The values for the chemotaxis index (CI) were calculated with at least ten replicates for each condition. To calculate the CI, the number of worms attracted to the test spot were subtracted by the number of worms in the control spot, and divided by the total number of males assayed. A CI of one indicates that all worms are attracted to the chemical in the test spot, whereas a CI close to zero indicates no attraction. Gonadal (Z1 – Z4) and vulva precursor cells (P5.p, P6.p and P7.p) of mid- L1 animals (females or hermaphrodites) were ablated using laser microsurgery. For ablation, worms were placed on agar pads on microscopic slides. Worms were recovered after ablation using a drop of M9 buffer and transferred to a normal seeded plate. Two days after recovery, laser ablated adult worms were used to collect supernatant for attraction assays
DOI: 10.6084/m9.figshare.1597657.v2
title: Prototype FICE comparison of ISAR and M-AERI aboard the Explorer of the Seas (Credit P. Minnett)

description: Prototype Field Inter Compasrison of ISAR and M-AERI aboard the Explorer of the Seas.
DOI: 10.6084/m9.figshare.1597655.v1
title: Sexes of Rhabditis sp.SB347 F1 from selfing or outcrossing parents.

description: To determine the sex of the F1 from selfing hermaphrodites, the self-progeny of 20 SB347 animals was collected throughout their lifespan (Fig. 2a). The hermaphrodite mothers were selected by first isolating dauers, which in SB347 always develop into hermaphrodites 32. Dauers were placed into single 6 cm agar plates seeded with E. coli OP50-1 and left to mature into adults. Every 8 h of their reproductive life, the hermaphrodite mothers were transferred to a new plate until they stopped laying eggs. To control more precisely for worms that may escape the plate before being scored, we sexed the progeny while they were at larval stages (two days after hatching). We scored the three sexes using several traits, including developmental rates and morphologies. Dauer larvae (destined to become hermaphrodites) are thin with darkly-pigmented guts. Larger larvae with long thin tails develop into females. Male larvae have a characteristically blunt tail.
DOI: 10.6084/m9.figshare.1597650
title: Attraction of Rhabditis sp. SB347 males to females in the fourth larval stage (L4) or as adults

description: Data from figure 3d. To quantify the degree of attraction of worms to conditioned medium produced by different sexes, we used chemotaxis assays. Conditioned medium (henceforth referred to as ‘supernatant’) was generated by placing 5-10 worms in 100 µL of M9 buffer for 12 h at room temperature. The supernatant was stored in 10 µL aliquots at -20 °C until required. The assay was performed either on a microscope slide with a layer of 1.5% agar placed on top of an empty plate, or on a 6 cm NGM plate. 3 µL of supernatant was added on one side of the slide and 3 cm apart from the control drop that just contained M9. 15 young-adults were placed on the midline between the spots. After 30 min, worms were scored on the basis of their location. The values for the chemotaxis index (CI) shown in figures 3a, 3d, 3e (in x axis) and S1 were calculated with at least ten replicates for each condition. To calculate the CI, the number of worms attracted to the test spot were subtracted by the number of worms in the control spot, and divided by the total number of males assayed. A CI of one indicates that all worms are attracted to the chemical in the test spot, whereas a CI close to zero indicates no attraction.
DOI: 10.6084/m9.figshare.1597649
title: Percentage of Rhabditis sp. SB347 males that attempt to mate to females over time after mating

description: Data from figure 3c. The male response efficiency assay measures the percentage of males that attempt to mate with the opposite sex. One day before the experiment, NGM plates were spotted with 13 µL of E. coli OP50-1 culture. Before the experiment, 5 males were placed for 10 min in the center of the ~ 5 mm diameter bacterial spot to let them acclimatize. 15 animals of the opposite sex (hermaphrodites or females) were added to the bacterial spot and observed for 4 min. If a male attempted to mate, as determined by the male tail scanning the body of the other sex, the male response was scored with the number 1. In case there was no attempt, the response was scored as 0. The behavior of each male was recorded only once. For each type of mating (male/hermaphrodite or male/female), 5 replicates were performed. 25 mated females were divided in 5 sets. 15 males were added at 5 time points (0, 6, 12, 18 and 24 h) after the initial mating to each set.