cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28936877.v1
title: Supplementary Material for: Artificial intelligence applied to ultrasound diagnosis of pelvic gynecological tumors: a systematic review and meta-analysis

description: Objective: To perform a systematic review on artificial intelligence (AI) studies focused on identifying and differentiating pelvic gynecological tumors on ultrasound scans.

Methods: Studies developing or validating AI models for diagnosing gynecological pelvic tumors on ultrasound scans were eligible for inclusion. We systematically searched PubMed, Embase, Web of Science, and Cochrane Central from their database inception until April 30th, 2024. To assess the quality of the included studies, we adapted the QUADAS-2 risk of bias tool to address the unique challenges of AI in medical imaging. Using multi-level random effects models, we performed a meta-analysis to generate summary estimates of the area under the receiver operating characteristic curve (AUC), sensitivity, and specificity. To provide a reference point of current diagnostic support tools for ultrasound examiners, we descriptively compared the pooled performance to that of the well-recognized ADNEX model on external validation. Subgroup analyses were performed to explore sources of heterogeneity. 

Results: From 9151 records retrieved, 44 studies were eligible: 40 on ovarian, three on endometrial, and one on myometrial pathology. Overall, 95% were at high risk of bias – primarily due to inappropriate study inclusion criteria, the absence of a patient-level split of training and testing image sets, and no calibration assessment. For ovarian tumors, the summary AUC for AI models distinguishing benign from malignant tumors was 0.89 (95% CI: 0.85-0.92). In lower-risk studies (at least three low-risk domains), the summary AUC dropped to 0.87 (0.83-0.90), with deep learning models outperforming radiomics-based machine learning approaches in this subset. Only five studies included an external validation, and six evaluated calibration performance. In a recent systematic review of external validation studies, the ADNEX model had a pooled AUC of 0.93 (0.91-0.94) in studies at low risk of bias. Studies on endometrial and myometrial pathologies were reported individually. 

Conclusion: Although AI models show promising discriminative performances for diagnosing gynecological tumors on ultrasound, most studies have methodological shortcomings that result in a high risk of bias. In addition, the ADNEX model appears to outperform most AI approaches for ovarian tumors. Future research should emphasize robust study designs – ideally large, multicenter, and prospective cohorts that mirror real-world populations – along with external validation, proper calibration, and standardized reporting.

Registration: This study was pre-registered with Open Science Framework (OSF): https://doi.org/10.17605/osf.io/bhkst.
DOI: 10.6084/m9.figshare.3561300.v1
title: Supplement 1. Data, R code and JAGS model description to repeat simulation study investigating power to detect population trends with correlated abundances between years, using the Markov and the log-linear trend model.

description: File List data.100m.R: (MD5: 25cca5e0b23be3915b197a50bcd1fb18) R data object containing data used in the hierarchical distance sampling analysis of island scrub-jay abundance by Sillett et al. (2012); loads the following objects covs: data frame with survey point covariates <br> Xall.100m: matrix with detections from fall survey, survey site by 100-m distance band<br> Xall.spring.100m: matrix with detections from spring survey, survey site by 100-m distance band Sollmann_et_al_R_script_Markovian_model.txt: (MD5: ) R script file with code to simulate, analyze, and summarize data under a Markovian abundance model where <i>N</i> at time <i>t</i> depends on <i>N</i> at time <i>t</i>-1, using the open-population hierarchical distance sampling model. Sollmann_et_al_Markovian_model_JAGS_code.txt: (MD5: ) JAGS model description of the open-population hierarchical distance sampling model used in the R script above. Sollmann_et_al_R_script_Markovian_data_log-linear_trend_model.txt: (MD5: ) R script file with code to simulate data under a Markovian abundance model (see above), and analyze and summarize it under a hierarchical distance sampling model with a log-linear time effect on abundance. Sollmann_et_al_Independent_years_model_JAGS_code.txt: (MD5: ) JAGS model description of the hierarchical distance sampling model with linear time effect used in the R script above. Description Data files and code are set up to repeat the simulation study investigating power to detect population trends with independent and correlated abundances between years, as presented in the Simulation section in the manuscript.
DOI: 10.6084/m9.figshare.6508253.v1
title: Supplementary Material for: A Novel Early Pregnancy Risk Prediction Model for Gestational Diabetes Mellitus

description: <b><i>Introduction:</i></b> Accurate early risk prediction for gestational diabetes mellitus (GDM) would target intervention and prevention in women at the highest risk. We evaluated novel biomarker predictors to develop a first-trimester risk prediction model in a large multiethnic cohort. <b><i>Methods:</i></b> Maternal clinical, aneuploidy and pre-eclampsia screening markers (PAPP-A, free hCGβ, mean arterial pressure, uterine artery pulsatility index) were measured prospectively at 11–13<sup>+6</sup> weeks’ gestation in 980 women (248 with GDM; 732 controls). Nonfasting glucose, lipids, adiponectin, leptin, lipocalin-2, and plasminogen activator inhibitor-2 were measured on banked serum. The relationship between marker multiples-of-the-median and GDM was examined with multivariate regression. Model predictive performance for early (&lt; 24 weeks’ gestation) and overall GDM diagnosis was evaluated by receiver operating characteristic curves. <b><i>Results:</i></b> Glucose, triglycerides, leptin, and lipocalin-2 were higher, while adiponectin was lower, in GDM (<i>p</i> &lt; 0.05). Lipocalin-2 performed best in Caucasians, and triglycerides in South Asians with GDM. Family history of diabetes, previous GDM, South/East Asian ethnicity, parity, BMI, PAPP-A, triglycerides, and lipocalin-2 were significant independent GDM predictors (all <i>p</i> &lt; 0.01), achieving an area under the curve of 0.91 (95% confidence interval [CI] 0.89–0.94) overall, and 0.93 (95% CI 0.89–0.96) for early GDM, in a combined multivariate prediction model. <b><i>Conclusions:</i></b> A first-trimester risk prediction model, which incorporates novel maternal lipid markers, accurately identifies women at high risk of GDM, including early GDM.
DOI: 10.6084/m9.figshare.7492991.v2
title: Data for "Generation and sampling of quantum states of light in a silicon chip"

description: Data for the paper "Generation and sampling of quantum states of light in a silicon chip" by Stefano Paesani et al.
DOI: 10.17632/8vxscfnpgc
title: Data for: Recent advances on the increased performances of methanol carbonylation into acetic acid.

description: Carbonylation reactions. Catalysis with noble metals
DOI: 10.6084/m9.figshare.14882262.v1
title: CHGCAR-JVASP-43906

description: CHGCAR
DOI: 10.6084/m9.figshare.23732718.v1
title: Origen del título del Proyecto de Aula de 2do. Grado 2023

description: Narración sobre el origen del tema del proyecto de aula del curso 204, titulado: "Los amigos increíbles y los valores de la bandera de Colombia", incluyendo una actividad de religión.Fecha: 21 de julio de 2023.Lugar: Institución Educativa Distrital Manuelita Sáenz.
DOI: 10.6084/m9.figshare.7843448.v1
title: Additional file 12: of Postcranial heterochrony, modularity, integration and disparity in the prenatal ossification in bats (Chiroptera)

description: Ossification sequence data used in this study. (XLS 40 kb)
DOI: 10.26188/28478285.v2
title: Anaemia intervention costing_Unit cost estimation worksheet

description: Supporting dataset for the following study:Estimated unit costs of anaemia interventions for women of reproductive age in 193 United Nations member states: a costing study.<b>Methods: </b>A micro-costing approach was used to estimate unit costs (per recipient per year) for six anaemia prevention and treatment interventions in 193 countries using data from secondary sources. A healthcare sector perspective and 1-year timeframe were adopted. Cost categories for each intervention included the commodity, supply chain, service delivery and administrative program costs. Impacts of parameter uncertainty were explored in deterministic sensitivity analyses. Costs are presented in 2023 United States dollars (USD).This file is the MS Excel file developed to estimate unit costsStudy authors and affiliations:Victoria L. Oliver<sup>1</sup>*, Yingying Wang<sup>1</sup>, Sumie Leung<sup>2</sup>, Robin Blythe<sup>3,4</sup>, Clare Glover-Wright<sup>1</sup>, Jacinta Holloway-Brown<sup>5</sup>, Michael Bode<sup>4</sup>, Sant-Rayn Pasricha<sup>1,2,6</sup>, Natalie Carvalho<sup>1</sup>Affiliations1. Melbourne School of Population and Global Health, University of Melbourne, Victoria, Australia, 30532. Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia, 30523. Duke-NUS Medical School, Singapore, 1698574. School of Mathematical Sciences, Queensland University of Technology, Queensland, Australia, 4001.5. School of Computer and Mathematical Sciences, University of Adelaide, South Australia, Australia, 50056. Department of Clinical Haematology, Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Parkville, Victoria, Australia, 3052
DOI: 10.6084/m9.figshare.11312873.v1
title: MULTICRITERIA ANALYSIS OF THE COMPLIANCE FOR THE IMPROVEMENT OF INFORMATION SECURITY

description: ABSTRACT Information security is a current issue of protection of information assets that considers significant variables of a strategic, organizational and IT governance nature, and that requires to analyze the compliance with international standards that regulate business actions. In this way, the work analyzes institutional compliance to improve information security applying the Analytic Hierarchy Process methodology to the specific practices defined in ISO/IEC 27002:2013. Expert Choice has been used as Decision Support Systems that has generated as a result the ranking of priorities of the criteria and alternatives used in the decisional process. It has been later applied in a medium-sized Brazilian industrial company. The results identify that the main security practice is the one related to the independent critical analysis of information security.
DOI: 10.6084/m9.figshare.25399516.v1
title: S3_Point counting artificial samples

description: This is the supplementary dataset S3 to the paper "How to quantify heavy mineral fertility from point-counting data". The dataset presents the results of point-couting artificial mixtures of grains (biotite, magnetite, quartz) using the Glagolev-Chayes method.
DOI: 10.17632/jxj2r45t2x
title: Honeys biological origin by GC-IMS

description: GC-IMS data set of authentic honeys from 3 biological origins: canola, acacia and honeydew. The files are in native .mea format and can e.g. be analyzed by our open source toolbox gc-ims-tools. An exemplary workflow can be found here: http://dx.doi.org/10.1016/j.foodres.2022.111779
DOI: 10.6084/m9.figshare.21916140.v1
title: Supplemental Files from: Environment-specific selection alters flowering-time plasticity and results in pervasive pleiotropic responses in maize

description: Article title: Environment-specific selection alters flowering-time plasticity and results in pervasive pleiotropic responses in maize Authors: Nicole E. Choquette, James B. Holland, Teclemariam Weldekidan, Justine Drouault, Natalia de Leon, Sherry Flint-Garcia, Nick Lauter, Seth C. Murray, Wenwei Xu, Randall J. Wisser <br> <strong>The following Supporting Files are available for this article. A separate README is also available for each data file.</strong> <br> <strong>---- Data files</strong> <strong>psge_combined_full.csv :</strong> Full dataset including design information and all trait measurements from 2014 to 2015. <strong>PSGE_Sel_emergence.csv :</strong> Planting dates and emergence dates for the selection environments. <strong>PSGE_Eval_emergence.csv :</strong> Planting dates and emergence dates for the evaluation environments. <strong>PSGE_transition.csv :</strong> Information for the estimated day of year for flowering time transition for each environment. <strong>PSGE_year_by_location_means.csv :</strong> Year-by-location means for all accessions/populations (flowering time). <strong>Crow_Flies_distances.csv :</strong> Geographical “as the crow flies” distances for all locations. <strong>PSGE_weather_windows.csv :</strong> Summary of weather variables over the three growth periods. <br> <strong>---- R scripts</strong> <strong>Step0_Weather_Summary.Rmd :</strong> Contains the analysis for summarizing the environmental variables over the three periods. Includes adding GDD to psge_combined.csv. <strong>Step1_Build_Model_Eq1.Rmd :</strong> Runs equation 1, estimates the 8x8 selection responses for flowering time traits, main effects for selection and evaluation locations, runs Wald tests, and saves as R objects. <strong>Step2_Sel_Eval_Effects.Rmd :</strong> Evaluates the previous R objects and runs the comparisons of the control populations. <strong>Step3_Responses_ForwardSel_Env.Rmd :</strong> Creates the individual generation by evaluation environment selection responses, runs forward selection, selects the final model, runs env PCA, and selection and evaluation correlations. Uses the summarized environmental files created in Step0_Weather_Summary.Rmd. <strong>Step4_Local_Adaptaiton_Distances.Rmd :</strong> Tests for local adaptation from the 8 x 8 interactions, isolates the interaction effects for the individual generation selection responses runs the forward selection on variable distances. Uses the summarized environmental files created in Step0_Weather_Summary.Rmd. <strong>Step5_Maladaptation_Syndrome.Rmd :</strong> Gets the G0 means for all traits, selection responses, and correlates the trait responses to GDD to silking selection responses. <strong>Step6_Piecewise_Regression.Rmd :</strong> Performs analysis of reaction norms. <br>
DOI: 10.6084/m9.figshare.28076054.v1
title: Topological Identification and Interpretation for Single-cell Epigenetic Regulation Elucidation in Multi-tasks using scAGDE

description: All processed datasets for benchmarking analysis and the human brain dataset used in scAGDE paper.
DOI: 10.6084/m9.figshare.4814698.v2
title: 4 objective problem test cases

description: A set of randomly generated 4 objective knapsack, assignment and travelling salesman problems used to test optimisation algorithms.<br><br>These are generated using similar techniques to those of Laumanns et al. (2006) (for knapsack problems), Przybylski et al. (2010) (for assignment problems), and Özpeynirci and Köksalan (2010) (for traveling salesman problems). A knapsack instance is generated by randomly assigned an integer weight (uniformly at random in the range {60, ... , 100}) to each of n items. The upper bound on the total weight of the selected items is set to be half of the total weight of all items. Each objective function is chosen in a similar manner, with the coefficients for each item drawn uniformly<br>at random from the range {[60, ... , 100}.<br><br>Assignment problems are generated in the manner of Przybylski et al. (2010), with objective function coefficients drawn uniformly at random from {0, ... , 20}. We also generate instances of the traveling salesman problem as per Özpeynirci and Köksalan (2010). We place cities on a 1000 × 1000 plane by assigning integer coordinates to cities, and round the Euclidean distance between any two cities to an integer value.<br><br>Finally some non-Euclidean traveling salesman problems are generated by assigning distances between towns uniformly at random from {20, ..., 180}. Note that these distances will not satisfy common properties of distances or norms (such as the triangle inequality).<br><br>Laumanns M, Thiele L, Zitzler E (2006) An efficient, adaptive parameter variation scheme for metaheuristics based on the epsilon-constraint method. European Journal of Operational Research 169(3):932 – 942, ISSN 0377-2217, URL http://dx.doi.org/http://dx.doi.org/10.1016/j.ejor.2004.08.029.<br><br>Przybylski A, Gandibleux X, Ehrgott M (2010) A two phase method for multi-objective integer programming and its application to the assignment problem with three objectives. Discrete Optimization 7(3):149 – 165, ISSN 1572-5286, URL http://dx.doi.org/https://doi.org/10.1016/j.disopt.2010.03.005.<br><br>Özpeynirci O, Köksalan M (2010) An exact algorithm for finding extreme supported nondominated points of multiobjective mixed integer programs. Management Science 56(12):2302–2315, URL http://dx.doi.org/10.1287/mnsc.1100.1248.<br><br>These use an extended LP file format where multiple objectives are defined as additional constraints after the original problem's constraints. The right-hand-side value of the last constraint defines the number of objectives.
DOI: 10.6084/m9.figshare.729084.v1
title: Visual data of patients with amblyopia of different ages treated with full-time occlusion therapy

description: Data of amblyopic patients’ Snellen's visual acuity scores assessed at regular periods during of full-time occlusion therapy, which was maintained over 32 weeks. Refractive error of the amblyopic eye is also provided. ET: amblyopic eye was esotropic, XT: amblyopic eye was exotropic.
DOI: 10.6084/m9.figshare.10305506.v1
title: Raw data for: Functional losses in ground spider communities due to habitat-structure degradation under tropical land-use change

description: Current dataset presents raw data on ground spider communities behind the research article "Functional losses in ground spider communities due to habitat-structure degradation under tropical land-use change" by Anton M. Potapov, Nadine Dupérré, Malte Jochum, Kerstin Dreczko, Bernhard Klarner, Andrew D. Barnes, Valentyna Krashevska, Katja Rembold, Holger Kreft, Ulrich Brose, Rahayu Widyastuti, Danilo Harms, Stefan Scheu, published in Ecology. <br>The study was conducted in the framework of the EFForTS project (http://www.uni-goettingen.de/en/310995.html), investigating ecological and socioeconomic changes associated with the transformation of lowland rainforest into agricultural systems. Four land-use systems – rainforest (forest, F), jungle rubber agroforest (J), rubber monoculture (R) and oil palm monoculture (O) were studied across two regions (Harapan and Bukit Duabelas landscape) in Jambi Province, Sumatra, Indonesia. <br>The data set consists of four files - two community matrices of spiders, one table describing the sampling sites and one table describing the taxonomy and traits of spiders. The data based on two collection events with different methods, different years and different sampling areas. Thus, the two community matrices are not directly comparable.
DOI: 10.6084/m9.figshare.12751931.v1
title: Rodriguésia - Material Suplementar / Supplementar Material

description: <b>Frutas nativas do Rio Grande do Sul Brasil: </b><b>riqueza e potencial alimentício</b> <i>Native fruits of Rio Grande do Sul, Brazil: richness and potential as food</i><i><br></i>
DOI: 10.6084/m9.figshare.26656750.v1
title: Additional file 6 of Characters evolution of Encyclia (Laeliinae-Orchidaceae) reveals a complex pattern not phylogenetically determined: insights from macro- and micromorphology

description: Additional file 6. A list of GenBank ID numbers. Table S9. A list of GenBank ID numbers for all DNA sequences used in the phylogenetic analyses, both from the NCBI database and obtained by the one of the co-authors. Table S10. A list of GenBank ID numbers only for new DNA sequences used in the phylogenetic analyses obtained by the one of the co-authors.
DOI: 10.6084/m9.figshare.28815281.v1
title: Les musiques tunisiennes d’aujourd’hui d’influence jazz

description: Le paysage sonore tunisien a connu de profonds changements au cours des dernières décennies, tant sur le plan social, politique, technologique et économique. Ces changements ont également eu un impact signifcatif sur la façon dont les gens perçoivent et apprécient la musique. De nos jours, les musiques occidentales continuent d’avoir un impact majeur sur notre relation à la musique, et plus particulièrement sur la manière dont nous l’apprécions. Dans ce réseau d’infuence, les musiques de jazz font leur apparition.
DOI: 10.17632/bnywhjwzh5
title: Diseases of the pancreas

description: The dataset is still replenishing with the help of the group of Professor Litvin A.A. from the Regional Clinical Hospital and Immanuel Kant Baltic Federal University (Surgery Department).
It includes "symptoms-diagnosis" of hospitalized patients at the arrival day,  three, five, seven, twelve-fifteen, 16-30 days later and on the day of the patient's discharge.  After the end of gathering information, it would be coded for testing of the Cognitive hybrid diagnostic system supporting decisions regarding health of patients with suspected cancer or chronic pancreatitis. The system is now being started to develop.
DOI: 10.6084/m9.figshare.24844344.v1
title: Microbiome single-cell transcriptomics reveal functional heterogeneity of metabolic niches covering more than 2,500 species in the rumen

description: Deciphering the activity of individual microbes within complex communities and environments remains a challenge. Here, we developed microbiome single-cell transcriptomics (MscT) using droplet-based single-cell RNA sequencing and pangenome-based computational analysis to characterize the functional heterogeneity of the rumen microbiome. We generated a microbial genome database (Bovine Gastro Microbial Genome Map, BGMGM) as a functional reference map for the construction of a single-cell transcriptomic atlas of the rumen microbiome. The atlas includes 174,531 microbial cells and 2,534 species, of which 172 were core active species grouped into 12 functional clusters. We detected single-cell level functional roles, including <i>Basfia succiniciproducens</i>, which has a key role in the carbohydrate metabolic niche of the rumen microbiome. Furthermore, we explored functional heterogeneity and revealed metabolic niche trajectories driven by biofilm formation pathway genes within <i>B. succiniciproducens</i>. Our results provide a resource for studying the rumen microbiome and illustrate the diverse functions of individual microbial cells that drive their ecological niche stability or adaptation within the ecosystem.
DOI: 10.6084/m9.figshare.25577217.v1
title: RNA-seq Data FPKM values

description: RNAseq Data report