cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/2rt8g6ndp3
title: Data for: Three-Dimensional Reconstruction of Wear Particle Surface Based on Photometric Stereo

description: the source code of 3D surface reconstruction based on Photometric stereo
DOI: 10.6084/m9.figshare.12730796.v2
title: Data for Sunday et al. 2020 submission

description: See Sunday et al., 2020 "Novel and familiar object recognition rely on the same ability" for details
DOI: 10.17632/zr7f72cgfb
title: Data from Systematic review of the caries treatment in primary teeth

description: To compare the performance of available treatments for cavitated caries lesion in outer half or middle third of primary teeth. The data were submitted to meta-analises in order to identify the best treatments in according with the surfaces involved and depth of cavity. The considered data were progression of caries lesion or success rate of treatments.
DOI: 10.6084/m9.figshare.13332914.v3
title: Data and Model for CaGIS

description: data and code for peer-review of CaGIS
DOI: 10.6084/m9.figshare.23715972.v1
title: Supplementary Material for: Rate-limiting enzymes in cardiometabolic health and aging in humans

description: Introduction. Rate-limiting enzymes (RLEs) are innate slow points in metabolic pathways, and many function in bioprocesses related to nutrient sensing. Many RLEs carry causal mutations relevant to inherited metabolic disorders. Because the activity of RLEs in cardiovascular health is poorly characterized, our objective was to assess their involvement in cardiometabolic health and disease, and where altered biophysical and biochemical functions can promote disease. Methods. A dataset of 380 human RLEs was compared to protein and gene datasets for factors likely to contribute to cardiometabolic disease, including proteins showing significant age-related altered expression in blood, and genetic loci with variants that associate with common cardiometabolic phenotypes. The biochemical reactions catalyzed by RLEs were evaluated for metabolites enriched in RLE subsets associating with various cardiometabolic phenotypes. Most significance tests were based on Z-score enrichment converted to P values with a normal distribution function. Results. Of 380 RLEs analyzed, 112 function in mitochondria, and 53 are assigned to inherited metabolic disorders. There was a depletion of RLE proteins known as aging biomarkers. At the gene level, RLEs were assessed for common genetic variants that associated with important cardiometabolic traits of LDL-cholesterol or any of the five outcomes pertinent to metabolic syndrome. This revealed several RLEs with links to cardiometabolic traits, from a minimum of 26 for HDL-cholesterol to a maximum of 45 for plasma glucose. Analysis of these GWAS-linked RLEs for enrichment of the molecular constituents of the catalyzed reactions disclosed a number of significant phenotype-metabolite links. These included blood pressure with acetate (P = 2.2x10-4) and NADP+ (P = 0.0091), plasma HDL-cholesterol and triglyceride with diacylglycerol (P = 2.6x10-5, 6.4x10-5, respectively) and diolein (P = 2.2x10-6, 5.9x10-6), and waist circumference with D-glucosamine 6-phosphate (P = 1.8x10-4). Conclusion. In the context of cardiometabolic health, aging and disease, these results highlight key diet-derived metabolites that are central to specific rate-limited processes that are linked to cardiometabolic health. These metabolites include acetate and diacylglycerol, pertinent to blood pressure and triglycerides, respectively, as well as diacylglycerol and HDL-cholesterol.
DOI: 10.6084/m9.figshare.3806355.v3
title: Python script for pattern search in Sox2 binding sequences

description: Cock PA, Antao T, Chang JT, Bradman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B and de Hoon MJL (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25, 1422-1423<br>Chapman BA and Chang JT (2000). Biopython: Python tools for computational biology. ACM SIGBIO Newsletter, 20, 15-19<br>Shirley MD, Ma Z, Pedersen B, Wheelan S. Efficient "pythonic" access to FASTA files using pyfaidx. PeerJ PrePrints 3:e1196. 2015.<br>Dhanusha Yesudhas, Muhammad Ayaz Anwar, Suresh Panneerselvam, Kim Han Kyul & Sangdun Choi*An approach to evaluate binding affinities of Sox2 with distinct DNA binding sequences by Umbrella Sampling (Manuscript under preparation)* http://sangdunchoi.openwetware.org/<br>Boyer, L. A. et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947-956, doi:10.1016/j.cell.2005.08.020 (2005).<br>
DOI: 10.6084/m9.figshare.5311252.v1
title: Supplementary Material for: The Prevalence of and Factors Related to Vascular Hyperintensity on T1-Weighted Imaging in Acute Ischemic Stroke

description: <b><i>Background:</i></b> Thrombus visualization in patients with acute ischemic stroke has been detected and reported using various imaging modalities. T1-weighted imaging (T1-WI) can depict thrombi as hyperintense signals within vessels. Moreover, in addition to thrombi, T1-WI hyperintensities in arteries may suggest arterial dissection. However, the frequency of and factors related to the T1-hyperintense vessel sign (T1-HVS) are not fully known. The aim of this study was to clarify the prevalence of and related factors for the T1-HVS in patients with acute ischemic stroke. <b><i>Methods:</i></b> From September 2014 through December 2015, consecutive acute ischemic stroke patients who were admitted to our stroke unit within 7 days from symptom onset were retrospectively recruited from the prospective registry. A T1-HVS was defined as the presence of a hyperintense signal, with intensity higher than surrounding brain, within the vessel lumen. Moreover, T1-HVSs were separated into filled T1-HVSs (hyperintensity fills whole vessel lumen) and non-filled T1-HVSs. The frequency of the T1-HVS and the timing of emersion and the relationship between the presence of the T1-HVS and arterial occlusion were assessed. <b><i>Results:</i></b> A total of 399 patients (139 women; median age 73 years; National Institutes of Health Stroke Scale score 3) were enrolled in the present study. Of these, 327 (82%) patients had T1-WI on admission. Two hundred and sixty-seven (67%) subjects had at least one follow-up T1-WI (median 6 days after admission), and 134 (34%) cases had ≥2 follow-up T1-WI examinations. The T1-HVS was observed in 18 patients during admission; therefore, the frequency of the T1-HVS in acute ischemic stroke patients was 4.5% (95% CI 2.5-6.5%). All but one (94%) of the T1-HVSs were first observed on follow-up imaging, and the median number of days from onset to T1-HVS appearance was 9. For patients having initial major artery occlusion and follow-up MRI (<i>n</i> = 95), sensitivity and specificity of the T1-HVS for persistent arterial occlusion on follow-up MR angiography were 22 and 100%, respectively. T1-HVS persisted for a few months and then normalized. Although there were no significant differences between filled and non-filled T1-HVS, more patients with non-filled T1-HVS had arterial dissection (43%) than those with filled T1-HVS (9%, <i>p</i> = 0.245). <b><i>Conclusion:</i></b> The T1-HVS was observed in 4.5% of acute ischemic stroke patients. T1-HVSs appeared in the subacute phase in arteries with persistent occlusion and remained for a few months.
DOI: 10.6084/m9.figshare.1509930.v1
title: Body Pattern Components in Aquarium-Raised Flamboyant Cuttlefish (Metasepia pfefferi)

description: These data were collected by video recording tank-raised flamboyant cuttlefish (<em>Metasepia pfefferi</em>). For more information on the methodology used to collect these data, see this manuscript: Thomas, A; MacDonald, C. 2016. Investigating body patterning in aquarium-raised flamboyant cuttlefish (<i>Metasepia pfefferi</i>). PeerJ. In press. Briefly, each number corresponds to the components observed from one flamboyant cuttlefish during a single, one-second video clip. All components were marked as either present (indicated by a "1") or absent (indicated by a "0"). Components that were not included in this study (i.e. components visible on the ventral surface) are indicated by solid black cells in the spreadsheet. The descriptions of each component are available in the above manuscript. Data were analyzed using AutoClass@IJM, available here during the writing of this manuscript:http://ytat2.ijm.univ-paris-diderot.fr//AutoclassAtIJM.htmlThe software is now "Autoclass@IMRB" and is available here: http://37.60.156.20//autoclass/AutoclassAtIMRB.html<br> In the Adobe Illustrator (.ai) file, open using Adobe Illustrator. Open the layers tab and toggle the visibility on each layer to reveal the various components of the cuttlefish. This file is also available as a supplemental PDF file in the associated manuscript.
DOI: 10.6084/m9.figshare.24161634.v1
title: Raw data for the Genomic Analysis of Singles and Pools (GASP) project. Code for analysis available in github: github.com/VishnuRaghuram94/GASP.

description: After addressing reviewer comments (Revision 1), changes here include addition of output files from StrainGE, Gubbins, and Kraken. We also removed the previous phylogeny (constructed using FastTree) and replaced it with a ML phylogeny (made by IQ-TREE) after masking recombinant regions with ClonalframeML and maskrc-svg.
DOI: 10.6084/m9.figshare.9729638.v1
title: Data for: "Tri-trophic interactions mediate the spread of a vector-borne plant pathogen"

description: This .csv file provides the raw data used for linear models and path analysis presented in the paper Clark et al. 2019 "Tri-trophic interactions mediate the spread of a vector-borne plant pathogen" in <i>Ecology.</i>
DOI: 10.17632/w68f9w6jmm
title: An image dataset for food waste in Bangladesh

description: The dataset comprises a collection of images documenting food waste from various contexts, such as restaurants, buffets, and events like weddings. These images aim to capture diverse scenarios of food waste to aid in understanding and analyzing waste patterns in different settings. The data collection process involved visiting multiple locations, including restaurants, buffet establishments, and weddings, and capturing pictures.
There are total 5 folder and the dataset contains 645 images. All the images are in .jpg format.
DOI: 10.6084/m9.figshare.16611607.v1
title: MSC .fcs data Figure 5

description: MSC .fcs data Figure 5<br><br>BM was analyzed with focus on MSCs
DOI: 10.6084/m9.figshare.17128607.v1
title: Supplementary Material for: Exploring the Policies Applied to Pharmaceutical Care Practice for Type 2 Diabetes over the Last Decade in European Community Pharmacies

description: In the last decade (2010–2020), more than half of European countries have improved their health policies within the primary care for type 2 <i>diabetes mellitus</i>. Community pharmacies have been and could continue to be essential actors in this evolution of fighting the disease by providing a set of pharmacotherapeutic follow-up services for the person with diabetes. These services, designated by the Pharmaceutical Group of the European Union as “<i>diabetes management</i>” and “<i>glucose measurement</i>”, have aimed to optimize adherence to therapy and improve health outcomes. However, to follow the European guidelines of Good Pharmacy Practice, providing these services implies having a normative framework or a legal basis. Thus, this study sought to analyze the normative and regulatory framework on which community pharmacies in 28 European countries were based on providing this health care over the last decade.
DOI: 10.6084/m9.figshare.16575194.v1
title: Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome. Meyer et. al 2022. ISME-J.

description: This is the data archive for: Meyer et al. 2022. Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome. ISME-J. Please cite this article when using these archived data.DOI: 10.1038/s41396-021-01184-6<br>Included are raw genetic sequences of the V5-V7 region of the 16S rRNA gene derived from experimental leaf surfaces of tomato, pepper, and bean plants.<br><br>Included in this archive are:Raw sequence data (RawFASTQ.zip)Reproducible R scripts (MeyerEtAl2021_RScript.R, VarPartSupplement.R)R objects corresponding to archived scripts (.RDS)Data for generating certain plots (PermanovaRValues.txt, PermanovaValuesByHost.txt, NeutralModelRValuesByHarvest.txt, VarPartHostEffects.txt)Sample metadata (NeighborhoodMetaData.txt)Phylogenetic Tree file for sample ASVs (PhyloTree.tre)Geographic distance matrix for distances between plots (GeodistNeighborhood.txt)ddPCR (microbial abundance) data (ddPCR_Neighborhood.csv)R script for rarefication function (Rarefy_mean.R)Taxonomic assignments for all ASVs in study (Taxonomy_Neighborhood.txt)R image files to load R environment instead of running script (MeyerEtAl2021_RScript.RData, VarPartSupplement.RData)<br><br><br>
DOI: 10.6084/m9.figshare.24512029.v1
title: Márton-et-al-Results-Pap12-6

description: Data were obtained from measurements of supernatant samples taken after treatment of primary hepatic cell cultures of chicken origin.
DOI: 10.6084/m9.figshare.25396372.v1
title: Source Data-Diamond with Sp2-Sp3 Composite Phase for Thermometry at Millikelvin Temperatures

description: Source Data for <b><i>Diamond with Sp2-Sp3 Composite Phase for Thermometry at Millikelvin Temperatures.</i></b>
DOI: 10.6084/m9.figshare.23100350.v2
title: Supplementary Tables and Data

description: All Supplementary Tables are provided in one Excel sheet. If you are loading these tables into R or python, you must remove the top rows, which contain a title, and sometimes a description of the fields.<br><b>Table ST1: </b>Descriptive statistics of taxa. Various descriptive statistics for subgenera of the genus <i>Lactobacillus</i> and genera detected in this study: number of ASVs within the (sub)genus (n_asvs), prevalence (occurrence), average relative abundance (mean_rel_abundance), frequency of being the most abundant taxon and greater than 0% abundant (top_and_gt0p), same as previous but greater than 30% abundant (top_and_gt30p), same as previous but greater than 50% abundant (top_and_gt50p), the previous three measures but in terms of relative frequencies (top_and_gtXp_rel).<br><b>Table ST2: </b>Table of the number of Isala participants per VALENCIA subCST.<br><b>Table ST3:</b> Taxa-taxa correlation network generated from sparcc for the Isala dataset. Each cell indicates the compositionality aware correlation between two taxa.<br><b>Table ST4: </b>Association tests between participant characteristics and their vaginal microbiome. Results of statistical tests for each tested questionnaire response. Results of association tests are provided for beta-diversity (Adonis tests), alpha-diversity, CSTs, eigentaxa and individual taxa. In addition to effect sizes, test statistics and p-values, the number of participants in each condition is provided.<br><b>Table ST5:</b> Supplementary meta-data for the Isala samples used in this study. Each ENA sample ID is linked to a participant’s age, whether intercourse occurred in the last 24 hours, technical covariates, and CST annotations. This file can be used in combination with the code available on github.<br><b>Table ST6:</b> Results of the PERMANOVA (Adonis2) tests between technical factors and the vaginal microbiome.<br><b>Table ST7:</b> Count data per (sub)genus per sample. Linked by identified to the meta data provided on EGA and Table ST5. This file can be used in combination with the code available on github.<br><b>Table ST8:</b> Relative abundance data per sample. Linked by identified to the meta data provided on EGA and Table ST5.<br><b>Table ST9: </b>Taxa classification specification per (sub)genus specified in Tables ST7 and ST8. This file can be used in combination with the code available on github.<br><b>Table ST10:</b> Count data per ASV per sample. Linked by identified to the meta data provided on EGA and Table ST3. This file can be used in combination with the code available on github.<br><b>Table ST11: </b>Taxa classification specification per ASV specified in Table ST10. This file can be used in combination with the code available on github.
DOI: 10.6084/m9.figshare.24903288.v1
title: <b>The Mediating Role of Anxiety in the Relationship Between Misophonia and Quality of Life: Findings from the Validated Turkish Version of MisoQuest</b>

description: Misophonia, characterized by an increased sensitivity to specific sounds and associated stimuli, is a condition that has received growing attention in recent years. However, there is still a lack of consensus in the literature on the nature of misophonia, which can have serious negative effects on individuals' lives, how it interacts with other psychological factors, and to what extent it affects individuals' quality of life. This study provides valuable insights into the relatively poorly understood misophonia and its implications on individuals' quality of life. The results of our research are important in several respects. Since there is no standard measurement tool to be used in the diagnosis and evaluation of misophonia, we think that making existing measurement tools available cross-culturally will contribute to the results of research in the misophonia literature becoming generalizable and comparable. For this, we adapted MisoQuest, a validated measurement tool, to our own culture. Second, results underscore the importance of recognizing misophonia as a potentially disruptive condition in people's lives. Third, our study highlights the critical role of anxiety in mediating the relationship between misophonia and quality of life. Our findings will provide a new perspective for interventions and supports to be developed for misophonia.
DOI: 10.17632/b6vc9j23hb
title: The power of social constructivism in teaching translation

description: The main objective of this study was to investigate the effectiveness of a suggested social constructivist program to develop translation proficiency and raise awareness of using translation strategies among fourth year English majors at College of Education. The study had a one group pretest-posttest design (n=40). The materials and tools of the study included a training social constructivist program in translation strategies, a pre-post translation strategy test for measuring awareness of translation strategies and a pre-post translation test for measuring translation proficiency. Results indicated that the suggested program was effective in improving translation proficiency of fourth year English majors, there was an increase in the awareness of translation strategies and there was a positive correlation between students' translation proficiency and their awareness of translation strategies. In the light of the results, it was recommended that pre-service, as well as in-service English teachers should be trained in social constructivist approach, a real shift from individual to collaborative learning should take place, the role of the teacher, in translation classes should be changed from a lecturer to a co-learner, Learners should have the chance of self-evaluation, and translation courses should integrate both translation theories with translation practices.
DOI: 10.6084/m9.figshare.14321878.v1
title: Influence of particle size distribution and content of ceramic tile polishing residues on mechanical performance of cementitious matrices

description: ABSTRACT This study aims to evaluate the influence of particle size distribution and the content of the replacement of cement by ceramic tile polishing residue on the mechanical strength of cementitious matrices. Eight types of mortars were produced in a ratio of 1:3 by weight (cement: sand) and water/fine (cement + residue) ratio of 0.48 with levels of replacement of 0; 10; 30 and 50% of ceramic tile polishing residue. It was adopted waste with two different particle size distributions: in natura and ground by 30 minutes in a ball mill. Residues were characterized by specific mass; laser diffraction analysis; X-ray diffraction and Chapelle modified method. In the fresh state, mortars were evaluated by tests of consistency, mass density and air content and in the hardened state by compression strength at 7, 28 and 150 days. The grinding of ceramic tile polishing residue was beneficial because it promoted the development of pozzolanic activity and an increase of the compression strength. The results showed that the replacement of 30% cement by ground residue resulted in compressive strength of 34 MPa at 28 days and it can reach 38MPa at 150 days. The replacement of cement by ceramic tile polishing residue with a controlled size particle distribution can be favorable to the industry because it possible reduce costs and environmental impact both by reuse of the residue or as a contribution to CO2 mitigation.
DOI: 10.6084/m9.figshare.24135174.v1
title: <b>Low-cost SNP array for genotype imputation optimized for breeding programs in the fish pacu </b><b><i>Piaractus mesopotamicus</i></b>

description: Pacu (<i>Piaractus mesopotamicus</i>) is one of the main native fish species for aquaculture in South America. Cost-effective genotyping strategies, involving low-density SNP arrays followed by genotype imputation, can facilitate the broader adoption of genomic selection for this species. In this study, we developed a 1K SNP array to be applied with genotype imputation strategies in breeding program of pacu. First, we assessed imputation accuracy across various SNP densities (9K, 7K, 5K, 2K, 1K, and 0.5K) from the commercial <i>Axiom 30 K SerraSNP</i> array to select the best subset for further analysis. Then, 15,166 (91.1%) imputed SNPs with high accuracy were obtained when we selected 1,068 SNPs to comprise the 1K SNP array (average accuracies of 0.90 ± 0.12 at the SNP level and 0.92 ± 0.06 for 290 genotyped individuals). The 1K SNP array was developed using the <i>Agriseq tGBS</i> platform. In the evaluation of array performance using 95 individuals, no discordant genotyping was observed between the <i>Agriseq tGBS</i> platform and the <i>Axiom 30 K SerraSNP</i> array. Ninety-one individuals had a call rate of 90% and above, and 92% of the SNPs were identified in at least 90% of the samples. Additionally, an average minor allele frequency (MAF) of 0.356 (± 0.108) and individual heterozygosity values ranging from 0.321 to 0.470 were found. The results showed that the constructed low-density SNP array exhibited high imputation accuracies and can explore genetic variations within pacu populations, making it a cost-effective tool for enhancing pacu production through genomic selection.
DOI: 10.6084/m9.figshare.23723829.v1
title: Qualitative Codebook: "Nonbelief Among Ex-Muslims in the United States: A Critical Grounded Theory Study"

description: This codebook includes the core categories, clusters, categories, and initial categories developed for a critical, grounded theory investigation of trajectories to nonbelief among ex-Muslims in the US.
DOI: 10.17632/3fcrdpr2gw
title: Data for: Mixed-effects Generalized Height–Diameter Model for Young Silver Birch Stands on Post-agricultural Lands

description: Data were collected from 80 pure silver birch stands growing on post-agricultural lands in the province of Mazowieckie in central Poland. Individual sample plots were located within silver birch stands that spontaneously and naturally regenerated, with the age ranging from 3–19 years. Tree heights (H) and the diameters at the breast heights (D) were measured for a random sample of trees using the VERTEX IV hypsometer (Häglofs, Sweden). 3,577 trees were measured in total. Data consists also the quadratic mean diameter at the breast height (Dg, cm) and basal area (BA, square meter per hectare) for each plot.