cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.988376_d265
title: Participant 4 in the WAY-EEG-GAL dataset.  328 grasp-and-lift trials with different weights and surfaces during which EEG, EMG, kinematics, and kinetics were recorded.

description: WAY-EEG-GAL is a dataset designed to allow critical tests of techniques to decode sensation, intention, and action from scalp EEG recordings in humans who perform a grasp-and-lift task. Twelve participants performed lifting series in which the object’s weight (165, 330, or 660g), surface friction (sandpaper, suede, or silk surface), or both, were changed unpredictably between trials, thus enforcing changes in fingertip force coordination. In each of a total of 3,936 trials, the participant was cued to reach for the object, grasp it with the thumb and index finger, lift it and hold it for a couple of seconds, put it back on the support surface, release it, and, lastly, to return the hand to a designated rest position. We recorded EEG (32 channels), EMG (five arm and hand muscles), the 3D position of both the hand and object, and force/torque at both contact plates.
DOI: 10.6084/m9.figshare.9961673.v1
title: holdout.json

description: Holdout from collection of user-generated online news comments published from 2015-2017 as part of a now-defunct commenting platform. For use in furthering research into online toxicity, bias, and harassment.
DOI: 10.17632/3c6ztw5nft
title: BaitBuster-Bangla: A Comprehensive Dataset for Clickbait Detection in Bangla with Multi-Feature and Multi-Modal Analysis

description: This dataset is a multi-feature and multi-modal dataset for Bangla clickbait detection in video sharing platforms. The dataset is collected from YouTube using its official public API with the objective of classifying clickbait content in the Bangla language. The dataset consists of 253,070 entries with 18 columns covering a curated list of 28 Not Clickbait, and 26 Clickbait Bangla youtube channels. The dataset provides valuable information for studying clickbait content and includes various metadata related to the videos, user engagement statistics, and labels. The dataset has been labeled in three different strategies: i) pre-defined auto labels, ii) labels by human annotator, and iii) labels by fine-tuned AI model. However, human labels are are available for 10000 entries. The dataset is available in three different formats: xlsx, csv, and parquet.
DOI: 10.6084/m9.figshare.25195910.v1
title: PRISMA-P checklist for dentin bone graft for socket preservation : systematic review

description: Socket preservation is a surgical procedure aimed at preserving the dimensions of the alveolar bone following tooth extraction. It is performed by filling the extraction socket with bone graft material either with or without a barrier membrane. Recently, dentine obtained from extracted teeth has been tried as an autograft for socket preservation. Studies have compared the use of dentin to other bone grafts, however, systematic reviews evaluating the efficacy of dentin for socket preservation are limited. Hence, this systematic review protocol is proposed to generate evidence on the efficacy of dentin as a viable alternative to other bone graft materials for socket preservation.
DOI: 10.17632/678mpp8vvw
title: Understanding the Boundless Potential of Infinite Numbers in Mathematics

description: By introducing infinite numbers, numerous
advantages arise, such as accurately representing limits, divergences in
integrals and infinite series, and extending calculations to infinity. This
mathematical advancement opens doors to exploring uncharted territories,
offering valuable insights and breakthroughs.
DOI: 10.6084/m9.figshare.14330255.v1
title: 6_HaplotypeDiversity

description: Haplotype Diversity Data
DOI: 10.6084/m9.figshare.14977281.v1
title: Tabula Sapiens Splicing

description: This h5ad contains splicing differences in the Tabula Sapiens atlas. For each cell, a splicing score, called the SpliZ, is assigned to each gene with enough informative splicing information (Olivieri et. al. 2021). This object contains both gene expression values (labeled with the gene name, e.g. “MYL6”) and splicing values (labeled with the gene name and “SpliZ”, e.g. “MYL6_SpliZ”). Low SpliZ values correspond to shorter introns on average across the gene, while high SpliZ values correspond to longer introns on average. The splice junctions for each gene in a cell have been called based on the SICILIAN method (Dehghannasiri et. al., 2020).
DOI: 10.6084/m9.figshare.25365508.v1
title: Image Super-resolution Inspired Electron Density Prediction

description: Pre-trained models in https://doi.org/10.48550/arXiv.2402.12335
DOI: 10.17632/9zsxjtzfr7
title: HTR-1.3 solver: Predicting electrified combustion using the hypersonic task-based research solver

description: This manuscript presents an updated open-source version of the Hypersonics Task-based Research (HTR) solver. The solver, whose main features are presented in Di Renzo et al. (2020) [9] and Di Renzo & Pirozzoli (2021) [10], is designed for direct numerical simulation of reacting flows at high Reynolds numbers. This new version extends the applications of the HTR solver to turbulent combustion in the presence of external electric fields. In particular, a new distributed Poisson solver compatible with heterogeneous architectures has been incorporated in the algorithm to compute the electric potential distribution in bi-periodic configurations. The drift fluxes of the electrically charged species are now included in the transport equations using a targeted essentially non-oscillatory scheme. A verification of these new features of the solver is provided using one-dimensional burner stabilized flames, whereas a three dimensional turbulent flame is utilized to discuss the scalability of the proposed numerical tool.
DOI: 10.6084/m9.figshare.21062545.v1
title: Supplementary Material for: Analysis of Barrett’s Esophagus and Its Risk Factors: A Cross-Sectional Study of 10,122 Subjects at a Japanese Health Examination Center

description: <b><i>Introduction:</i></b> <i>Helicobacter pylori</i> eradication is expected to significantly change the prevalence of Barrett’s esophagus (BE). However, few reports on this relationship exist. We analyzed the risk factors of BE using the current consensus on length of BE considering <i>H. pylori</i> infection status. <b><i>Methods:</i></b> We analyzed 10,122 individuals (5,962 men; mean age = 52.9 ± 9.9 years) who had undergone esophagogastroduodenoscopy as part of a medical checkup. Correlations among factors including <i>H. pylori</i> infectious status, endoscopic findings, and BE ≥1 cm were analyzed. <b><i>Results:</i></b> Prevalence of BE, long-segment BE, and esophageal adenocarcinoma was 22.5%, 0.014%, and 0%, respectively. Logistic regression analysis showed that the risk factors for BE were hiatal hernia (odds ratio [OR]: 2.89 [2.59–3.24]), female sex (OR: 0.52 [0.46–0.59]), social drinking (OR:0.77 [0.68–0.87]), <i>H. pylori</i> eradication therapy (OR: 1.34 [1.19–1.51]), proton pump inhibitor (PPI) use (OR: 1.52 [1.18–1.96]), bile reflux (OR: 1.18 [1.04–1.33]), age ≥50 years (OR: 1.13 [1.02–1.26]), and nonsteroidal anti-inflammatory drug (NSAID) use (OR: 1.29 [1.02–1.62]). Although reflux esophagitis (RE) was more common in <i>H. pylori</i>-negative patients (17.2%) than in those after <i>H. pylori</i> eradication therapy (11.8%, <i>p</i> &lt; 0.00001), the latter was correlated with BE, disputing RE as a strong risk factor for BE. Therefore, we conducted a subgroup analysis; most of the risk factors except for PPI use (<i>p</i> = 0.75), H2-receptor antagonist use (<i>p</i> = 0.078), and atrophic gastritis absence (<i>p</i> = 0.72) were positively correlated with BE after <i>H. pylori</i> eradication therapy compared with <i>H. pylori</i>-negative status. <b><i>Conclusions:</i></b> <i>H. pylori</i> eradication, bile reflux, PPI use, and NSAID use were risk factors for BE along with hiatal hernia, male sex, and older age.
DOI: 10.6084/m9.figshare.28874474.v1
title: <b>Convergent patterns of horizontal gene transfer among holoparasitic plants: driving the evolution of parasitic lifestyle</b>

description: The protein sequences of horizontally transferred genes and associated phylogenetic trees in 1four independently evolved parasitic plant lineages.
DOI: 10.6084/m9.figshare.12516640.v1
title: hgcAB_concatenated_alignment

description: Concatenated alignment of 650 select hgcAB sequences used in phylogeny with 4 fused hgcAB sequences to root the tree
DOI: 10.6084/m9.figshare.1539609.v2
title: Fileset to accompany "The relationship between cancer incidence, stage, and poverty in the United States"

description: This fileset contains 3 data sets referenced in the paper, "The relationship between cancer incidence, stage, and poverty in the United States", submitted as a preprint in September 2015 to the University at Albany preprint server.
DOI: 10.17632/9dbd9jcdvs
title: Facebook Audience Insight on Food Choice

description: We collected the data through an online platform by performing a query search on Facebook Audience Insights Interests. The keywords that we use in the question quest are based on the United Nations Food and Agriculture Organisation (FAO) Food Balance Sheet (FBS) which is retrieved from FAOStat in May 2020. The data was gathered between 15 May and 2 July 2020. With a sample size of 100-150 million viewers or about 36.95 per cent-55.43 percent of Indonesia's 2019 population, we limited our sample to Indonesia. The dataset is made up of ten tables that can be separately analyzed. For each table, we carry out exploratory data analysis (EDA) to provide more insights.
DOI: 10.17632/cvk8wnfm36
title: Supplemental movies

description: These movies are supplemental material used for the article submitted as a preprint here : https://www.biorxiv.org/content/10.1101/2022.12.19.521111
DOI: 10.6084/m9.figshare.695950.v36
title: Data of torque meter experiments

description: Pre-analyzed data and metadata of self-learning experiments.
DOI: 10.17632/pxvh6jhtvt
title: Code for ``Strategic Digitization in Currency and Payment Competition" by Lin William Cong and Simon Mayer

description: This repository provides the code used for the numerical solution in the paper ``Strategic Digitization in Currency and Payment Competition." 

Please unpack the zip code and follow the instructions of the Readme file to replicate the figures in the paper.
DOI: 10.6084/m9.figshare.12443414.v1
title: H3K27ac Signal Track for H1376, PAEC (ECS), DHL4, and ARPE

description: Genome-wide signal tracks for each sample were generated in two stages: (i) assess ChIP–seq quality and obtain the predominant fragment length using phantompeakqualtools (https://code.google.com/archive/p/phantompeakqualtools/); (ii) use align2rawsignal (https://code.google.com/archive/p/align2rawsignal/wikis/Method.wiki) to generate signal track (parameters: -n = 5, -k = epanechnikov, -l = [frag-ment length from step (i)], -w = 150, -f = 0).
DOI: 10.6084/m9.figshare.25943893.v2
title: <b>An interpretable deep learning framework for genome-informed precision oncology</b>

description: Cancers result from aberrations in cellular signaling systems, typically resulting from driver somatic genome alterations (SGAs) in individual tumors. Precision oncology requires understanding the cellular state and selecting medications that induce vulnerability in cancer cells under such conditions. To this end, we developed a computational framework consisting of two components: 1) A representation-learning component, which learns a representation of the cellular signaling systems when perturbed by SGAs, using a biologically motivated and interpretable deep learning model. 2) A drug-response-prediction component, which predicts drug response by leveraging the information of the cellular state of the cancer cells derived by the first component. Our cell-state-oriented framework significantly improves drug response prediction accuracy compared to models using SGAs directly in cell lines. Moreover, our model performs well with real patient data. Importantly, our framework enables the prediction of response to chemotherapy agents based on SGAs, thus expanding genome-informed precision oncology beyond molecularly targeted drugs.
DOI: 10.17632/mpf3sfncjm
title: Panel dataset of fossil fuel extraction and electricity generation across commuting zones in the contiguous U.S.: 2004 to 2021

description: Dataset used for 'Stack & O'Rourke (2024). Concentrated Declines, Distributed Growth, and the Challenges of Balancing the Green Energy Transition in the US.' The purpose of this dataset is to understand how the geography of primary energy production is changing, and the implications of this for energy policy, regional development, and a just transition.

It measures energy production in commuting zones in the contiguous U.S. from 2004 to 2021. The contiguous U.S. includes 48 states and Washington D.C., while excluding Hawaii, Alaska, and U.S. overseas territories. This dataset measures energy production in these regions, including coal extraction, oil extraction, natural gas extraction. It also includes a range of utility-scale electricity generation, including: solar, wind, oil, natural gas, coal, nuclear, hydro, and several others.
DOI: 10.6084/m9.figshare.11890263.v1
title: Time series data of microbial communities

description: Time series abundances of bacterial prey species and their morphotypes appearing in time with and without a protist predator species. All microcosms were started with equal abundance for all prey species either with or without the predator (See "Notes" section in the data file for the descriptions of species). Static microcosms consisted of 20 mL Brunner-CR2 medium in 50-mL cell culture flasks, incubated at 25°C. Prey and predator numbers were adjusted in the experimental medium to 1.8 x 10<sup>7 </sup>cells mL<sup>-1</sup> and 4.2 x 10<sup>4</sup> cells mL<sup>-1</sup>, respectively. During the experiment, we performed daily 10-fold dilutions by transferring 10% of the community into fresh medium. All microcosms were sampled 32 times (from 3 to 34 days ). All bacterial species were quantified by plating on Brunner CR-2 medium. All visible, differently coloured colonies were recorded after 2 days of incubation at 25°C using different dilutions from 10<sup>3</sup> to 10<sup>8</sup>. Cell numbers of protist predator were estimated by counting cells fixed with 0.2% Lugol’s iodine solution under an inverted microscope with a counting chamber.
DOI: 10.6084/m9.figshare.19508938.v3
title: Electronic datasets associated with Snake Predators of Bird Eggs: A Review and Bibliography. Journal of Field Ornithology.

description: Electronic datasets S1 and S2 from Barends and Maritz 2022. Snake Predators of Bird Eggs: A Review and Bibliography. Journal of Field Ornithology. In Press.<br>
DOI: 10.6084/m9.figshare.4036077.v1
title: Lake Victoria Atlantis model files

description: This is a complete model setup and files that were used for Prediction of Lake Victoria's response to varied fishing regimes using the Atlantis ecosystem model
DOI: 10.17632/pgk6k3b7j8
title: Crust-mantle interaction during continental deep subduction: evidence from light Mo isotopes in post-collisional mafic igneous rocks from the East Kunlun orogen

description: supplementary materials
DOI: 10.6084/m9.figshare.11825871.v1
title: Comprehensive understanding of co-evolution and fitness cost of mcr-1 and mcr-3 in E. coli strains via long-read sequencing

description: The complete genome sequences of five E. coli strains coharboring mcr-1 and mcr-3 variants were submitted here for reference.<br>
DOI: 10.6084/m9.figshare.26505922.v1
title: Glomerular circadian transcriptomics (meta2d BHQ &lt;0.1)Podocyte circadian transcriptomics (meta2d BHQ &lt;0.1)Kidney circadian proteomics meta2d (p val &lt;0.05)

description: For circadian kidney collection, eight-week-old male and female wildtype (C57BL/6J) mice were kept in Dark-Dark for 36 h prior to the onset of tissue collection and until they were sacrificed by cervical neck dislocation. Circadian time (CT) corresponds to administration of light in the animal room in normal Light-Dark schedule; CT0 indicates 6am. Kidneys were harvested at 4 h intervals for 48 h and immediately snap frozen and stored at -80<sup>o</sup>C for later processing. For the glomerular circadian transcriptomics, glomeruli were sieve-isolated from thawed kidneys and RNA was isolated using TRIzol. RNA was checked for quality and prepared for sequencing in the Genomic Technologies Core Facility in Manchester. RNA-seq counts were normalized using DESeq2 (v1.28.1) and rhythmic genes were identified with MetaCycle. For the kidney circadian proteomics, kidneys from eight-week-old male and female wildtype (C57BL/6J) mice harvested during the time-series tissue collection described above were used for mass spectrometry-based proteomics. Mouse kidneys were enriched for matrix proteins and peptide samples were analyzed by liquid chromatography (LC)-tandem mass spectrometry using a Thermo Exploris 480 mass spectrometer (Thermo Fisher Scientific). The meta2d function from Metacycle was used to identify rhythmic proteins detected in at least 2 out of the 3 replicates per circadian time.For the time-series cell collection, primary podocytes were cultured from kidneys of wildtype mice (C57BL/6J, aged eight weeks) for 14 days. Podocytes were harvested in BL buffer containing 0.1% 1-Thioglycerol (Promega) and immediately snap-frozen at 4 h intervals for 48 h starting at 15 h post-synchronization with dexamethasone. RNA was isolated and purified using a ReliaPrep RNA Cell Miniprep System (Promega) as per manufacturers protocol. RNA was checked for quality and prepared for sequencing in the Genomic Technologies Core Facility in Manchester. RNA-seq counts were normalized using DESeq2 (v1.28.1) and rhythmic genes were identified with MetaCycle.
DOI: 10.6084/m9.figshare.29040771.v1
title: S4 R studio code reproduce Lyons et al 2025 phylogeny from Spider Venom Potency Exhibits Phylogenetic Prey-specificity but Does Not Trade-off with Body Size or Silk Use in Prey Capture.

description: S4 contains the R studio script and base phylogeny used to produce the phylogeny used as part of Lyons et al analyses. The final phylogeny .tre file is also located in S4 folder.
DOI: 10.6084/m9.figshare.9118952.v1
title: Analyzing the Students’ Perception of UML Diagrams: Results of the TAM (Technology Acceptance Model)

description: Models taught in Software Engineering disciplines can facilitate the communication and understanding of systems by practitioners. These models can be expressed by Unified Modeling Language (UML). In the literature, existing reports how professionals perceive the adoption of UML in practice. However, little is known about the students’ perception regarding these models. In this technical report, we present the students’ answers to the Technology Acceptance Model (TAM) questionnaires for five UML diagrams.
DOI: 10.6084/m9.figshare.9739199.v1
title: OPTIMIZATION OF FERMENTATIVE CONDITIONS OF PICHIA MEMBRANIFACIENS FOR SECOND GENERATION ETANOL PRODUCTION

description: Technologies developed in the last decade have made viable the use of lignocellulosic materials for the production of ethanol. However, to improve the fermentative yield some improvements are necessary, among them the search for new microorganisms capable of fermenting sugars with five carbons. Thus, the present research aimed to determine the best pH and temperature for Pichia membranifaciens LJ04 in synthetic medium containing pentose, aiming at the biotechnological production of ethanol from hemicellulosic hydrolysate. The experimental design was completely randomized in Split-Split-Plot, with 3 replicates. The main treatments were pHs (3.5, 4.0 and 4.5), the secondary were temperatures (32 ºC, 37 ºC and 40 ºC) and the tertiary were fermentation periods (0, 6, 12 and 24 hours). It was determined in this study that the ideal conditions were temperature of 32 ºC and pH 4.0-4.5. With these conditions there was higher xylose consumption, high ethanol production, low production of secondary compounds and high rates of cell viability during fermentation.
DOI: 10.17632/5sbwbcmndh
title: Temperature-dependent differences in male and female life history responses to a period of food limitation during development

description: With climate change, animals face both rising temperatures and more variable food availability. Many species have evolved an adaptative response to historic variation in food availability: they grow faster after a period of diet restriction (“compensatory growth”). However, higher temperatures may reduce the capacity for compensatory growth in ectotherms because individuals require more resources to support their increased metabolism. We experimentally tested how higher temperature affects compensatory growth by raising guppies (Poecilia reticulata) at a high or control temperature, and on a normal or temporarily restricted diet during early development. At the control temperature guppies on the restricted diet grew faster once their diet returned to normal. Both sexes showed compensatory growth. At the high temperature, both sexes also increased their growth rates after dietary restriction ended, but the life history outcomes differed. Males at the high temperature matured earlier and were smaller than males reared at the control temperature. In contrast, females at the high temperature matured later and were bigger than females at the control temperature. Our study highlights that rising temperatures could reduce the ability of fish to compensate for periods of low food availability, and that males and females can have different responses to the same environmental stressors.
DOI: 10.17632/r9z37s29wz
title: The Superiority and Feasibility of Fresh Single Blastocyst Transfer in the Gonadotropin-Releasing Hormone Antagonist Protocol

description: The single blastocyst transfer strategy ensures a favorable live birth rate and a low multiple pregnancy rate in fresh embryo transfer cycles.
DOI: 10.6084/m9.figshare.11663811.v2
title: data_phenotyping_and_genotypes_DEDpathogens_Hessenauer&Fijarczyk

description: Hybridization and resulting introgression can drive the success of invasive species via the rapid acquisition of adaptive traits. The Dutch Elm Disease (DED) pandemics in the past 100 years were caused by three fungal lineages with permeable reproductive barriers: Ophiostoma ulmi, Ophiostoma novo-ulmi subsp. novo-ulmi and Ophiostoma novo-ulmi subsp. americana. Using whole genome sequences and growth phenotyping of a worldwide collection of isolates, we show that introgression has been the main driver of genomic diversity and that it impacted fitness related traits. Introgressions contain genes involved in host-pathogen interactions and reproduction. Introgressed isolates have enhanced growth rate at high temperature and produce different necrosis sizes on an in vivo model for pathogenicity. In addition, lineages diverge in many pathogenicity-associated genes and exhibit differential mycelial growth in the presence of a proxy of a host defence compound, implying an important role of a host tree in molecular and functional differentiation of pathogens.<br>This dataset includes the phenotyping results of this study as well as the genotypes in VCF format, please refer to Hessenauer&Fijarczyk 2020 for more details