cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7087451.v1
title: A model of hardwood tree colonization among forest fragments: predicting migration across human-dominated landscapes

description: We developed a model of hardwood tree colonization in forest patches. We began with a basic model of species’ recruitment density calculated as a function of seed production and juvenile survivorship. Survivorship probability was expressed as a function of seed size, using seed-sowing data for a wide variety of species. To account for dispersal, we used an exponential distance-decay function based on empirical colonization data for species classified by dispersal mechanism and seed mass. The basic model reasonably predicted observed recruitment densities at or near forest edges, except for small seeded, wind-dispersed species with strong establishment constraints, for which it over-predicts. Our dispersal term yielded predictions that were not statistically different from observed colonization. However, species with large seeds and unspecialized dispersal mechanism appear to have distinct thresholds beyond which <i>no</i> dispersal occurs. Further research should better account for establishment constraints among small-seeded species, dispersal constraints among large-seeded species and unspecialized dispersers, and improve the dispersal functions to better reflect vectors such as birds. Nevertheless, the present model is adequate for the prediction of colonization probabilities in fragmented forests, requiring only an estimate of the abundance of source trees of a species and the mean inter-fragment distances.
DOI: 10.6084/m9.figshare.7087418
title: Sungazer ACTH and MAD data

description: ACTH Challenge conducted on 2 female and 1 male adult Sungazer lizards (Smaug giganteus). <br>Four enzyme immunoassays tested.<br>Also included is the mean absolute deviation van the baseline faecal glucocorticoid metabolite concentrations for each of the four tested enzyme immunoassays
DOI: 10.6084/m9.figshare.7087418.v1
title: Sungazer ACTH and MAD data

description: ACTH Challenge conducted on 2 female and 1 male adult Sungazer lizards (Smaug giganteus). <br>Four enzyme immunoassays tested.<br>Also included is the mean absolute deviation van the baseline faecal glucocorticoid metabolite concentrations for each of the four tested enzyme immunoassays
DOI: 10.6084/m9.figshare.7087415
title: Supplementary Material for: Distinct Clinical Factors in Hospitalized Patients with Diverticular Bleeding and Diverticulitis

description: <b><i>Background/Aims:</i></b> It is unclear why colonic diverticular bleeding and diverticulitis rarely coexist. This study compared the characteristics of these conditions. <b><i>Methods:</i></b> This single-center retrospective study examined 310 consecutive patients hospitalized with an episode of diverticular disease (cases) and outpatients without a diverticular episode (controls) from January 2012 to December 2015. We investigated distinct clinical factors in hospitalized patients with diverticular bleeding and diverticulitis. <b><i>Results:</i></b> We identified 183 patients with 263 episodes of diverticular bleeding and 127 patients with 135 episodes of diverticulitis during the study period. Patients with diverticular bleeding were significantly older than those with diverticulitis (median age 76 vs. 56 years) and had more cardiovascular disease, hypertension, diabetes, cerebrovascular disease, chronic kidney disease, lipid disorder, or a poorer performance status. Significantly more diverticular bleeding patients were taking antiplatelet drugs, anticoagulant drugs, proton pump inhibitors, or laxative agents. Multivariate analysis revealed that an age &gt; 65 years (OR 5.42), and antiplatelet agent use (OR 7.29) were more significant risk factors for diverticular bleeding than for diverticulitis. <b><i>Conclusions:</i></b> Elderly people using antiplatelet drugs may be more susceptible to diverticular bleeding than diverticulitis.
DOI: 10.6084/m9.figshare.7087376
title: Strube et al. subsequent testing data 2019-2020

description: Behavioral beadstask data and sociodemographic, clinical and neuropsychological characteristics for 252 participants analyzed in Strube et al. 2019.
DOI: 10.6084/m9.figshare.7087373
title: Vitamin D supplementation for the management of knee osteoarthritis: a systematic review of randomized controlled trials

description: Table describing the study design characteristics and baseline characteristics of patients included in studies
DOI: 10.6084/m9.figshare.7087373.v1
title: Vitamin D supplementation for the management of knee osteoarthritis: a systematic review of randomized controlled trials

description: Table describing the study design characteristics and baseline characteristics of patients included in studies
DOI: 10.6084/m9.figshare.7087376.v1
title: Excelmaster of beadstask data Strube et al 2019

description: Behavioral beadstask data and sociodemographic, clinical and neuropsychological characteristics for 252 participants analyzed in Strube et al. 2019.
DOI: 10.6084/m9.figshare.7087376.v3
title: Excelmaster of beadstask data Strube et al 2019

description: Behavioral beadstask data and sociodemographic, clinical and neuropsychological characteristics for 252 participants analyzed in Strube et al. 2019.
DOI: 10.6084/m9.figshare.7087376.v2
title: Excelmaster of beadstask data Strube et al 2019

description: Behavioral beadstask data and sociodemographic, clinical and neuropsychological characteristics for 252 participants analyzed in Strube et al. 2019.
DOI: 10.6084/m9.figshare.7087259
title: MOESM2 of Control of directionality of chromatin folding for the inter- and intra-domain contacts at the Tfap2c–Bmp7 locus

description: Additional file 2. Table S1. List of ENCODE files of the CTCF binding peaks used in the study. Table S2. List of the CRISPR target sequences and their genomic coordinates, using the mm9 assembly. Table S3. Combination of CRISPR targets used to introduce mutations in this study. The IDs of the targets are given in Additional File 2: Table S2. See also Additional File S1: Figure S4. Table S4. Primer pairs used to confirm the CRISPR mutations. Table S5. Primer pairs used for the qPCR assay. Table S6. Primers used to prepare the 4C-seq libraries. Table S7. List of the 4C-seq libraries prepared and analyzed in this study. The IDs of primers used for the 1st and 2nd PCR are given in Additional File 2: Table S6. Table S8. List of intervals utilized for counting mapped reads, and their coordinates using the mm9 assembly.
DOI: 10.6084/m9.figshare.7087259.v1
title: MOESM2 of Control of directionality of chromatin folding for the inter- and intra-domain contacts at the Tfap2c–Bmp7 locus

description: Additional file 2. Table S1. List of ENCODE files of the CTCF binding peaks used in the study. Table S2. List of the CRISPR target sequences and their genomic coordinates, using the mm9 assembly. Table S3. Combination of CRISPR targets used to introduce mutations in this study. The IDs of the targets are given in Additional File 2: Table S2. See also Additional File S1: Figure S4. Table S4. Primer pairs used to confirm the CRISPR mutations. Table S5. Primer pairs used for the qPCR assay. Table S6. Primers used to prepare the 4C-seq libraries. Table S7. List of the 4C-seq libraries prepared and analyzed in this study. The IDs of primers used for the 1st and 2nd PCR are given in Additional File 2: Table S6. Table S8. List of intervals utilized for counting mapped reads, and their coordinates using the mm9 assembly.
DOI: 10.6084/m9.figshare.7087127
title: Data from: Anti-predator defences of a bombardier beetle: is bombing essential for successful escape from frogs?

description: Sugiura (2018) Anti-predator defences of a bombardier beetle: is bombing essential for successful escape from frogs? PeerJ 6:e5942 http://dx.doi.org/10.7717/peerj.5942<br>
DOI: 10.6084/m9.figshare.7087127.v1
title: Data from: Anti-predator defences of a bombardier beetle: is bombing essential for successful escape from frogs?

description: Sugiura (2018) Anti-predator defences of a bombardier beetle: is bombing essential for successful escape from frogs? PeerJ 6:e5942 http://dx.doi.org/10.7717/peerj.5942<br>
DOI: 10.26180/5b9b27134050a
title: Data to support Fig 3 of the manuscript "Wide dynamic range of cellular flow through early αβ T-cell selection in the thymus"

description: The file contains mouse T cell receptor (TCR) sequences obtained by multiplex PCR amplification of cDNA molecules followed by Illumina sequencing. Sequences were aligned to the mouse genome using MIGEC software (see doi: 10.1038/nmeth.2960 for details). Sequences with a read count of &lt;3 were excluded. Except for the header row, each row contains information about a unique TCR nucleotide sequence. Columns 1-11 contain output from MIGEC software. Columns 12-15 contain information about sample origin, detailed as follows: column 12 "sample_id" is an identifier for the sample of origin; column 13 "tcr_b" specifies the TCR beta chain status of donor mouse ("poly" = C57BL/6 inbred mouse strain); column 14 “mouse” is an identifier for the individual mouse of origin and column 15 "subset" specifies the T cell subset of origin ("t_1" = Type A IELp thymocytes; "t_4" = CD4+ naive thymocytes; "t_8" = CD8+ naive thymocytes). For materials and methods refer to Wirasinha et al Immunol Cell Biol. 2018 Jul;96(6):553-561. doi: 10.1111/imcb.12047. PMID: 29726044.
DOI: 10.6084/m9.figshare.7087073
title: MATLAB results

description: Results of simulations for CO2 natural convection in dual porosity media.<br>the convention of names:Results_Ra number_Da number_xi_alpha*
DOI: 10.6084/m9.figshare.7087073.v1
title: MATLAB results

description: Results of simulations for CO2 natural convection in dual porosity media.<br>the convention of names:Results_Ra number_Da number_xi_alpha*
DOI: 10.6084/m9.figshare.7086920
title: Bowel Symptoms in HTLV-1

description: Bowel Symptoms in HTLV-1 infected individuals
DOI: 10.6084/m9.figshare.7086920.v1
title: Bowel Symptoms in HTLV-1

description: Bowel Symptoms in HTLV-1 infected individuals
DOI: 10.6084/m9.figshare.7087064
title: Dataset for: Latent trait shared parameter mixed-models for missing ecological momentary assessment data

description: Latent trait shared-parameter mixed-models (LTSPMM) for ecological momentary assessment (EMA) data containing missing values are developed in which data are collected in an intermittent manner. In such studies, data are often missing due to unanswered prompts. Using item response theory (IRT) models, a latent trait is used to represent the missing prompts and modeled jointly with a mixed-model for bivariate longitudinal outcomes. Both one- and two-parameter LTSPMMs are presented. These new models offer a unique way to analyze missing EMA data with many response patterns. Here, the proposed models represent missingness via a latent trait that corresponds to the students' "ability" to respond to the prompting device. Data containing more than 10,300 observations from an EMA study involving high-school students' positive and negative affect are presented. The latent trait representing missingness was a significant predictor of both positive affect and negative affect outcomes. The models are compared to a missing at random (MAR) mixed-model. A simulation study indicates that the proposed models can provide lower bias and increased efficiency compared to the standard MAR approach commonly used with intermittently missing longitudinal data.
DOI: 10.6084/m9.figshare.7086791
title: Walking trials (2x, C3D)

description: C3D file for the first walking trial
DOI: 10.6084/m9.figshare.7087064.v1
title: Dataset for: Latent trait shared parameter mixed-models for missing ecological momentary assessment data

description: Latent trait shared-parameter mixed-models (LTSPMM) for ecological momentary assessment (EMA) data containing missing values are developed in which data are collected in an intermittent manner. In such studies, data are often missing due to unanswered prompts. Using item response theory (IRT) models, a latent trait is used to represent the missing prompts and modeled jointly with a mixed-model for bivariate longitudinal outcomes. Both one- and two-parameter LTSPMMs are presented. These new models offer a unique way to analyze missing EMA data with many response patterns. Here, the proposed models represent missingness via a latent trait that corresponds to the students' "ability" to respond to the prompting device. Data containing more than 10,300 observations from an EMA study involving high-school students' positive and negative affect are presented. The latent trait representing missingness was a significant predictor of both positive affect and negative affect outcomes. The models are compared to a missing at random (MAR) mixed-model. A simulation study indicates that the proposed models can provide lower bias and increased efficiency compared to the standard MAR approach commonly used with intermittently missing longitudinal data.
DOI: 10.6084/m9.figshare.7086791.v1
title: Walking trial 1 (C3D)

description: C3D file for the first walking trial
DOI: 10.6084/m9.figshare.7086788
title: Standing calibration trial (C3D)

description: C3D file for the standing calibration trial
DOI: 10.6084/m9.figshare.7086788.v1
title: Standing calibration trial (C3D)

description: C3D file for the standing calibration trial
DOI: 10.26180/5b9abfe5687e3
title: Data- Gordon et al. PLoS Biology 2019

description: Data underlying the figures in Gordon et.al PLoS Biology 2019.Details in DataReadme file (including small correction from version 1).<br><br><br><b></b><i></i><sub></sub><sup></sup><br><b></b><i></i><sub></sub><sup></sup><b></b><i></i><sub></sub><sup></sup><b></b><i></i><sub></sub><sup></sup><b></b><i></i><sub></sub><sup></sup><b></b><i></i><sub></sub><sup></sup><br>
DOI: 10.6084/m9.figshare.7083494.v1
title: D.mel_sim_DP(1;Y).xlsx

description: Raw courtship frequency data for parents, reciprocal F1's, duplication hybrids, and overlapping strains.
DOI: 10.6084/m9.figshare.7083389
title: PopPUNK Listeria monocytogenes dataset

description: This is an example set of 128 Listeria monocytogenes genomes, reported in https://doi.org/10.1016/j.cmi.2016.12.008.<br>They are used to demonstrate the function of the software PopPUNK https://poppunk.readthedocs.io/
DOI: 10.6084/m9.figshare.7083386
title: TDE7n53g53

description: Sim data<br>
DOI: 10.6084/m9.figshare.7083389.v1
title: PopPUNK Listeria monocytogenes dataset

description: This is an example set of 128 Listeria monocytogenes genomes, reported in https://doi.org/10.1016/j.cmi.2016.12.008.<br>They are used to demonstrate the function of the software PopPUNK https://poppunk.readthedocs.io/
DOI: 10.6084/m9.figshare.7083386.v1
title: TDE7n53g53

description: Sim data<br>
DOI: 10.6084/m9.figshare.7083242
title: SynthAer - a synthetic dataset of semantically annotated aerial images

description: SynthAer is a dataset consisting of synthetic aerial images with pixel-level semantic annotations from a suburban scene generated using the 3D modelling tool Blender. SynthAer contains three time-of-day variations for each image - one for lighting conditions at dawn, one for midday, and one for dusk.
DOI: 10.6084/m9.figshare.7083254
title: R scripts for Poirier et al Food Microbiome datasetdataset

description: Graphical R scripts based on Phyloseq and ggplot packages for the analysis of Poirier et al Food microbiome dataset<br>
DOI: 10.6084/m9.figshare.7083242.v1
title: SynthAer - a synthetic dataset of semantically annotated aerial images

description: SynthAer is a dataset consisting of synthetic aerial images with pixel-level semantic annotations from a suburban scene generated using the 3D modelling tool Blender. SynthAer contains three time-of-day variations for each image - one for lighting conditions at dawn, one for midday, and one for dusk.
DOI: 10.6084/m9.figshare.7083209
title: POIRIER_ET_AL_DATASET_FOODMICROBIOME_V2.xlsx

description: Dataset associated with the publication Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: a comparative analysis with 16S rDNA V3-V4 amplicon sequencing.<br>
DOI: 10.6084/m9.figshare.7083164
title: Supplementary Material for: Evidence of Cross-Reactivity between Different Seed Storage Proteins from Hazelnut (<b><i>Corylus avellana</i></b>) and Walnut (<b><i>Juglans regia</i></b>) Using Recombinant Allergen Proteins

description: Seed storage proteins are extremely stable allergens in nuts, seeds, and legumes and are responsible for the most severe allergic reactions to these foods. The cross-reactivity between seed storage proteins from different sources has not been studied at a molecular level so far. This study aimed to ascertain the cross-reactivity between walnut and hazelnut seed storage proteins using recombinant allergens. Sera from 13 consecutive patients with severe primary walnut and/or hazelnut allergy and hypersensitive to both nuts were studied. IgE specific for rCor a 9, rCor a 14, and rJug r 1 was measured, and inhibition experiments were carried out by measuring IgE reactivity after absorption of patients’ sera with freshly prepared walnut extract. All 13 sera showed strong IgE reactivity against walnut 2S albumin, Jug r 1, 12 reacted to hazelnut 2S albumin, Cor a 14, and 8 to the hazelnut legumin, Cor a 9. In inhibition experiments, absorption of sera with whole walnut extract led to the complete disappearance of IgE reactivity to Jug r 1 in 12/13 cases, as expected, but also to the complete disappearance of specific IgE to Cor a 14 in 9/12 sera, and of IgE reactivity to Cor a 9 in 7/8. In the remaining cases a dramatic drop in IgE reactivity was observed. The study shows that patients primarily allergic to either walnut or hazelnut showing a skin or serological reactivity to the other nut also are potentially at risk of severe allergic reactions caused by cross-reactivity between 2S albumins and legumins.
DOI: 10.6084/m9.figshare.7083164.v1
title: Supplementary Material for: Evidence of Cross-Reactivity between Different Seed Storage Proteins from Hazelnut (<b><i>Corylus avellana</i></b>) and Walnut (<b><i>Juglans regia</i></b>) Using Recombinant Allergen Proteins

description: Seed storage proteins are extremely stable allergens in nuts, seeds, and legumes and are responsible for the most severe allergic reactions to these foods. The cross-reactivity between seed storage proteins from different sources has not been studied at a molecular level so far. This study aimed to ascertain the cross-reactivity between walnut and hazelnut seed storage proteins using recombinant allergens. Sera from 13 consecutive patients with severe primary walnut and/or hazelnut allergy and hypersensitive to both nuts were studied. IgE specific for rCor a 9, rCor a 14, and rJug r 1 was measured, and inhibition experiments were carried out by measuring IgE reactivity after absorption of patients’ sera with freshly prepared walnut extract. All 13 sera showed strong IgE reactivity against walnut 2S albumin, Jug r 1, 12 reacted to hazelnut 2S albumin, Cor a 14, and 8 to the hazelnut legumin, Cor a 9. In inhibition experiments, absorption of sera with whole walnut extract led to the complete disappearance of IgE reactivity to Jug r 1 in 12/13 cases, as expected, but also to the complete disappearance of specific IgE to Cor a 14 in 9/12 sera, and of IgE reactivity to Cor a 9 in 7/8. In the remaining cases a dramatic drop in IgE reactivity was observed. The study shows that patients primarily allergic to either walnut or hazelnut showing a skin or serological reactivity to the other nut also are potentially at risk of severe allergic reactions caused by cross-reactivity between 2S albumins and legumins.
DOI: 10.6084/m9.figshare.7082990
title: Supplementary Material for: Clear Liquids versus Polyethylene Glycol Preparation for Video Capsule Endoscopy of the Small Bowel: A Randomized Controlled Trial

description: <b><i>Background:</i></b> An effective bowel cleanse can improve the imaging quality of video capsule endoscopy (VCE). We aimed to further investigate the optimal small bowel cleanse method by comparing the efficacy of 4 L of clear liquids, 2 L of polyethylene glycol (PEG), and 4 L of PEG on the image quality of VCE. <b><i>Methods:</i></b> A randomized controlled, non-inferiority trial was performed comparing 4 L of clear liquids (Group A), 2 L of PEG (Group B), and 4 L of PEG (Group C). The primary endpoint was image quality between the groups. The secondary endpoints included patient tolerability and side effects. <b><i>Results:</i></b> Eighty-one patients were analyzed in group A, 84 patients were analyzed in group B, and 80 patients were analyzed in group C. Image quality scores revealed 4 L of clear liquids to be non-inferior to 2 L of PEG, and 2 L of PEG to be non-inferior to 4 L of PEG (<i>p</i> &lt; 0.0167). Group A had a lower difficulty of completion rate than Group B and Group C and a lower rate of side effects when compared to Group C (<i>p</i> &lt; 0.0167). <b><i>Conclusion:</i></b> Four liters of clear liquids should be considered a routine method for small bowel preparation prior to VCE.
DOI: 10.6084/m9.figshare.7082990.v1
title: Supplementary Material for: Clear Liquids versus Polyethylene Glycol Preparation for Video Capsule Endoscopy of the Small Bowel: A Randomized Controlled Trial

description: <b><i>Background:</i></b> An effective bowel cleanse can improve the imaging quality of video capsule endoscopy (VCE). We aimed to further investigate the optimal small bowel cleanse method by comparing the efficacy of 4 L of clear liquids, 2 L of polyethylene glycol (PEG), and 4 L of PEG on the image quality of VCE. <b><i>Methods:</i></b> A randomized controlled, non-inferiority trial was performed comparing 4 L of clear liquids (Group A), 2 L of PEG (Group B), and 4 L of PEG (Group C). The primary endpoint was image quality between the groups. The secondary endpoints included patient tolerability and side effects. <b><i>Results:</i></b> Eighty-one patients were analyzed in group A, 84 patients were analyzed in group B, and 80 patients were analyzed in group C. Image quality scores revealed 4 L of clear liquids to be non-inferior to 2 L of PEG, and 2 L of PEG to be non-inferior to 4 L of PEG (<i>p</i> &lt; 0.0167). Group A had a lower difficulty of completion rate than Group B and Group C and a lower rate of side effects when compared to Group C (<i>p</i> &lt; 0.0167). <b><i>Conclusion:</i></b> Four liters of clear liquids should be considered a routine method for small bowel preparation prior to VCE.
DOI: 10.6084/m9.figshare.7082948
title: Data from - Learning from others: an invasive lizard uses social information from both conspecifics and heterospecifics

description: Dataset from a study that investigated the ability of the invasive Italian wall lizard (Podarcis sicula) to solve a novel foraging task when social information was available from both a conspecific and an unfamiliar heterospecific (Podarcis bocagei).<br><br>
DOI: 10.17028/rd.lboro.7082888
title: Accelerated electric curing of steel fibre reinforced concrete - associated data

description: All the data from laboratory testing undertaken for the publication "Accelerated electric curing of steel-fibre reinforced concrete". This includes:- mechanical testing with raw data and graphs- curing data including electrical and temperature both raw and graphical
DOI: 10.17028/rd.lboro.7082888.v1
title: Accelerated electric curing of steel fibre reinforced concrete - associated data

description: All the data from laboratory testing undertaken for the publication "Accelerated electric curing of steel-fibre reinforced concrete". This includes:- mechanical testing with raw data and graphs- curing data including electrical and temperature both raw and graphical