cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22280632.v2
title: Supplemental Materials for: A standardized quantitative analysis strategy for stable isotope probing metagenomics DOI: https://doi.org/10.1128/msystems.01280-22

description: <strong>Table S1. </strong><em>E. coli</em> AFE (%) in each treatment condition. <strong>Table S2. </strong>Characteristics of pre-centrifugation spike-ins. To produce distinct distribution patterns along the density gradient, some spike-ins were artificially enriched with 13C through PCR by adjusting the ratio of unlabeled dNTPs and uniformly-labeled 13C dNTPs. Theoretical AFE values are reported based on the ratio of labeled dNTPs, but actual AFE values were not experimentally confirmed. <strong>Table S3. </strong>Comparison of various abundance estimation strategies. All results were derived from the qSIP analysis method. Sensitivity and specificity were averaged across the seven treatment conditions. <strong>Table S4. </strong>Average total coverage across all fractions for <em>E. coli</em> in different treatment conditions after subsampling from 100% to 0.001% of the original <em>E. coli </em>sequence reads. <strong>Table S5.</strong> Comparison of MW-HR-SIP and qSIP methods for detecting isotopic labeling of <em>E. coli</em> at different levels of total genome coverage across the density gradient. ‘True’ indicates <em>E. coli</em> was correctly identified to be isotopically labeled (true positive), and ‘false’ indicates <em>E. coli</em> was incorrectly identified as unlabeled (false negative). NA corresponds to the failure of the MW-HR-SIP algorithm with that dataset. <strong>Table S6.</strong> The impact of genome coverage levels on detecting isotope incorporation using the qSIP model. <strong>Table S7.</strong> Comparison of MAGs retained and the number of false positives detected using the qSIP method after applying different minimum genome coverage thresholds. MAGs were retained if their average total coverage in the unlabeled controls exceeded the coverage threshold. <em>E. coli </em>was the only true positive and had a coverage of 1029X, thus no false negatives were detected using the coverage thresholds below. <strong>Table S8.</strong> Comparison of specificity, sensitivity, and balanced accuracy of the qSIP method after applying minimum AFE thresholds. To be identified as isotopically labeled, the lower 95% CI interval of a genome’s estimated AFE must be greater than the minimum AFE threshold. <strong>Table S9. </strong>Comparison of false positives MAGs identified by the MW-HR-SIP, qSIP, and ΔBD methods. Names of the false positive MAGs are listed in each column. <strong>Table S10. </strong>Comparison of <em>E. coli</em> AFE confidence intervals estimated using qSIP alone, qSIP after first applying MW-HR-SIP, and qSIP after first applying ΔBD method to identify a subset of putatively labeled MAGs. Condition B (“20pct_20ng”) was removed as it <em>E coli </em>was never identified as an isotope incorporator in this condition.
DOI: 10.6084/m9.figshare.25719732.v2
title: Can geodemographic clustering be fair? Incorporating social fairness in crisp and fuzzy approaches through a unified framework

description: Geodemographic analysis involves clustering geographic areas into socio-demographically homogeneous groups. However, most existing methods prioritize overall effectiveness, measured by minimizing total costs, potentially misrepresenting specific subgroups within the data. Despite a growing literature on fair clustering, it focuses almost exclusively on crisp clustering, failing to address the inherent fuzziness of the real world. This study addresses these gaps by introducing a socially-fair geodemographic clustering (SFGC) framework, which modifies the classical fuzzy-c means (FCM) by incorporating a new cost function that, instead of minimizing total costs, minimizes the maximum average cost across all subgroups. SFGC also introduces a gradient descent-based algorithm to optimize this new cost function. In addition, SFGC can be directly adapted to crisp clustering, facilitating practical implementation and comparison of clustering algorithms.
DOI: 10.6084/m9.figshare.5907496.v1
title: Millikan and the contact potential question on the photoelectric effect experiment

description: Abstract It will be presented in this paper the theoretical and experimental Millikan's approach to the contact potential question in his experiments about the photoelectric effect. The 1923 Nobel prize won by Millikan, had as motivation his experiments which resulted on the electron charge (oil drop experiment) and Planck constant (photoelectric effect experiment) measurements. The precision with which Millikan obtained the Planck constant is due to the importance Millikan attributed to the contact potential between two electrically connected metals. Presenting his calculations on the contact potential in one of his 1916 papers, Millikan showed one result subtly wrong, apparently not perceived by the scholars of the subject. In 1921, Millikan corrected the erroneous equation without mention the 1916 mistake. If this mistake was not due to bad digitation, apparently there is no plausible justification for their occurency.
DOI: 10.6084/m9.figshare.5909998.v1
title: Data and code from: Ecosystem functional response across precipitation extremes in a sagebrush steppe

description: <b>usses_water: Experimental Test of Climate Change Impacts on Grassland ANPP</b><br>Research project data and code for an analysis of drought and irrigation experiment at US Sheep Experiment State (USSES) near Dubois, ID.Goal is to quantify the impact of a 50% increase/decrease of precipitation on:<br>* ANPP through time* Relationship of ANPP to soil moisture* Species composition<br><b>Running the code</b><br><br>To fully run this code you will need R and a number of R packages.Running `00_source_usses_water_scripts` in the `code/` directory will run all necessary scripts to complete the analysis.The code will also stop and send errors letting you know what R packages need to be installed.Once all packages are installed, the code should run all the way through.<br>You must source the script from RStudio, rather than from command line, because we use some Rstudio-specific commands to set working directories.<br><b>Citation information</b><br>This work has been accepted for publication in PeerJ (https://peerj.com/).It is currently in press, so for now please cite as<br>Tredennick, A.T., A.R. Kleinhesselink, J.B. Taylor, and P.B. Adler. (In press). Ecosystem functional response across precipitation extremes in a sagebrush steppe. <i>PeerJ</i>.<br>The preprint can be found at: https://www.biorxiv.org/content/early/2018/01/24/195594.<br>Additionally, please cite the Figshare fileset if reusing data or code as:<br>Tredennick, A.T., A.R. Kleinhesselink, J.B. Taylor, and P.B. Adler. Data and code from: Ecosystem functional response across precipitation extremes in a sagebrush steppe. Figshare. 10.6084/m9.figshare.5909998 <br>
DOI: 10.6084/m9.figshare.7097675.v1
title: Data with Warming and Grazing.xlsx

description: Grazing buffers the effect of climatic change on species diversity of seedlings in an alpine meadow on the Tibetan Plateau
DOI: 10.17632/3c9sgsk8mz
title: Supplemental Data Parathyroidectomy improves bone density in women with primary hyperparathyroidism and preoperative osteopenia

description: Supplemental Table 1, Figure 1 et Figure 2
DOI: 10.17632/96v329bg7g
title: Multiple Early Factors Anticipate Post-Acute COVID-19 Sequelae. Su et al

description: Post-acute sequelae of COVID-19 (PASC) represent an emerging global crisis. However, quantifiable risk-factors for PASC and their biological associations are poorly resolved. We executed a deep multi-omic, longitudinal investigation of 309 COVID-19 patients from initial diagnosis to convalescence (2-3 months later), integrated with clinical data, and patient-reported symptoms. We resolved four PASC-anticipating risk factors at the time of initial COVID-19 diagnosis: type 2 diabetes, SARS-CoV-2 RNAemia, Epstein-Barr virus viremia, and specific autoantibodies. In patients with gastrointestinal PASC, SARS-CoV-2-specific and CMV-specific CD8+ T cells exhibited unique dynamics during recovery from COVID-19. Analysis of symptom-associated immunological signatures revealed coordinated immunity polarization into four endotypes exhibiting divergent acute severity and PASC. We find that immunological associations between PASC factors diminish over time leading to distinct T3 immune states. Detectability of most PASC factors at COVID-19 diagnosis emphasizes the importance of early disease measurements for understanding emergent chronic conditions and suggests PASC treatment strategies.
DOI: 10.6084/m9.figshare.18318890.v1
title: Mature_immature_analysis.R

description: Here we provide the script needed to reproduce the kernel density plots and gamlss analysis of mature and immature elasmobranch both generla pattern and comparing PPAs and UPAs
DOI: 10.6084/m9.figshare.21701231.v1
title: PSY-COVID PSS-4 Dataset

description: This is the dataset of the online survey PSY-COVID in its third wave (2022) used in the study "Psychometric properties of the Perceived Stress Scale-4 (PSS-4) in Colombians with university education". It contains data provided by 1,911 Colombians with university studies. The data set contains data on sociodemographic variables (age, gender, status, economic and employment) and clinical variables (stress, depression, anxiety, resilience, post-traumatic growth).
DOI: 10.17035/d.2024.0312242926
title: Assessing the quality of plasma etched InP laser facets - data

description: Broad area InP lasers were manufactured utilising both etched and cleaved facets with a variety of different cavity lengths. AFM topography data of eight sampled etched facets, four near the wafer centre and four near the wafer edge, have been provided for all five wafers in the form of .spm files. These files can be viewed with free and open access software e.g. Gwyddion. The “DeviceLookup.csv” file contains details on the p-contact dimensions, cavity lengths, the type of facets used by the device (EE for etched facets and CC for cleaved) along with the file name for the corresponding PIV data. The remaining .csv files contain the pulsed optical power versus current (PI) and current-voltage (IV) data measured using a calibrated integrating sphere at a controlled temperature of 21 degC. Current is measured in A, power in W and voltage in V
DOI: 10.17632/53j3vrhddj
title: Opposing regulation of the STING pathway in hepatic stellate cells by NBR1 and p62 determines the progression of hepatocellular carcinoma

description: Hepatocellular carcinoma (HCC) emerges from chronic inflammation to which activation of hepatic stellate cells (HSCs) contributes by shaping a pro-tumorigenic microenvironment. Key to this process is p62, whose inactivation leads to enhanced hepatocarcinogenesis. Here, we show that while p62 positively regulates STING ubiquitination by TRIM32 by displacing NBR1, which results in the activation of the interferon (IFN) cascade, NBR1 prevents TRIM32 interaction with and the activation of STING, leading to impaired IFN synthesis. NBR1 also antagonizes STING function by promoting its trafficking from the Golgi to the endosome-lysosomal degradative cascade independent of autophagy. Importantly, NBR1 deletion completely reverts the tumor-promoting function of p62-deficient HSCs. The upregulation of the STING-IFN pathway by NBR1 deficiency enhances the anti-tumor response mediated by CD8+ T cells. These results identify NBR1 as a synthetic vulnerability of p62-deficiency in HSCs. NBR1 loss, by promoting the STING/IFN pathway, boosts anti-tumor CD8+ T cell responses to restrain HCC.
Nbr1 knock-out and wild-type hepatic stellate cells were profiled in three biological replicates under normal conditions.
DOI: 10.6084/m9.figshare.18133829.v1
title: 配比表.xlsx

description: This file is the mix proportions of CA-UHPCs in this study.
DOI: 10.6084/m9.figshare.25764189.v1
title: Feature enhanced ensemble modeling with voting optimization for credit risk assessment

description: The ChinaZJB dataset consists of 1,329 valid samples of SMEs after merging the non-financial behavioral information and soft information on credit rating with the financial information, loan information, and non-financial basic information found in the annual loan ledger data. Among them, 108 SMEs have default records, while 1,221 SMEs have no default records, resulting in an imbalanced ratio of approximately 1:11.Five datasets from the UC Irvine (UCI) machine-learning repository, that is, the Polish 1, Polish 2, Polish 3 , Australian, and Taiwan credit datasets, were used for robustness checks.
DOI: 10.17632/d4tj3vx88m
title: Clinical characteristics and genetic analysis of 14 patients affected with acne fulminans and hidradenitis suppurativa: ASH syndrome, a new phenotypic entity

description: Legend of Mendeley Supplementary figures: 1A Left axilla HS lesions at Day 0, 1B Left axilla HS lesions at remission after 7 months of targeted antibiotherapy, 1C Acne fulminans at Day 0, 1D Acne fulminans after 6 weeks of targeted antibiotherapy.

Mendeley supplemental table. Variants identified in 16 of the 74 genes from a panel of genes associated with acne, auto-inflammation and antimicrobial activity
DOI: 10.6084/m9.figshare.14095927.v1
title: driving style

description: this is the original data of bus driver and taxi drivers and driving style
DOI: 10.6084/m9.figshare.27600417.v1
title: RAST Annotation Results for <i>Bremerella cremea</i> LHWP2

description: This file contains RAST annotation results, including gene functions, pathways, and subsystem categories for the genome of Bremerella cremea LHWP2
DOI: 10.6084/m9.figshare.28326886.v1
title: Degree-heterogeneous Latent Class Analysis for High-dimensional Discrete Data

description: The latent class model is a widely used mixture model for multivariate discrete data. Besides the existence of qualitatively heterogeneous latent classes, real data often exhibit additional quantitative heterogeneity nested within each latent class. The modern latent class analysis also faces extra challenges, including the high-dimensionality, sparsity, and heteroskedastic noise inherent in discrete data. Motivated by these phenomena, we introduce the Degree-heterogeneous Latent Class Model and propose an easy-to-implement <i>HeteroClustering</i> algorithm for it. HeteroClustering uses heteroskedastic PCA with l2 normalization to remove degree effects and perform clustering in the top singular subspace of the data matrix. We establish the result of exact clustering under minimal signal-to-noise conditions. We further investigate the estimation and inference of the high-dimensional continuous item parameters in the model, which are crucial to interpreting and finding useful markers for latent classes. We provide comprehensive procedures for global testing and multiple testing of these parameters with valid error controls. The superior performance of our methods is demonstrated through extensive simulations and applications to three diverse real-world datasets from political voting records, genetic variations, and single-cell sequencing.
DOI: 10.17632/8jdpbj69sm
title: Dados financeiros das empresas listadas em 2023

description: Base de dados financeiros das empresas listadas na B3, em setores não financeiros, contendo nome, tipo de ativo e setor de atuação de todas as empresas. Base de dados em construção para execução do Trabalho de conclusão de Curso.
DOI: 10.17632/dwfmg6jdhg
title: Social Preferences in the Public Goods Game –  An Agent-Based Simulation with EconSim

description: Dataset of the EconSim agent-based model for "Social Preferences in the Public Goods Game"
DOI: 10.6084/m9.figshare.1453184.v1
title: Three Drug Study Dataset

description: Guide and dataset accompanying Wardle, Marcus & de Wit (under review). "A preliminary investigation of individual differences in subjective responses to d-amphetamine, alcohol, and delta-9-tetrahydrocannabinol"
DOI: 10.6084/m9.figshare.25308796.v1
title: Hyperspectral pressure-volume curves to estimate leaf turgor loss

description: Turgor Loss Point (TLP) is an important proxy for plant drought tolerance, species habitat suitability, and drought-induced plant mortality risk. Thus, TLP serves as a critical tool for evaluating climate change impacts on plants, making it imperative to develop high-throughput and in-situ methods to measure TLP. We developed hyperspectral pressure-volume curves to estimate TLP using leaf spectral reflectance. First, we developed PLSR models to estimate leaf water potential (WP or psi) and relative water content (RWC) using spectral reflectance (400-2400 nm). We used estimated values to construct hyperspectral PV-curves and compared the accuracy of estimating TLP from reflectance to empirical PV-curves using the Pressure-Volume Analysis Spreadsheet tool (PVAST, the most widely used analytical method; Sack et al., 2010). Additionally, we compared TLPs extracted from PVAST to TLPs automatically extracted by segmented regression, a tool commonly used to automatically parameterize physiological.
DOI: 10.6084/m9.figshare.5554528.v1
title: Experiment CLA-SubjectE-160119-3States

description: Experiment in which subject performed 3 imageries of left and right hand motion and a passive state.
DOI: 10.17632/7cgsh88krx
title: Mobile phone hardware component dataset

description: Mobile phone components from Android phones were collected to create this dataset. There are total eight folder (based on mobile phone brand Name) and each of these folder contains 13 sub-folders (based on mobile phone component name). Therefore, a total of 206 images have been collected.
DOI: 10.17632/97brdz5339
title: Dr

description: The raw data and code accompanies the manuscript: K. Andraka, K. Kondrakiewicz, K. Rojek-Sito, K. Ziegart-Sadowska, K. Meyza, T. Nikolaev, A. Hamed, M. Kursa, M. Wójcik, K. Danielewski, M. Wiatrowska, E. Kublik, M. Bekisz, T. Lebitko, D. Duque, T. Jaworski, H. Madej, W. Konopka, P. M. Boguszewski, E. Knapska "Central amygdala circuits activated by social stimuli indicating imminent vs remote danger promote different defensive behaviors"
DOI: 10.17632/hgskyckxb7
title: Gut microbiome alterations in high-fat-diet-fed mice are associated with antibiotic tolerance

description: Raw Metabolomics data, the data set is related to figure 3d, Extended Data Fig. 5 and 6.
DOI: 10.17632/yshpvk5kyt
title: Gelinas_Data_Stable Carbon Isotope Values of Bacteria-Specific Fatty Acids

description: Dataset for the article: "Stable Carbon Isotope Values of Bacteria-Specific Fatty Acids to Assess the Reactivity of Terrestrial and Marine Organic Matter in Sediment of the St. Lawrence Estuary and Gulf" by Frédéric Leone, Yeganeh Mirzaei, Anic Imfeld, Bahar Pakseresht, Brandon Findlay, Yves Gélinas
DOI: 10.6084/m9.figshare.11907081.v3
title: The Histoire ancienne jusqu’à César: A Digital Edition (The Values of French)

description: <i>The</i> Histoire ancienne jusqu’à César: <i>A Digital Edition</i>, ed. by Hannah Morcos, Simon Gaunt, Simone Ventura, Maria Teresa Rachetta, Henry Ravenhall, Natasha Romanova, and Luca Barbieri; technical ed. Paul Caton, Ginestra Ferraro, Marcus Husar, and Geoffroy Noël (ISBN: 978-1-912466-15-3). <br>The latest version of the text can be browsed on <i>The Values of French </i>website: http://www.tvof.ac.uk/textviewer/ (available until 2030).<br>This edition is the primary output of the ERC-funded project <i>The Values of French Language and Literature in the European Middle Ages</i> (EU Horizon 2020, grant agreement no. 670726), directed by Prof. Simon Gaunt (PI) and hosted by the Department of French, King's College London. For more information, visit https://tvof.ac.uk/ (available until 2030).<br>
DOI: 10.6084/m9.figshare.11916720.v1
title: High-throughput Density Functional Perturbation Theory and Machine Learning Predictions of Infrared, Piezoelectric and Dielectric Responses

description: Many technological applications depend on the response of materials to electric fields, but available databases of such responses are limited. Here, we explore the infrared, piezoelectric and dielectric properties of inorganic materials by combining high-throughput density functional perturbation theory and machine learning approaches. We compute {\Gamma}-point phonons, infrared intensities, Born-effective charges, piezoelectric, and dielectric tensors for 5015 materials in the JARVIS-DFT database. We find 3230 and 1943 materials with at least one far and mid-infrared mode, respectively. We identify 577 high-piezoelectric materials, using a threshold of 0.5 C/m2. Using a threshold of 20, we find 593 potential high-dielectric materials. Importantly, we analyze the chemistry, symmetry, dimensionality, and geometry of the materials to find features that help explain variations in our datasets. Finally, we develop high-accuracy regression models for the highest infrared frequency and maximum Born-effective charges, and classification models for maximum piezoelectric and average dielectric tensors to accelerate discovery.
DOI: 10.6084/m9.figshare.22201882.v1
title: Dormouse FEA

description: Finite element models, project files, script files, and results files for the mandibles of five dormouse species: Eliomys quercinus (mainland garden dormouse), Eliomys quercinus ophiusae (giant subspecies of garden dormouse from Formentera), Hypnomys onicensis (extinct giant dormouse from the Balearic islands), Hypnomys morpheus (extinct giant dormouse from the Balearic islands), and Leithia melitensis (extinct giant dormouse from Sicily.
DOI: 10.6084/m9.figshare.25634952.v1
title: Fully Inductive N-ary Link Prediction Datasets

description: Datasets for Paper "Fully Inductive Link Prediction on N-ary Relational Facts via Semantic Hypergraph Reasoning"
DOI: 10.6084/m9.figshare.9887528.v1
title: Human Nasal Cavity - Male 33 years old - Septal Deviation - CT-Data

description: In this data set the computed tomography image data of a 33 year old patient with deviation of the nasal septum is provided. Additional information, as for example the segmentation of the nasal cavity will be provided subsequently.
DOI: 10.17632/3jg3z44fnj
title: Using In Vitro Gastrointestinal (GI) Tract Digestive Products to Investigate Fermentation Dynamics of Lactobacillus rhamnosus GG, Bifidobacterium animalis subsp. lactis BB-12, and Escherichia coli

description: The raw data obtained from this experiment are presented in the document, including bacterial cell activity as well as some metabolite concentrations.
DOI: 10.17632/7xy79mnsd9
title: HF Dataset

description: It consist of 898 Patients Dataset with 13 different features including Death Rate (output).
DOI: 10.17632/vd7f9fzbt6
title: Data for: Structural health monitoring and performance analysis of a 12-story recycled aggregate concrete structure
DOI: 10.6084/m9.figshare.13014299.v1
title: A dataset of remote-sensed Forel-Ule Index for global inland waters during 2000–2018

description: We present the first time series FUI dataset for large global lakes from 2000–2018 based on MODIS observations. This dataset provides significant information on spatial and temporal changes of water colour for global large lakes during the past 19 years. It will be valuable to studies in search of the drivers of global and regional lake colour change, and the interaction mechanisms between water colour, hydrological factors, climate change, and anthropogenic activities.