cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28595732.v1
title: Supplementary Material for: C-reactive protein and metabolic syndrome in obese and normal weight Hungarian children

description: Introduction: It is well known that obese children frequently have high C- reactive protein (CRP) values. There are controversies about the association of the CRP and components of the metabolic syndrome (MetS). The aim of this study was to determine among children and adolescents the link between the most routinely used inflammation marker, CRP, and components of the MetS.
Methods: The study recruited 506 obese/overweight and 249 normal weight participants (ages 4–18 years) with complete fasting laboratory and anthropometric data. Statistical analyses, including multinomial logistic regression, were conducted in R, with significance set at p&lt;0.05.
Results: Children were divided into three groups according to CRP concentration (low &lt;1 mg/l, medium: 1–3 mg/l, high &gt;3 mg/l). The children were also classified whether they had MetS (n =249) or were free of MetS (n = 421). We found highly significant difference between CRP groups in the occurrence of the MetS components (p &lt; 0.001), hypertension (p &lt; 0.001), hypertriglyceridemia (p &lt; 0.001), and low high-density lipoprotein (HDL) cholesterol (p = 0.001), waist circumference (p &lt; 0.001), body mass index(BMI) z-score (p &lt; 0.001), fasting plasma glucose (p &lt;0.001), homeostasis model assessment of insulin resistance (p &lt;0.001) respectively. However, when BMI z-score was included in the model this relationship disappeared, suggesting that BMI has a more significant effect on the MetS components than CRP.
Conclusion: Our results demonstrate that BMI z-score is the main determinant of the MetS and its components. However, CRP remains an important factor to be checked in overweight and obese children.
DOI: 10.6084/m9.figshare.28755569.v1
title: Within-night training data

description: This repository contains the data used for training and deploying gradient boosted trees that analyze the associations between bird migration intensity and predictor variables. By integrating radar (NEXRAD) data with weather and terrestrial factors within 2-hour segments, we are able to assess changes in these associations within a single migration night, as birds transition between terrestrial and atmospheric habitat. Due to the large size of the input datasets (hundreds of GB), we have only included a subset of the data for the year 2012.<br>We include code for analyzing these data as well as a suggested data storage structure on GitHub [https://github.com/a-khalighifar/migration_forecast/tree/main/within-night].<br><b>Description of files included</b><i>01_cell-coordinates/1_all-trainingPoints-fromStations.csv</i>: This csv includes training points for within the coverage of each NEXRAD radar station.Unique.ID - A numerical identifier for each training pointRadar Station - The four-letter abbreviation for each NEXRAD radar siteX - The longitude or easting coordinate of each pointY - The latitude or northing coordinate of each point*Note - we also include coordinates for points at varying distances and directions from each sampling point, denoted in the header title (e.g. X.75.N = longitude coordinate for point 75km north of a given sampling point).<i>02_Radar_Atm_combined_Annual/2012/2012.rds</i>: Full dataset of predictor variables for sampling points in 2012.<br>
DOI: 10.6084/m9.figshare.5829318.v2
title: Argonaute2 and LaminB modulate gene expression by controlling chromatin topology

description: Code and supplemental data Nazer et al 2018 PLOS Genetics.<br><br><b>nazer_et_al.zip</b>: contains the code and instructions for regenerating the figures.<br><b><br>nazer_et_al_generated_figures.zip</b>: contains the figures and reports created by running the above code.<br>
DOI: 10.6084/m9.figshare.19624239.v1
title: remotesensing-1681545-dataset.zip

description: GPS-TEC and DEMETER data for study of seismo-ionospheric anomaly
DOI: 10.6084/m9.figshare.9777653.v1
title: Supplementary Material for: Diffusion-Weighted Imaging Patterns According to the Right-to-Left Shunt Amount in Cryptogenic Stroke

description: <b><i>Background:</i></b> Although patent foramen ovale (PFO) is considered to be the main cause of cryptogenic stroke, it is difficult to define “true” PFO-related stroke. <b><i>Objective:</i></b> In this study, we evaluated comprehensive diffusion-weighted imaging (DWI) findings in patients with cryptogenic stroke according to the right-to-left shunt (RLS) amounts on transcranial Doppler (TCD) sonography. <b><i>Methods:</i></b> We assessed consecutive patients with cryptogenic stroke between October 2010 and 2018. The RLS amount on TCD was assessed according to the International Consensus Criteria (ICC). Massive RLS was defined as the highest category of ICC (Curtain pattern). We assessed DWI findings, including the location of lesions, involved vascular territory, and DWI lesion patterns. <b><i>Results:</i></b> A total of 100 consecutive patients with cryptogenic stroke were assessed, and PFO was found in 59 patients. In multivariable analyses, massive RLS was noted to be positively associated with the presence of cortical lesion (adjusted OR [aOR] 15.75, 95% CI 1.94–127.71, <i>p</i> = 0.010), multiple territory involvement (aOR 5.24, 95% CI 1.57–17.53, <i>p</i> = 0.007), and number of DWI lesions (beta 0.713, 95% CI 0.245 to 1.181, <i>p</i> = 0.003) after adjusting for confounders. Conversely, massive RLS showed inverse correlations with posterior circulation involvement (aOR 0.22, 95% CI 0.06–0.87, <i>p</i>= 0.031) and number of large DWI lesions (beta –0.328, 95% CI –0.629 to –0.026, <i>p</i> = 0.034). <b><i>Conclusions:</i></b> We demonstrated that massive RLS on TCD was associated with multiple, small-scattered cortical lesion in patients with cryptogenic stroke. These DWI pattern is highly suggestive of PFO-related stroke.
DOI: 10.15468/dl.755eh5
title: Occurrence Download

description: A dataset containing 132 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Observation, Human Observation, Machine Observation, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Panzeria rudis (Fallén, 1810)"
 ]
}

 The dataset includes 132 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009572-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.22762076.v6
title: Targeted S-gene Sequencing Supplemental Material

description: The SARS-CoV-2 spike protein is a highly immunogenic and mutable protein that is the target of vaccine prevention and antibody therapeutics. This makes the encoding S-gene an important sequencing target. The SARS-CoV-2 sequencing community overwhelmingly adopted tiling amplicon-based strategies for sequencing the entire genome. As the virus evolved, primer mismatches inevitably led to amplicon drop-out. Given the exposure of the spike protein to host antibodies, mutation occurred here most rapidly, leading to amplicon failure over the most insightful region of the genome. To mitigate this, we developed a targeted method to amplify and sequence the S-gene. We evaluated 20 distinct primer designs through iterative <i>in silico</i> and <i>in vitro</i> testing to select the optimal primer pairs and run conditions. Once selected, periodic <i>in silico</i> analysis monitor primer conservation as SARS-CoV-2 evolves. Despite being designed during the Beta wave, the selected primers remain &gt; 99% conserved through Omicron as of 2023-10-19. To validate the final design, we compared targeted S-gene data to National SARS-CoV-2 Strain Surveillance whole-genome data for 321 matching samples. Consensus sequences for the two methods were highly identical (99.998%) across the S-gene. This method can serve as a complement to whole-genome surveillance or be leveraged where only S-gene sequencing is of interest.
DOI: 10.6084/m9.figshare.26255297.v3
title: LC-MS results.docx

description: LC-MS data for sponge extracts
DOI: 10.5522/04/22580047.v1
title: Qualitative study on exploring beliefs and practices regarding cognitive and socio-emotional caregiving practices among caregivers of Dhanusha district, Nepal

description: This qualitative dataset was collected in Nepal’s Dhanusha district in the plains of Nepal in June 2012. It arose from a study that aimed to explore and learn about beliefs and practices prevalent in households and communities regarding cognitive and socio-emotional caregiving practices among mothers and grandmothers in rural areas of Dhanusha district, Nepal. The record consists of seven semi-structured interviews (SSIs) (four with mothers and three with grandmothers) of children under three years of age and four Focus Group Discussions (FGDs) with mothers. All SSIs and FGDs with caregivers were conducted in the local Maithili language by eight experienced field coordinators, working in groups of two. Field coordinators were fluent in Maithili and Nepali. For analysis, all data were transcribed verbatim into Nepali and translated into English. We have anonymised all data for open-access publication. This data contributes to the paper <strong>“</strong>Children learn on their own by observing and imitating”: a qualitative exploration of caregivers’ perspectives on cognitive and socio-emotional caregiving practices for children 0-3 years in lowland Nepal”
DOI: 10.6084/m9.figshare.22361098.v1
title: Supplementary Material for: Culprit plaques of large parent arteries, rather than cerebral small vessel disease, contribute to early neurological deterioration in stroke patients with intracranial branch atheromatous disease

description: Introduction: Intracranial branch atheromatous disease (BAD) has been applied to occlusions that occur at the origin of large caliber penetrating arteries due to the microatheromas or large parent artery plaques. This study aimed to explore the association between culprit plaques of large parent arteries, neuroimaging markers of cerebral small vessel disease (CSVD), and the risk of early neurological deterioration (END) in stroke patients with BAD. Methods: A total of 97 stroke patients with BAD in the vascular territories of the lenticulostriate arteries or paramedian pontine arteries, diagnosed using high-resolution magnetic resonance imaging (HRMRI), were prospectively recruited in this observational study. A culprit plaque in the middle cerebral artery was defined as the only arterial plaque on the ipsilateral side of an infarction visible on diffusion-weighted imaging. A culprit plaque in the basilar artery (BA) was identified when it was observed within the same axial slices of an infarction or on the adjacent upper or lower slice, whereas a plaque within the BA located in the ventral region was considered non-culprit. If more than one plaque was present in the same vascular territory, the most stenotic plaque was chosen for the analysis. Four CSVD neuroimaging markers, including white matter hyperintensity (WMH), lacunes, microbleeds, and enlarged perivascular spaces (EPVS), were evaluated in accordance with the total CSVD score. The associations between neuroimaging features of lesions within large parent arteries, neuroimaging markers of CSVD, and the risk of END in stroke patients with BAD were investigated using logistic regression analysis. Results: END occurred in 41 stroke patients (42.27%) with BAD. The degree of large parent artery stenosis (P&lt;0.001), culprit plaques of large parent arteries (P&lt;0.001), and plaque burden (P&lt;0.001) were significantly different between the END and non-END groups in stroke patients with BAD. In logistic regression analysis, culprit plaques of large parent arteries (OR, 32.258; 95% CI, 4.140-251.346) were independently associated with the risk of END in stroke patients with BAD. Conclusions: Culprit plaques of large parent arteries could predict the risk of END in stroke patients with BAD. These results suggest that lesions in the large parent arteries, rather than damage to the cerebral small vessels, contribute to END in stroke patients with BAD.
DOI: 10.17608/k6.auckland.14958228.v1
title: SymbioLCD - Datasets

description: <b>Overview:</b>Three new datasets available here represent normal household areas with common objects - <b>lounge, kitchen and garden</b> - with varying trajectories.<br><br><b><br></b><b>Description:</b>Lounge: The lounge dataset with common household objects.Lounge_oc: The lounge dataset with object occlusions near the end of trajectory.Kitchen: The kitchen dataset with common household objects.Kitchen_oc: The kitchen dataset with object occlusions near the end of trajectory.Garden: The garden dataset with common household objects.Garden_oc: The garden dataset with object occlusions near the end of trajectory.convert.py: Python script to convert a video file into jpgs.<br><br><br><b>Paper</b>:The datasets were used for the paper "<b>SymbioLCD: Ensemble-Based Loop Closure Detection using CNN-Extracted Objects and Visual Bag-of-Words</b>", accepted at 2021 IEEE/RSJ International Conference on Intelligent Robots and Systems.<br><br><b>Abstract:</b><br>Loop closure detection is an essential tool of Simultaneous Localization and Mapping (SLAM) to minimize drift in its localization. Many state-of-the-art loop closure detection (LCD) algorithms use visual Bag-of-Words (vBoW), which is robust against partial occlusions in a scene but cannot perceive the semantics or spatial relationships between feature points. CNN object extraction can address those issues, by providing semantic labels and spatial relationships between objects in a scene. Previous work has mainly focused on replacing vBoW with CNN derived features.In this paper we propose SymbioLCD, a novel ensemble-based LCD that utilizes both CNN-extracted objects and vBoW features for LCD candidate prediction. When used in tandem, the added elements of object semantics and spatial-awareness creates a more robust and symbiotic loop closure detection system. The proposed SymbioLCD uses scale-invariant spatial and semantic matching, Hausdorff distance with temporal constraints, and a Random Forest that utilizes combined information from both CNN-extracted objects and vBoW features for predicting accurate loop closure candidates. Evaluation of the proposed method shows it outperforms other Machine Learning (ML) algorithms - such as SVM, Decision Tree and Neural Network, and demonstrates that there is a strong symbiosis between CNN-extracted object information and vBoW features which assists accurate LCD candidate prediction. Furthermore, it is able to perceive loop closure candidates earlier than state-of-the-art SLAM algorithms, utilizing added spatial and semantic information from CNN-extracted objects.<br><b>Citation</b>:Please use the <b>bibtex</b> below for citing the paper:<br>@inproceedings{kim2021symbiolcd,title = {SymbioLCD: Ensemble-Based Loop Closure Detection using CNN-Extracted Objects and Visual Bag-of-Words},author = {Jonathan Kim and Martin Urschler and Pat Riddle and J\"{o}rg Wicker},year = {2021},date = {2021-09-27},booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems},keywords = {},pubstate = {forthcoming},tppubtype = {inproceedings}}
DOI: 10.6084/m9.figshare.14248580.v1
title: Supplemental_dataset_S1.xlsx

description: Supplementary dataset containing microbiome profile data (ASV tables) for skin and skin-associated surfaces.
DOI: 10.6084/m9.figshare.22710160.v1
title: Career Decision Self-Efficacy: The Influence of Film and Television Business Coursework on Young Film/TV Professionals

description: Based on the research question, the study’s approach was quantitative, specifically utilizing a non-experimental, cross-sectional design. All young film/TV professionals constituted the population, with the authors using random selection to sample 500 of the 4,761 members from Awesome Assistants, a Facebook group that allows followers to discuss news and careers in the film/TV industry. A 25-question survey called the Career Decision Self-Efficacy Scale-Short Form (CDSES-SF) captured data, with the authors asking demographic questions about age and film/TV business coursework. The authors received 267 individual responses. Subjects under 18 years old, or over 35 years old, were not considered during the analysis. Respondents who did not answer their age or at least one item from each subscale within the CDSES-SF were also eliminated. For the remaining 240 subjects, the authors ran descriptive statistics and a t test using IBM Statistical Product and Service Solutions (SPSS) Statistics 27. A p-value less than .05 constituted statistical significance.
DOI: 10.6084/m9.figshare.21655784.v1
title: MDD2 (MDD2018) GWAS sumstats w/o UKBB

description: GWAS summary statistics for major depressive disorder from the PGC. MDD2 (Wray et al.) excluding 23andMe and UK Biobank. Cite Wray et al 2018 (source of cohort summary stastics) and Howard et al 2019 (source of UKB/PGC overlap resolution).
DOI: 10.6084/m9.figshare.25713852.v1
title: Additional file 5 - scripts for microbiota analysis

description: Microbiota analysis was carried out in R using the DADA2 pipeline (Callahan et al., 2016), and taxonomic categories were assigned using the Silva Database (release 138.1) as a reference for the assignment (Quast et al., 2012). Alpha (Shannon, Chao1, and Simpson indices) and Beta diversity (calculated as Bray Curtis distance matrix), as well as the abundance of taxonomic categories, were calculated and analysed with R software 3.6, using the PhyloSeq (McMurdie et al., 2013), Vegan (Dixon, 2003), and microbiomeMarker (Cao et al., 2022) packages. Differences between groups regarding Alpha diversity indices were tested using a linear mixed model that included category (IUGR, NORM), time (T1, T2, T3, T4), and their interaction as fixed factors, with the litter of origin considered as a random factor. Then, a separate model within each time point was performed including only the category as a fixed factor and the litter of origin as a random factor. For Beta diversity, a dissimilarity matrix was constructed using the Bray–Curtis distance matrix as metrics, and the results were plotted using a non-metric multidimensional scaling (NMDS) plot. Furthermore, the betadisper test was conducted to test differences in the samples’ dispersion among the groups. Differences were tested using a PERMANOVA (Adonis) model with 9,999 permutations, including category, time, and their interaction, and litter of origin as factors. A second PERMANOVA model was then performed within each time point, including the category as a factor. For the differential analysis of taxa, the LEfSe algorithm was used at the genus level. Specifically, taxa were considered significant if they possessed a Linear Discriminant Analysis (LDA) score &gt; 4 and a Padj &lt; 0.05 within each time point, including the category as a factor.References:Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP: DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods 2016, 13:581-583.Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO: The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 2012, 41:D590-D596.McMurdie PJ, Holmes S: phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PloS One 2013, 8:e61217.Dixon P: VEGAN, a package of R functions for community ecology. Journal of Vegetation Science 2003, 14:927-930.Cao Y, Dong Q, Wang D, Zhang P, Liu Y, Niu C: microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization. Bioinformatics 2022, 38:4027-4029.
DOI: 10.6084/m9.figshare.5915113.v3
title: Mice TCR datasets

description: TCR repertoires data for mice of various age groups
DOI: 10.6084/m9.figshare.19126814.v4
title: Datasets For Pipeline

description: This repository contains big datasets for the multi-omic analysis pipeline that cannot be uploaded to github.
DOI: 10.6084/m9.figshare.7924046.v1
title: gVCF_HG03738

description: 1000 Genomes gVCF mapped to hs37d5 for HG03738. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.22581628.v1
title: Embryonic SynProteome MIA_AYotova

description: Embryonic-Synaptic-Proteome_MIA-0-5mg/kg-Poly(IC)_Pool/M/F_LiliLi-AnnaYYotovaProteomic data (Spectronaut v18) - Raw + Full & Cleaned/Filtered Candidate Lists (w/ stats)
DOI: 10.6084/m9.figshare.14754123.v13
title: Supplementary Material for: Dental Health Inequalities among Indigenous Populations: A Systematic Review and Meta-Analysis

description: The aim of this systematic review and meta-analysis was to document the disparity in dental caries experiences among indigenous and nonindigenous populations globally by measuring dental caries prevalence and severity. An electronic database (MEDLINE) was initially searched using relevant keywords. This was followed by use of the search string in the following electronic databases: Scopus, EBSCOhost, Cochrane, and Open Grey. Two independent reviewers conducted the study search and screening, quality assessment, and data extraction, which was facilitated using JBI SUMARI software. The primary outcome was the decayed missing filled teeth (DMFT) score and dental caries prevalence. Subgroup analysis was done by country of publication to identify causes of heterogeneity. Forest plots were used with the standardized mean difference (SMD) and publication bias was assessed using the Egger test with funnel plot construction. For the final review, 43 articles were selected and 34 were meta-analyzed. The pooled mean DMFT for both the permanent dentition (SMD = 0.26; 95% CI 0.13–0.39) and deciduous dentition (SMD = 0.67; 95% CI 0.47–0.87) was higher for the Indigenous population than for the general population. Indigenous populations experienced more decayed teeth (SMD = 0.44; 95% CI 0.25–0.62), a slightly higher number of missing teeth (SMD = 0.11&lt; 95% CI –0.05 to 0.26), and lesser filled teeth (SMD = –0.04; 95% CI –0.20 to 0.13) than their nonindigenous counterparts. The prevalence of dental caries (SMD = 0.27; 95% CI 0.13–0.41) was higher among indigenous people. Globally, indigenous populations have a higher caries prevalence and severity than nonindigenous populations. The factors which have led to such inequities need to be examined.
DOI: 10.6084/m9.figshare.1577551.v1
title: AR.nex

description: sequences
DOI: 10.6084/m9.figshare.28852544.v1
title: Blended Learning as a Novel Teaching Learning Activity: Student Perceptions, Engagement, and Performance Outcomes - research data from LMS

description: Blended Learning as a Novel Teaching Learning Activity: Student Perceptions, Engagement, and Performance Outcomes - this data sheet include the data gather from the LMS system regarding students' performance and participation