cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10006595
title: Ixodes scapularis 5'-COI DNA barcode sequences

description: 5'-COI DNA barcode multiple sequence alignment for deer tick (Ixodes scapularis) used in Phillips et al. (submitted)
DOI: 10.6084/m9.figshare.10006595.v1
title: Ixodes scapularis 5'-COI DNA barcode sequences

description: 5'-COI DNA barcode multiple sequence alignment for deer tick (Ixodes scapularis) used in Phillips et al. (submitted)
DOI: 10.6084/m9.figshare.10006625.v1
title: Genetic interactions derived from high-throughput phenotyping of 7,350 yeast cell cycle mutants

description: This dataset is derived from high-throughput phenotyping of over 7,000 yeast cell cycle mutants on six different media types. Multiple independent biological replicates (average of 12) were created for every possible double mutant combination of 36 cell cycle genes. Those mutants were phenotyped by measuring growth rates over time on six different media types.
DOI: 10.6084/m9.figshare.10006625.v2
title: Genetic interactions derived from high-throughput phenotyping of 7,350 yeast cell cycle mutants

description: This dataset is derived from high-throughput phenotyping of over 7,000 yeast cell cycle mutants on six different media types. Multiple independent biological replicates (average of 12) were created for every possible double mutant combination of 36 cell cycle genes. Those mutants were phenotyped by measuring growth rates over time on six different media types.
DOI: 10.6084/m9.figshare.10006571
title: Clinical features and natural history of idiopathic peptic ulcers: a retrospective case–control study

description: <b>Objectives:</b> Peptic ulcer disease (PUD) is still common worldwide and is characterized by high mortality and morbidity. Following the decline of <i>Helicobacter pylori</i> infection, the detection of idiopathic PUD (IPUD) has become more frequent, making diagnosis and treatment more difficult. In this study, the clinical features and natural history of IPUD were analyzed. <b>Methods:</b> This was a retrospective case‒control study conducted in a tertiary care setting (University of Sassari, Italy). Records of 9,212 patients undergoing upper endoscopy from 2002 to 2018 were analyzed. Following the exclusion of <i>H. pylori</i>, NSAIDs, and unusual PUD causes, the remaining were labelled as IPUD. Cases (IPUD) and controls (PUD negative) were compared, adjusting for several covariates through multivariate logistic regression models. <b>Results:</b> Among 380 PUD, 95 were considered IPUD. The proportion rose over the study period in contrast to the decline of <i>H. pylori</i>-PUD. Factors significantly associated with IPUD, after adjusting for all covariates, were age (OR, 3.520; 95% CI, 1.634 − 7.585), male sex (OR, 3.126; 95% CI, 1.888 − 5.176), hospitalization (OR, 2.968; 95% CI, 1.926 − 4.575), and number of medications (OR, 2.808; 95% CI, 1.178 − 6.735). A clinical history positive for PUD was the major risk associated with IPUD (OR, 3.729; 95% CI, 2.050 − 6.785). Patients with IPUD were treated with the highest proton pump inhibitor (PPI) dose for 40–60 days. Follow up endoscopy showed a cure rate of 97.6%. <b>Conclusion:</b> The relative proportion of IPUD is increasing in our population in contrast to the drop of <i>H. pylori</i>-PUD. Treatment with high-dose PPI, and for a long duration, heals IPUD and protects from recurrence.
DOI: 10.6084/m9.figshare.10006571.v1
title: Clinical features and natural history of idiopathic peptic ulcers: a retrospective case–control study

description: <b>Objectives:</b> Peptic ulcer disease (PUD) is still common worldwide and is characterized by high mortality and morbidity. Following the decline of <i>Helicobacter pylori</i> infection, the detection of idiopathic PUD (IPUD) has become more frequent, making diagnosis and treatment more difficult. In this study, the clinical features and natural history of IPUD were analyzed. <b>Methods:</b> This was a retrospective case‒control study conducted in a tertiary care setting (University of Sassari, Italy). Records of 9,212 patients undergoing upper endoscopy from 2002 to 2018 were analyzed. Following the exclusion of <i>H. pylori</i>, NSAIDs, and unusual PUD causes, the remaining were labelled as IPUD. Cases (IPUD) and controls (PUD negative) were compared, adjusting for several covariates through multivariate logistic regression models. <b>Results:</b> Among 380 PUD, 95 were considered IPUD. The proportion rose over the study period in contrast to the decline of <i>H. pylori</i>-PUD. Factors significantly associated with IPUD, after adjusting for all covariates, were age (OR, 3.520; 95% CI, 1.634 − 7.585), male sex (OR, 3.126; 95% CI, 1.888 − 5.176), hospitalization (OR, 2.968; 95% CI, 1.926 − 4.575), and number of medications (OR, 2.808; 95% CI, 1.178 − 6.735). A clinical history positive for PUD was the major risk associated with IPUD (OR, 3.729; 95% CI, 2.050 − 6.785). Patients with IPUD were treated with the highest proton pump inhibitor (PPI) dose for 40–60 days. Follow up endoscopy showed a cure rate of 97.6%. <b>Conclusion:</b> The relative proportion of IPUD is increasing in our population in contrast to the drop of <i>H. pylori</i>-PUD. Treatment with high-dose PPI, and for a long duration, heals IPUD and protects from recurrence.
DOI: 10.6084/m9.figshare.10006541
title: Amp_res_Ecoli_data

description: forward raw reads - E.coli amp resistant
DOI: 10.6084/m9.figshare.10006523
title: Study 2 dataset

description: Dataset of the Study 2
DOI: 10.6084/m9.figshare.10006625.v4
title: Genetic interactions derived from high-throughput phenotyping of 7,350 yeast cell cycle mutants

description: This dataset is derived from high-throughput phenotyping of over 7,000 yeast cell cycle mutants on six different media types. Multiple independent biological replicates (average of 12) were created for every possible double mutant combination of 36 cell cycle genes. Those mutants were phenotyped by measuring growth rates over time on six different media types.
DOI: 10.6084/m9.figshare.10006520
title: Study 1 data

description: Dataset from Study 1 - development of the Importance and Perception of the Character Strengths Scale
DOI: 10.6084/m9.figshare.10006523.v1
title: Study 2 dataset

description: Dataset of the Study 2
DOI: 10.6084/m9.figshare.10006418
title: Supplemental files_Paul Katongole et al_v2.XLSX

description: We determined the different phylogenetic groups of UPEC and their antimicrobial susceptibility patterns
DOI: 10.6084/m9.figshare.10006412
title: R script for simulation study from Effects of marker type and filtering criteria on <i>Q</i><sub>ST</sub>-<i>F</i><sub>ST</sub> comparisons

description: Comparative studies of quantitative and neutral genetic differentiation (<i>Q</i><sub>ST</sub>-<i>F</i><sub>ST</sub> tests) provide means to detect adaptive population differentiation. However, Q<sub>ST</sub>-<i>F</i><sub>ST</sub> tests can be overly liberal if the markers used deflate <i>F</i><sub>ST</sub> below its expectation, or overly conservative if methodological biases lead to inflated <i>F</i><sub>ST</sub> estimates. We investigated how marker type and filtering criteria for marker selection influence <i>Q</i><sub>ST</sub>-<i>F</i><sub>ST</sub> comparisons through their effects on <i>F</i><sub>ST</sub> using simulations and empirical data on over 18 000 <i>in silico</i> genotyped microsatellites and 3.8 million SNP loci from four populations of nine-spined sticklebacks (<i>Pungitius pungitius</i>). Empirical and simulated data revealed that <i>F</i><sub>ST</sub> decreased with increasing marker variability, and was generally higher with SNPs than with microsatellites. The estimated baseline <i>F</i><sub>ST</sub> levels were also sensitive to filtering criteria for SNPs: both minor alleles and linkage disequilibrium (LD) pruning influenced <i>F</i><sub>ST</sub> estimation, as did marker ascertainment. However, in the case of stickleback data used here where <i>Q</i><sub>ST</sub> is high, the choice of marker type, their genomic location, ascertainment and filtering made little difference to outcomes of <i>Q</i><sub>ST</sub>-<i>F</i><sub>ST</sub> tests. Nevertheless, we recommend that <i>Q</i><sub>ST</sub>-<i>F</i><sub>ST</sub> tests using microsatellites should discard the most variable loci, and those using SNPs should pay attention to marker ascertainment and properly account for LD before filtering SNPs. This may be especially important when level of quantitative trait differentiation is low and levels of neutral differentiation high.
DOI: 10.6084/m9.figshare.10006418.v1
title: Supplemental files_Paul Katongole et al_v2.XLSX

description: We determined the different phylogenetic groups of UPEC and their antimicrobial susceptibility patterns
DOI: 10.6084/m9.figshare.10006409
title: R script for selection analysis from Effects of marker type and filtering criteria on <i>Q</i><sub>ST</sub>-<i>F</i><sub>ST</sub> comparisons

description: Comparative studies of quantitative and neutral genetic differentiation (<i>Q</i><sub>ST</sub>-<i>F</i><sub>ST</sub> tests) provide means to detect adaptive population differentiation. However, Q<sub>ST</sub>-<i>F</i><sub>ST</sub> tests can be overly liberal if the markers used deflate <i>F</i><sub>ST</sub> below its expectation, or overly conservative if methodological biases lead to inflated <i>F</i><sub>ST</sub> estimates. We investigated how marker type and filtering criteria for marker selection influence <i>Q</i><sub>ST</sub>-<i>F</i><sub>ST</sub> comparisons through their effects on <i>F</i><sub>ST</sub> using simulations and empirical data on over 18 000 <i>in silico</i> genotyped microsatellites and 3.8 million SNP loci from four populations of nine-spined sticklebacks (<i>Pungitius pungitius</i>). Empirical and simulated data revealed that <i>F</i><sub>ST</sub> decreased with increasing marker variability, and was generally higher with SNPs than with microsatellites. The estimated baseline <i>F</i><sub>ST</sub> levels were also sensitive to filtering criteria for SNPs: both minor alleles and linkage disequilibrium (LD) pruning influenced <i>F</i><sub>ST</sub> estimation, as did marker ascertainment. However, in the case of stickleback data used here where <i>Q</i><sub>ST</sub> is high, the choice of marker type, their genomic location, ascertainment and filtering made little difference to outcomes of <i>Q</i><sub>ST</sub>-<i>F</i><sub>ST</sub> tests. Nevertheless, we recommend that <i>Q</i><sub>ST</sub>-<i>F</i><sub>ST</sub> tests using microsatellites should discard the most variable loci, and those using SNPs should pay attention to marker ascertainment and properly account for LD before filtering SNPs. This may be especially important when level of quantitative trait differentiation is low and levels of neutral differentiation high.
DOI: 10.6084/m9.figshare.10006394
title: Project Data from Social wasps are effective biocontrol agents of key lepidopteran crop pests

description: Experiment 1 & 2 datasets; wasp marking ID.
DOI: 10.6084/m9.figshare.10006403
title: R script for QST-FST analysis from Effects of marker type and filtering criteria on <i>Q</i><sub>ST</sub>-<i>F</i><sub>ST</sub> comparisons

description: Comparative studies of quantitative and neutral genetic differentiation (<i>Q</i><sub>ST</sub>-<i>F</i><sub>ST</sub> tests) provide means to detect adaptive population differentiation. However, Q<sub>ST</sub>-<i>F</i><sub>ST</sub> tests can be overly liberal if the markers used deflate <i>F</i><sub>ST</sub> below its expectation, or overly conservative if methodological biases lead to inflated <i>F</i><sub>ST</sub> estimates. We investigated how marker type and filtering criteria for marker selection influence <i>Q</i><sub>ST</sub>-<i>F</i><sub>ST</sub> comparisons through their effects on <i>F</i><sub>ST</sub> using simulations and empirical data on over 18 000 <i>in silico</i> genotyped microsatellites and 3.8 million SNP loci from four populations of nine-spined sticklebacks (<i>Pungitius pungitius</i>). Empirical and simulated data revealed that <i>F</i><sub>ST</sub> decreased with increasing marker variability, and was generally higher with SNPs than with microsatellites. The estimated baseline <i>F</i><sub>ST</sub> levels were also sensitive to filtering criteria for SNPs: both minor alleles and linkage disequilibrium (LD) pruning influenced <i>F</i><sub>ST</sub> estimation, as did marker ascertainment. However, in the case of stickleback data used here where <i>Q</i><sub>ST</sub> is high, the choice of marker type, their genomic location, ascertainment and filtering made little difference to outcomes of <i>Q</i><sub>ST</sub>-<i>F</i><sub>ST</sub> tests. Nevertheless, we recommend that <i>Q</i><sub>ST</sub>-<i>F</i><sub>ST</sub> tests using microsatellites should discard the most variable loci, and those using SNPs should pay attention to marker ascertainment and properly account for LD before filtering SNPs. This may be especially important when level of quantitative trait differentiation is low and levels of neutral differentiation high.
DOI: 10.6084/m9.figshare.10006394.v1
title: Project Data from Social wasps are effective biocontrol agents of key lepidopteran crop pests

description: Experiment 1 & 2 datasets; wasp marking ID.
DOI: 10.6084/m9.figshare.10006391
title: Supplementary Figure & Tables from Social wasps are effective biocontrol agents of key lepidopteran crop pests

description: Figure S1 (experimental setup); Table S1 (random effect variance); Table S2 (temperature effects); Table S3 (model 4 results).
DOI: 10.6084/m9.figshare.10006403.v1
title: R script for QST-FST analysis from Effects of marker type and filtering criteria on <i>Q</i><sub>ST</sub>-<i>F</i><sub>ST</sub> comparisons

description: Comparative studies of quantitative and neutral genetic differentiation (<i>Q</i><sub>ST</sub>-<i>F</i><sub>ST</sub> tests) provide means to detect adaptive population differentiation. However, Q<sub>ST</sub>-<i>F</i><sub>ST</sub> tests can be overly liberal if the markers used deflate <i>F</i><sub>ST</sub> below its expectation, or overly conservative if methodological biases lead to inflated <i>F</i><sub>ST</sub> estimates. We investigated how marker type and filtering criteria for marker selection influence <i>Q</i><sub>ST</sub>-<i>F</i><sub>ST</sub> comparisons through their effects on <i>F</i><sub>ST</sub> using simulations and empirical data on over 18 000 <i>in silico</i> genotyped microsatellites and 3.8 million SNP loci from four populations of nine-spined sticklebacks (<i>Pungitius pungitius</i>). Empirical and simulated data revealed that <i>F</i><sub>ST</sub> decreased with increasing marker variability, and was generally higher with SNPs than with microsatellites. The estimated baseline <i>F</i><sub>ST</sub> levels were also sensitive to filtering criteria for SNPs: both minor alleles and linkage disequilibrium (LD) pruning influenced <i>F</i><sub>ST</sub> estimation, as did marker ascertainment. However, in the case of stickleback data used here where <i>Q</i><sub>ST</sub> is high, the choice of marker type, their genomic location, ascertainment and filtering made little difference to outcomes of <i>Q</i><sub>ST</sub>-<i>F</i><sub>ST</sub> tests. Nevertheless, we recommend that <i>Q</i><sub>ST</sub>-<i>F</i><sub>ST</sub> tests using microsatellites should discard the most variable loci, and those using SNPs should pay attention to marker ascertainment and properly account for LD before filtering SNPs. This may be especially important when level of quantitative trait differentiation is low and levels of neutral differentiation high.
DOI: 10.6084/m9.figshare.10006388
title: Supplementary tables - performance of swarms in additional scenarios from Testing the limits of pheromone stigmergy in high-density robot swarms

description: Logistic fits to performance curves
DOI: 10.6084/m9.figshare.12866585.v1
title: Spatial density of adolescents aged 14 years old, victims of dental: a longitudinal study

description: <b>Abstract</b> <b>Background/Aim: </b>Knowledge about the spatial density of the domiciles of dental trauma victims can enable the identification of the most vulnerable areas and contribute to the planning of prevention, promotion, control and treatment actions, focusing on the most affected areas. The study aimed to analyze the spatial density of domiciles of 14-year-old adolescents, victims of dental trauma, in the city of Diamantina, southeastern Brazil, after two years of follow-up. <b></b> <b>Material and Methods: </b>This longitudinal study was carried out with 584 adolescents between 2013 and 2015. Dental trauma (Andreasen classification), overjet and lip protection (O'Mullane) were assessed by two examiners trained and calibrated (K&gt; 0.70). Information about binge drinking was collected among the adolescents through the Alcohol Use Disorders Identification Test and sociodemographic indicators were obtained through a questionnaire answered by the adolescent’s caregivers. The spatial analyses were performed to evaluate the spatial density of adolescents with dental trauma and the independent variables of interest according to the domicile using the Ripley’s K function and Kernel Map. <b>Results</b>: The Ripley's K function showed spatial aggregation of the domiciles of adolescent victims of dental trauma in relation to males, binge drinking and overjet, with a confidence level of 95%. The higher density of domiciles with adolescents with two or more traumatized teeth was found in the northeast region of the city. Boys were the most affected, their homes were located in the north, northwest and southeast regions at the baseline and follow-up. The largest density of domiciles of adolescents with overjet greater than 5 mm and inadequate lip protection was in the northeast region. Similar spatial distribution was identified for binge drinking for both years. <b>Conclusion: </b>The majority of adolescents with dental trauma lived in the northeast and southeast regions, characterized by high population density and higher social vulnerability.<br>
DOI: 10.6084/m9.figshare.10006058
title: MOESM2 of Surface rupture and characteristics of a fault associated with the 2011 and 2016 earthquakes in the southern Abukuma Mountains, northeastern Japan, triggered by the Tohoku-Oki earthquake

description: Additional file 2. KML files showing locations of features associated with the 2011 and 2016 events. Red pins indicate tectonic surface ruptures, green pins indicate other minor cracks, and yellow stars indicate the locations of FFZs.
DOI: 10.6084/m9.figshare.10006058.v1
title: MOESM2 of Surface rupture and characteristics of a fault associated with the 2011 and 2016 earthquakes in the southern Abukuma Mountains, northeastern Japan, triggered by the Tohoku-Oki earthquake

description: Additional file 2. KML files showing locations of features associated with the 2011 and 2016 events. Red pins indicate tectonic surface ruptures, green pins indicate other minor cracks, and yellow stars indicate the locations of FFZs.
DOI: 10.6084/m9.figshare.10006010
title: MOESM1 of Genomic analysis on broiler-associated Clostridium perfringens strains and exploratory caecal microbiome investigation reveals key factors linked to poultry necrotic enteritis

description: Additional file 1. Supplementary tables.
DOI: 10.6084/m9.figshare.10006010.v1
title: MOESM1 of Genomic analysis on broiler-associated Clostridium perfringens strains and exploratory caecal microbiome investigation reveals key factors linked to poultry necrotic enteritis

description: Additional file 1. Supplementary tables.
DOI: 10.6084/m9.figshare.10005971
title: Data for 2019JG005240

description: This dataset belongs to a JGR-Biogeosciences manuscript entitled 'Isotope constraints on the sources of particulate organics in a subtropical deep reservoir'.
DOI: 10.6084/m9.figshare.10005974
title: MOESM1 of First report of hare treponematosis seroprevalence of European brown hares (Lepus europaeus) in the Czech Republic: seroprevalence negatively correlates with altitude of sampling areas

description: Additional file 1: Table S1. A list of European brown hares (Lepus europaeus) sampled in the Czech Republic, 2015 to 2017, that were tularemia-negative. Hares were tested for the presence of hare treponematosis by the TPHA and FTA-ABS tests. Abbreviations: a.s.l.: above sea level; non: non-evaluable; P: positive; N: negative; 4+: strongly reacting in both dilutions; 3+: strongly reacting in 1:8 dilution, weakly reacting in 1:64 dilution; 2+: weakly reacting in both dilutions; 1+: weakly reacting solely in 1:8 dilution.
DOI: 10.6084/m9.figshare.10005974.v1
title: MOESM1 of First report of hare treponematosis seroprevalence of European brown hares (Lepus europaeus) in the Czech Republic: seroprevalence negatively correlates with altitude of sampling areas

description: Additional file 1: Table S1. A list of European brown hares (Lepus europaeus) sampled in the Czech Republic, 2015 to 2017, that were tularemia-negative. Hares were tested for the presence of hare treponematosis by the TPHA and FTA-ABS tests. Abbreviations: a.s.l.: above sea level; non: non-evaluable; P: positive; N: negative; 4+: strongly reacting in both dilutions; 3+: strongly reacting in 1:8 dilution, weakly reacting in 1:64 dilution; 2+: weakly reacting in both dilutions; 1+: weakly reacting solely in 1:8 dilution.
DOI: 10.6084/m9.figshare.10005977
title: MOESM2 of First report of hare treponematosis seroprevalence of European brown hares (Lepus europaeus) in the Czech Republic: seroprevalence negatively correlates with altitude of sampling areas

description: Additional file 2: Table S2. The correlation between true seroprevalence of TPeL and altitude median estimated at three levels: (1) grouped districts; (2) districts; (3) villages grouped according to the altitude. Eight out of 12 districts (for grouped districts and districts) and 27 out of 59 altitude levels (i.e. 39 out of 73 villages) were selected for the correlation analyses, the criterion was ≥20 and ≥ 4 of samples available, respectively. A negative correlation (r &lt; − 0.5) between estimated true seroprevalence of TPeL and altitude median was observed at the district level. Abbreviations: No: number; CI: confidence interval; r: Pearson correlation coefficient; p: p value; BV: Břeclav; HB: Havlíčkův Brod; HO: Hodonín; PE: Pelhřimov; SY: Svitavy; TA: Tábor; UO: Ústí nad Orlicí; ZR: Žďár nad Sázavou.
DOI: 10.6084/m9.figshare.10005977.v1
title: MOESM2 of First report of hare treponematosis seroprevalence of European brown hares (Lepus europaeus) in the Czech Republic: seroprevalence negatively correlates with altitude of sampling areas

description: Additional file 2: Table S2. The correlation between true seroprevalence of TPeL and altitude median estimated at three levels: (1) grouped districts; (2) districts; (3) villages grouped according to the altitude. Eight out of 12 districts (for grouped districts and districts) and 27 out of 59 altitude levels (i.e. 39 out of 73 villages) were selected for the correlation analyses, the criterion was ≥20 and ≥ 4 of samples available, respectively. A negative correlation (r &lt; − 0.5) between estimated true seroprevalence of TPeL and altitude median was observed at the district level. Abbreviations: No: number; CI: confidence interval; r: Pearson correlation coefficient; p: p value; BV: Břeclav; HB: Havlíčkův Brod; HO: Hodonín; PE: Pelhřimov; SY: Svitavy; TA: Tábor; UO: Ústí nad Orlicí; ZR: Žďár nad Sázavou.