cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12736823
title: Additional file 1 of Genome-wide evolutionary characterization and expression analysis of SIAMESE-RELATED family genes in maize

description: Additional file 1. Gene ID and Sequence of ZmSMRs.
DOI: 10.6084/m9.figshare.12736829
title: Additional file 3 of Genome-wide evolutionary characterization and expression analysis of SIAMESE-RELATED family genes in maize

description: Additional file 3 The number of various cis-acting elements in ZmSMR promoters.
DOI: 10.6084/m9.figshare.12736823.v1
title: Additional file 1 of Genome-wide evolutionary characterization and expression analysis of SIAMESE-RELATED family genes in maize

description: Additional file 1. Gene ID and Sequence of ZmSMRs.
DOI: 10.6084/m9.figshare.12736829.v1
title: Additional file 3 of Genome-wide evolutionary characterization and expression analysis of SIAMESE-RELATED family genes in maize

description: Additional file 3 The number of various cis-acting elements in ZmSMR promoters.
DOI: 10.6084/m9.figshare.12736820
title: Additional file 11 of Genome-wide evolutionary characterization and expression analysis of SIAMESE-RELATED family genes in maize

description: Additional file 11 Primers for qRT-PCR to investigate the ZmSMR genes.
DOI: 10.6084/m9.figshare.12736820.v1
title: Additional file 11 of Genome-wide evolutionary characterization and expression analysis of SIAMESE-RELATED family genes in maize

description: Additional file 11 Primers for qRT-PCR to investigate the ZmSMR genes.
DOI: 10.6084/m9.figshare.12736766
title: Supplementary Material for: Hybrid Percutaneous-Endoscopic Removal (HPER) of Cholelithiasis

description: Acute cholecystitis (AC) affects over 20 million Americans annually, leading to annual costs exceeding USD 6 billion. Optimal treatment is early cholecystectomy. However, patients deemed high surgical risk undergo percutaneous cholecystostomy tube (PCT) placement as a bridge to surgery or more commonly as a definitive therapy. We hereby describe our experience with a new procedure named “Hybrid Percutaneous Endoscopic Removal (HPER) of cholelithiasis” that is meant for patients with chronic indwelling PCT. This procedure is an effective alternative to EUS-guided gallbladder drainage in high-risk patients. It does not require special expertise or technology and is simply performed by placing a fully covered metal stent conduit through the existing mature percutaneous tract allowing the endoscopic removal of gallstones through this conduit. This procedure can prevent the recurrence of gallstone-related complications as well as chronic PCT-related costs and adverse events. In our video, we present a case series and long-term follow-up of patients who underwent HPER as an alternative definitive therapy for calculous AC.
DOI: 10.6084/m9.figshare.12736769
title: Fiscal rules and budget deficit: does democracy matter? (Dataset)

description: This dataset is a compilation of macroeconomics, institutional and fiscal rules data to determine the role of democracy on fiscal rules effectiveness in budget deficit reducing.
DOI: 10.6084/m9.figshare.12736769.v1
title: Fiscal rules and budget deficit: does democracy matter? (Dataset)

description: This dataset is a compilation of macroeconomics, institutional and fiscal rules data to determine the role of democracy on fiscal rules effectiveness in budget deficit reducing.
DOI: 10.6084/m9.figshare.12736562
title: Pupae behavior

description: This dataset has records on behavior of mosquito pupae (<i>Aedes aegypti</i>) when wriggling and at the water surface and its space use pattern when exposed to non-lethal predation threat from guppy fish (<i>Poecilia reticulata</i>)<br>
DOI: 10.6084/m9.figshare.12736604
title: Supplemental Data_L-00522-2019R1.pdf

description: <b>This is the ONLINE DATA SUPPLEMENT for the communicated paper titled </b> <b> "</b>Non-canonical role for Ku70/80 in the prevention of allergic airway inflammation via maintenance of airway epithelial cell organelle homeostasis:. This has been communicated to AJP-Lung Cellular and Molecular Physiology.
DOI: 10.6084/m9.figshare.12736562.v1
title: Pupae behavior

description: This dataset has records on behavior of mosquito pupae (<i>Aedes aegypti</i>) when wriggling and at the water surface and its space use pattern when exposed to non-lethal predation threat from guppy fish (<i>Poecilia reticulata</i>)<br>
DOI: 10.6084/m9.figshare.12736235
title: Tree_phylobayes

description: Model: MtArt
DOI: 10.6084/m9.figshare.12736235.v1
title: Tree_phylobayes

description: Model: MtArt
DOI: 10.6084/m9.figshare.12736238
title: Data Matrix_48_10AA

description: 48taxa11AAaligned with transXConcatenate with Phylosuite
DOI: 10.6084/m9.figshare.12736238.v1
title: Data Matrix_48_10AA

description: 48taxa11AAaligned with transXConcatenate with Phylosuite
DOI: 10.6084/m9.figshare.12736232
title: Bankit

description: Sqn<br>Biosample tableSRA table
DOI: 10.6084/m9.figshare.12736226
title: Sequence Assembly and Base composition

description: Assembly note including failure of CR Base composition table
DOI: 10.25400/lincolnuninz.12736217
title: Evolutionary divergence of the insect disease-encoding Serratia plasmid pADAP Supplementary Materials

description: Documents in support of statements made in the PhD thesis "Evolutionary divergence of the insect disease-encoding <i>Serratia</i> plasmid pADAP" by Thomas Lesley Sitter<br>Abstract for the thesis<br>The larvae of the New Zealand grass-grub (<i>Costelytra givenii</i>), cause significant damage to New Zealand’s pastures. Two diseases of grass-grub larvae, instigated by strains of <i>Serratia</i> <i>entomophila</i> and <i>S.</i> <i>proteamaculans</i>, have been identified and are being used as commercial biocontrol agents. The main virulence determinants of these <i>Serratia</i> strains, an Anti-feeding-prophage and an ABC-toxin-complex, are encoded on a 153-kb conjugative plasmid pADAP. Recently 75 <i>Serratia</i> strains with atypical disease phenology were sequenced with the goal of defining evolutionary points of divergent between plasmid variants and define potential co-evolution between plasmid and host. Phylogenetic analysis of the conserved plasmid “backbone”, residing between a conserved integrase (Int2) and the end of a conjugative pili cluster (PilL), revealed clustering of all the <i>S. entomophila</i> plasmids. Within the predicted backbone region, several intergenic replication and conjugation regions contained DNA inserts, one of which, positioned between TraG and TraC, demarcates chronic disease related plasmids from the non-chronic plasmids. These inserted regions were used as a marker to track the evolutionary divergence between the plasmids variants. A key finding was that all ABC-toxin-complex variants are co-located with a fimbria cluster, eluding to a role of fimbriae for the proper functionality of the ABC-toxin-complex. <br> <b>Keywords:</b> Insecticidal activity, plasmids, evolutionary divergence, horizontal gene transfer, pan-genome, genome wide association study, grass grub, pADAP, Sep, Afp. <br>
DOI: 10.6084/m9.figshare.12736226.v1
title: Sequence Assembly and Base composition

description: Assembly note including failure of CR Base composition table
DOI: 10.6084/m9.figshare.12736232.v1
title: Bankit

description: Sqn<br>Biosample tableSRA table
DOI: 10.25400/lincolnuninz.12736217.v1
title: Evolutionary divergence of the insect disease-encoding Serratia plasmid pADAP Supplementary Materials

description: Documents in support of statements made in the PhD thesis "Evolutionary divergence of the insect disease-encoding <i>Serratia</i> plasmid pADAP" by Thomas Lesley Sitter<br>Abstract for the thesis<br>The larvae of the New Zealand grass-grub (<i>Costelytra givenii</i>), cause significant damage to New Zealand’s pastures. Two diseases of grass-grub larvae, instigated by strains of <i>Serratia</i> <i>entomophila</i> and <i>S.</i> <i>proteamaculans</i>, have been identified and are being used as commercial biocontrol agents. The main virulence determinants of these <i>Serratia</i> strains, an Anti-feeding-prophage and an ABC-toxin-complex, are encoded on a 153-kb conjugative plasmid pADAP. Recently 75 <i>Serratia</i> strains with atypical disease phenology were sequenced with the goal of defining evolutionary points of divergent between plasmid variants and define potential co-evolution between plasmid and host. Phylogenetic analysis of the conserved plasmid “backbone”, residing between a conserved integrase (Int2) and the end of a conjugative pili cluster (PilL), revealed clustering of all the <i>S. entomophila</i> plasmids. Within the predicted backbone region, several intergenic replication and conjugation regions contained DNA inserts, one of which, positioned between TraG and TraC, demarcates chronic disease related plasmids from the non-chronic plasmids. These inserted regions were used as a marker to track the evolutionary divergence between the plasmids variants. A key finding was that all ABC-toxin-complex variants are co-located with a fimbria cluster, eluding to a role of fimbriae for the proper functionality of the ABC-toxin-complex. <br> <b>Keywords:</b> Insecticidal activity, plasmids, evolutionary divergence, horizontal gene transfer, pan-genome, genome wide association study, grass grub, pADAP, Sep, Afp. <br>
DOI: 10.6084/m9.figshare.12736199
title: Saturation

description: AA saturationPCGs_N saturation
DOI: 10.6084/m9.figshare.12736199.v1
title: Saturation

description: AA saturationPCGs_N saturation
DOI: 10.23641/asha.12735935
title: IPS in healthy adults (Bhutada et al., 2020)

description: <b>Purpose:</b> The purpose of this study was to investigate factors influencing the initiation of pharyngeal swallow (IPS) in healthy, nondysphagic adults.<b>Method:</b> A total of 195 healthy participants ranging in age from 21 to 89 years participated in a modified barium swallow study. IPS was quantified using the Modified Barium Swallow Impairment Profile standardized scoring system across nine swallowing tasks observed in the lateral viewing plane for each participant.<b>Results:</b> Large variability for bolus head location at time of hyoid burst (IPS) was observed within this healthy cohort, ranging from the ramus of the mandible to the pyriform sinuses. Significant effects of bolus volume, viscosity, sex, and race were also observed.<b>Conclusion: </b>Study findings indicate that IPS is variable in healthy adults and influenced by volume, viscosity, sex, and race. Thus, variability in IPS may be considered typical in otherwise nondysphagic adults. The clinical significance of high Modified Barium Swallow Impairment Profile IPS scores in dysphagic patients, therefore, must be considered within the context of other swallowing impairments.<br><b>Supplemental Material S1.</b> Summary of regression analysis for variables predicting IPS scores across swallow tasks for age category, sex and race (Caucasian; African American).<br><b>Supplemental Material S2. </b>Odds ratios (95% confidence interval [lower bound, upper bound]) of IPS scores across swallow tasks for age category, sex and race (Caucasian; African American).<br>Bhutada, A. M., Dey, R., Martin-Harris, B., & Garand, K. L. (2020). Factors influencing initiation of pharyngeal swallow in healthy adults.<i> American Journal of Speech-Language Pathology.</i> Advance online publication. https://doi.org/10.1044/2020_AJSLP-20-00027
DOI: 10.23641/asha.12735935.v1
title: IPS in healthy adults (Bhutada et al., 2020)

description: <b>Purpose:</b> The purpose of this study was to investigate factors influencing the initiation of pharyngeal swallow (IPS) in healthy, nondysphagic adults.<b>Method:</b> A total of 195 healthy participants ranging in age from 21 to 89 years participated in a modified barium swallow study. IPS was quantified using the Modified Barium Swallow Impairment Profile standardized scoring system across nine swallowing tasks observed in the lateral viewing plane for each participant.<b>Results:</b> Large variability for bolus head location at time of hyoid burst (IPS) was observed within this healthy cohort, ranging from the ramus of the mandible to the pyriform sinuses. Significant effects of bolus volume, viscosity, sex, and race were also observed.<b>Conclusion: </b>Study findings indicate that IPS is variable in healthy adults and influenced by volume, viscosity, sex, and race. Thus, variability in IPS may be considered typical in otherwise nondysphagic adults. The clinical significance of high Modified Barium Swallow Impairment Profile IPS scores in dysphagic patients, therefore, must be considered within the context of other swallowing impairments.<br><b>Supplemental Material S1.</b> Summary of regression analysis for variables predicting IPS scores across swallow tasks for age category, sex and race (Caucasian; African American).<br><b>Supplemental Material S2. </b>Odds ratios (95% confidence interval [lower bound, upper bound]) of IPS scores across swallow tasks for age category, sex and race (Caucasian; African American).<br>Bhutada, A. M., Dey, R., Martin-Harris, B., & Garand, K. L. (2020). Factors influencing initiation of pharyngeal swallow in healthy adults.<i> American Journal of Speech-Language Pathology.</i> Advance online publication. https://doi.org/10.1044/2020_AJSLP-20-00027
DOI: 10.23641/asha.12735875
title: Speech amplification devices for hypophonia (Knowles et al., 2020)

description: <b>Purpose: </b>This study compared the performance of three amplification devices hypothesized to improve speech communication in individuals with hypophonia (HP), as well as to identify individuals’ device preferences.<b>Method: </b>Twenty-two individuals with HP and their primary communication partners participated in a cross-over design study comparing three different speech amplification devices: a wired portable amplifier (Device A), a wireless stationary amplifier (Device B), and a one-way personal communication system (Device C). Participants attended one laboratory visit followed by 1-week trial periods with each device. At the first visit, HP participants completed speech tasks with and without the devices, in quiet and in noise. Following the in-laboratory test period, participants trialed each device at home for approximately 1 week per device. Following completion of the study, participants indicated whether or not they would like to continue using a device.<b>Results: </b>Overall, in the presence of noise, all three devices demonstrated significant improvements in speech-to-noise levels and speech intelligibility compared to no device. A clear device hierarchy emerged such that the personal communication device (Device C) was associated with significantly better speech outcomes compared to the other two devices. The majority of participants elected to continue using a device at the completion of the study. Device preferences, however, did not clearly reflect the objective device hierarchy that was found for the objective speech measures. Each of the three devices was selected as a preferred device by at least three participants at the completion of the study.<b>Conclusion: </b>Results from this study demonstrated clear differences in device performance in three distinct forms of amplification devices for individuals with HP. Findings suggest that amplification device use may be beneficial for this clinical population and underscore the potential to improve device availability and device selection criteria in future research.<b><br></b><b>Supplemental Material S1. </b>Pairwise comparisons for the speech-to-noise (SNR) model results.<br><b>Supplemental Material S2. </b>Pairwise comparisons for the familiar listener intelligibility model results.<br><b>Supplemental Material S3. </b>Pairwise comparisons for the naïve listener intelligibility model results.<br>Knowles, T., Adams, S. G., Page, A., Cushnie-Sparrow, D., & Jog, M. (2020). A comparison of speech amplification and personal communication devices for hypophonia.<i> Journal of Speech, Language, and Hearing Research.</i> https://doi.org/10.1044/2020_JSLHR-20-00085
DOI: 10.23641/asha.12735875.v1
title: Speech amplification devices for hypophonia (Knowles et al., 2020)

description: <b>Purpose: </b>This study compared the performance of three amplification devices hypothesized to improve speech communication in individuals with hypophonia (HP), as well as to identify individuals’ device preferences.<b>Method: </b>Twenty-two individuals with HP and their primary communication partners participated in a cross-over design study comparing three different speech amplification devices: a wired portable amplifier (Device A), a wireless stationary amplifier (Device B), and a one-way personal communication system (Device C). Participants attended one laboratory visit followed by 1-week trial periods with each device. At the first visit, HP participants completed speech tasks with and without the devices, in quiet and in noise. Following the in-laboratory test period, participants trialed each device at home for approximately 1 week per device. Following completion of the study, participants indicated whether or not they would like to continue using a device.<b>Results: </b>Overall, in the presence of noise, all three devices demonstrated significant improvements in speech-to-noise levels and speech intelligibility compared to no device. A clear device hierarchy emerged such that the personal communication device (Device C) was associated with significantly better speech outcomes compared to the other two devices. The majority of participants elected to continue using a device at the completion of the study. Device preferences, however, did not clearly reflect the objective device hierarchy that was found for the objective speech measures. Each of the three devices was selected as a preferred device by at least three participants at the completion of the study.<b>Conclusion: </b>Results from this study demonstrated clear differences in device performance in three distinct forms of amplification devices for individuals with HP. Findings suggest that amplification device use may be beneficial for this clinical population and underscore the potential to improve device availability and device selection criteria in future research.<b><br></b><b>Supplemental Material S1. </b>Pairwise comparisons for the speech-to-noise (SNR) model results.<br><b>Supplemental Material S2. </b>Pairwise comparisons for the familiar listener intelligibility model results.<br><b>Supplemental Material S3. </b>Pairwise comparisons for the naïve listener intelligibility model results.<br>Knowles, T., Adams, S. G., Page, A., Cushnie-Sparrow, D., & Jog, M. (2020). A comparison of speech amplification and personal communication devices for hypophonia.<i> Journal of Speech, Language, and Hearing Research.</i> https://doi.org/10.1044/2020_JSLHR-20-00085
DOI: 10.6084/m9.figshare.12735860
title: Differentially regulated genes E14.5 spial cord NFIX KO vs WT

description: The rationale behind this profiling experiment was to understand transcriptional changes arising in the developing spinal cord in the absence of <i>Nfix. </i>To do this, <i>Nfix<sup>-/-</sup></i> mice and their wild-type littermates were used in this study. These mice were maintained on a C57Bl/6J genetic background. Heterozygous male and female mice were placed together overnight to produce time-mated litters. The presence of a vaginal plug the following day indicated a successful mating was likely, and this was designated E0.5. Pregnant dams were euthanized by cervical dislocation. Embryos were removed and placed on ice. Whole spinal cords were dissected from E14.5 <i>Nfix<sup>-/-</sup></i> and wild-type mouse embryos and snap frozen using dry ice. An RNeasy Micro Kit (QIAGEN) was used to extract total RNA from these samples, which were then diluted to 80 ng/μL and sent to the Ramaciotti Centre (University of New South Wales, Australia) for microarray analysis on a Mouse Transcriptome Array 2.0ST (Affymetrix). Raw microarray data in the form of .CEL files were received from the Ramaciotti Centre and initially processed by running an SST-RMA (gene level) analysis on all samples using the Affymetrix Expression Console software (build 1.4.1.46). The resulting .CHP files were then imported into the Affymetrix Transcription Analysis Console (TAC) software and sample files were compared in differential gene expression analyses between <i>Nfix<sup>-/-</sup></i> and wild-type samples. Algorithm parameters selected included: genome version mm10, one-way between-subject ANOVA (unpaired) and ANOVA <i>p</i>-value (condition pair) &lt;0.05. Differential gene expression analyses were performed using Affymetrix Transcription Analysis Console (TAC) software. Gene expression levels between <i>Nfix<sup>-/-</sup></i> and wild-type samples were compared using a one-way between-subject ANOVA (unpaired) and corrected for FDR. A <i>p-</i>value &lt;0.05 denoted a statistically significant difference in gene expression between samples. A fold change cut-off for differential expression of &gt; ± 1.5 was also used to stratify differentially expressed genes.
DOI: 10.6084/m9.figshare.12735860.v1
title: Differentially regulated genes E14.5 spial cord NFIX KO vs WT

description: The rationale behind this profiling experiment was to understand transcriptional changes arising in the developing spinal cord in the absence of <i>Nfix. </i>To do this, <i>Nfix<sup>-/-</sup></i> mice and their wild-type littermates were used in this study. These mice were maintained on a C57Bl/6J genetic background. Heterozygous male and female mice were placed together overnight to produce time-mated litters. The presence of a vaginal plug the following day indicated a successful mating was likely, and this was designated E0.5. Pregnant dams were euthanized by cervical dislocation. Embryos were removed and placed on ice. Whole spinal cords were dissected from E14.5 <i>Nfix<sup>-/-</sup></i> and wild-type mouse embryos and snap frozen using dry ice. An RNeasy Micro Kit (QIAGEN) was used to extract total RNA from these samples, which were then diluted to 80 ng/μL and sent to the Ramaciotti Centre (University of New South Wales, Australia) for microarray analysis on a Mouse Transcriptome Array 2.0ST (Affymetrix). Raw microarray data in the form of .CEL files were received from the Ramaciotti Centre and initially processed by running an SST-RMA (gene level) analysis on all samples using the Affymetrix Expression Console software (build 1.4.1.46). The resulting .CHP files were then imported into the Affymetrix Transcription Analysis Console (TAC) software and sample files were compared in differential gene expression analyses between <i>Nfix<sup>-/-</sup></i> and wild-type samples. Algorithm parameters selected included: genome version mm10, one-way between-subject ANOVA (unpaired) and ANOVA <i>p</i>-value (condition pair) &lt;0.05. Differential gene expression analyses were performed using Affymetrix Transcription Analysis Console (TAC) software. Gene expression levels between <i>Nfix<sup>-/-</sup></i> and wild-type samples were compared using a one-way between-subject ANOVA (unpaired) and corrected for FDR. A <i>p-</i>value &lt;0.05 denoted a statistically significant difference in gene expression between samples. A fold change cut-off for differential expression of &gt; ± 1.5 was also used to stratify differentially expressed genes.
DOI: 10.6084/m9.figshare.12735791
title: Impact of 2019–2020 mega-fires on Australian fauna habitat

description: This r code creates figure 2 from MS.
DOI: 10.6084/m9.figshare.12735791.v1
title: Impact of 2019–2020 mega-fires on Australian fauna habitat

description: This r code creates figure 2 from MS.
DOI: 10.6084/m9.figshare.12735692
title: FishingForPlasmids_databases

description: This repository contains blastn databases part of the Fishing For Plasmids tool. More information about the tool and how to use the databases is available on: https://github.com/Visser-M/FishingForPlasmids.git<br>