cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25497445.v2
title: <b>A deep</b><b> </b><b>learning framework </b><b>for </b><b><i>in silico</i></b><b> screening of anticancer drugs at the single-cell level</b>

description: Tumor heterogeneity plays a pivotal role in tumor progression and resistance to clinical treatment. Single-cell RNA sequencing (scRNA-seq) enables us to explore heterogeneity within a cell population and identify rare cell types, thereby improving our design of targeted therapeutic strategies. Here, we use a pan-cancer and pan-tissue single-cell transcriptional landscape to reveal heterogeneous expression patterns within malignant cells, precancerous cells, as well as cancer-associated stromal and endothelial cells. We introduce a deep learning framework named Shennong for <i>in silico</i> screening of anticancer drugs for targeting each of the landscape cell clusters. Utilizing Shennong, we could predict individual cell responses to pharmacologic compounds, evaluate drug candidates’ tissue damaging effects, and investigate their corresponding action mechanisms. Prioritized compounds in Shennong’s prediction results include FDA-approved drugs currently undergoing clinical trials for new indications, as well as drug candidates reporting anti-tumor activity. Furthermore, the tissue damaging effect prediction aligns with documented injuries and terminated discovery events. This robust and explainable framework has the potential to accelerate the drug discovery process and enhance the accuracy and efficiency of drug screening.
DOI: 10.6084/m9.figshare.26405008.v1
title: <b><i>De novo </i></b><b>transcriptome assembly of </b><b><i>Acartia tonsa </i></b><b>adults</b><b><i> </i></b><b>using Nanopore long-read sequencing</b>

description: <i>Acartia tonsa </i>is a calanoid copepod with a cosmopolitan distribution. It generally reaches relatively high abundances and often becomes the dominant zooplankton species during summer, making it the most numerous taxon in several ecosystems. Its ecological relevance makes it a useful bioindicator organism for assessing the toxicity of various compounds. However, transcriptomic assemblies of <i>A. tonsa</i> using long-read technologies have not yet been described. The use of long-read sequencing technologies in transcriptomics allows the study of alternative splicing, structural variations and alternative polyadenylation sites. In this study, we present a <i>de novo </i>transcriptome of <i>A. tonsa </i>adult copepods exposed to different neonicotinoids obtained from Nanopore sequences. Our transcriptome exhibits higher completeness and longer sequences than the largest assemblies reported previously. We also provide a complete annotation by sequence homology (NR database), domain identification (InterProScan) and functional classification (Gene Ontology). Our transcriptome represents a solid baseline for further transcriptomic studies on this copepod and, specifically, its response to currently used pesticides.
DOI: 10.6084/m9.figshare.5128663.v1
title: Supplementary Material for: Remote Ischemic Preconditioning May Attenuate Renal Ischemia-Reperfusion Injury in a Porcine Model of Supraceliac Aortic Cross-Clamping

description: <b><i>Aim:</i></b> The effect of remote ischemic preconditioning (RIPC) in decreasing renal ischemia-reperfusion injury (IRI) during a suprarenal aortic cross-clamping was examined in a swine model. <b><i>Materials and Methods:</i></b> Four groups of pigs were examined: (a) ischemia-reperfusion (IR) group, renal IRI produced by 30 min of supraceliac aortic cross-clamping; (b) RIPC I group, the same renal IRI following RIPC by brief occlusion of the infrarenal aorta (15 min ischemia and 15 min reperfusion); (c) RIPC II group, the same renal IRI following RIPC by brief occlusion of the infrarenal aorta (3 cycles of 5 min ischemia and 5 min reperfusion); (d) sham group. Renal function was assessed before and after IRI by examining creatinine, neutrophil gelatinase-associated lipocalin (NGAL), TNF-α, malondialdehyde (MDA), cystatin C and C-reactive protein (CRP) from renal vein blood samples at specific time intervals. <b><i>Results:</i></b> Both RIPC groups presented significantly less impaired results compared to the IR group when considering MDA, cystatin C, CRP and creatinine. Between the two RIPC groups, RIPC II presented a better response with regard to CRP, NGAL, TNF-α, MDA and cystatin C. <b><i>Conclusions:</i></b> Remote IR protocols and mainly repetitive short periods of cycles of IR ameliorate the biochemical kidney effects of IRI in a model of suprarenal aortic aneurysm repair.
DOI: 10.6084/m9.figshare.14161313.v1
title: Data for Paper "An elasticity-curvature illusion decouples cutaneous and proprioceptive cues in active exploration of soft objects"

description: Experimental data for finite element analysis and human-subjects experiments
DOI: 10.6084/m9.figshare.7523426.v2
title: Stress of worm under flow

description: Stress of worm under flow<br>
DOI: 10.11583/dtu.19689025.v1
title: Onshore wind generation time series for technology SP335 HH200 at resource grade A (PECD 2021 update)

description: This data (csv file) provides simulated hourly time series of onshore wind generation with specific power (SP) 335 W/m2 turbines at hub height (HH) of 200 m for the regions shown in the attached map. The analysed wind power plants are sited at the best 10 % of locations in each region, i.e., in resource grade (RG) A. The map shows the resulting capacity factors (annual mean). The Excel file gives a rough indication if this wind technology is suitable for the different regions for this RG or not. The available land considers all onshore land area of a region, except lakes, cities, and very high elevation locations. The possible impact of any existing onshore wind installations in the region is not considered. Wake losses are modeled, with additional 5 % of other losses and unavailability considered. The time stamps are in GMT; the variable (column) names relate to the region names shown in the maps. The data include also country-level aggregations, e.g., UK00 is the aggregated onshore wind generation of all the UK regions (weighted by regional installed capacities). The data are part of the variable renewable energy generation time series created for ENTSO-E in the 2021 update of the Pan-European Climate Database (PECD) dataset. ENTSO-E has used the data in ERAA 2021 and Winter Outlook 2021-2022 assessments, and they are used in TYNDP 2022. The simulations are carried out by DTU Wind Energy, with the future technology selection and data validation discussed and agreed with ENTSO-E and its members. The linked journal paper (1st link) describes the simulation methodology (combination of ERA5 and GWA data is used). It is requested that the paper is cited when the data are used. The linked related journal paper (2nd link) describes the concept of resource grades and how they can be applied in energy system analyses. This item is part of a larger collection of wind and solar data: https://doi.org/10.11583/DTU.c.5939581
DOI: 10.6084/m9.figshare.28559201.v2
title: <b>Dataset: Mood States and Spatiotemporal Gait Parameters in Healthy Young Adults</b>

description: This dataset contains spatiotemporal gait parameters and concurrent mood assessments from 16 healthy young adults across multiple sessions during an academic semester. Data were collected to examine relationships between naturally occurring mood states and walking characteristics, accounting for time-of-day variations and individual differences. For detailed protocol information, please refer to the published manuscript.Dataset Contents<b>gait_data.csv</b> (n=73 observations):Spatiotemporal parameters (temporal, spatial, phase organization)Gait variability measuresAnthropometric data<b>mood_data.csv</b> (n=67 observations):Individual emotion ratingsComposite affect scores<b>gait_mood_merged.csv</b> (matched observations):Combined dataset for direct analysis of mood-gait relationshipsTechnical NotesParticipant identifiers anonymizedTemporal relationships preserved through relative study daysSession timing (morning/afternoon) maintainedAll measurements standardized and quality-controlled
DOI: 10.6084/m9.figshare.12440417.v1
title: Supplementary Tables - Levade et al. 2020

description: Supplementary Tables S1-S9
DOI: 10.17632/5d6th74drd
title: Data for: Unraveling sedimentary processes in fluvial sediments from two basalt dominated watersheds in northern Idaho, USA.

description: Tables and Reference Values.
DOI: 10.6084/m9.figshare.17705036.v1
title: Dataset_ProjectGovernance

description: Dataset is used for research.
DOI: 10.6084/m9.figshare.20237802.v2
title: DATA AVAILABILITY: Machine Learning and Singularity Analysis Reveal Zircon Fertility and Magmatic Intensity: Implications for Porphyry Copper Potential

description: Zhou et al., 2022. Machine Learning and Singularity Analysis Reveal Zircon Fertility and Magmatic Intensity: Implications for Porphyry Copper Potential. Natural Resources Research. <br> <strong>Table S1. </strong>U-Pb age and trace element composition database for global compiled igneous zircons <strong>Table S2.</strong> U-Pb age and trace element composition database for compiled detrital zircons in the eastern Gangdese belt
DOI: 10.6084/m9.figshare.26104981.v1
title: Supplementary Material for: Whole exome sequencing indicating GGCCTG hexanucleotide repeat in patients with spinocerebellar ataxia type 36

description: Introduction: Spinocerebellar ataxia type 36 (SCA36) is caused by large GGCCTG repeat expansion in the NOP56 gene. The genetic diagnosis based on Southern blot is expensive and time-consuming. This study aimed to evaluate the reliability and effectiveness of whole exome sequencing (WES) for routine genetic diagnosis of suspected SCA36 patients.
Methods: Pathogenic repeat expansions for SCAs including SCA36 were first analyzed based on WES data using ExpansionHunter in five probands from SCA families, then the results were confirmed by triplet repeat primed polymerase chain reaction (TP-PCR) and Southern blot.
Results: GGCCTG repeat expansion in NOP56 was indicated in all five probands by WES, then it was found in 11 SCA patients and three asymptomatic individuals by TP-PCR. The sizes of GGCCTG repeat expansions were confirmed to be 1390-1556 by Southern blot. The mean age at onset of the patients was 51.0 ± 9.3 (ranging from 41 to 71), and they presented slowly progressive cerebellar ataxia, atrophy and fasciculation in tongue or limb muscles.
Conclusion: The patients were clinically and genetically diagnosed as SCA36. This study proposed that WES could be a rapid, reliable, and cost-effective routine test for the preliminarily detection of SCA36 and other ataxia diseases.
DOI: 10.17632/nc52p2wj9c
title: LINF_160005000

description: ASF1-like protein; Leishmania infantum (strain JPCM5)
DOI: 10.15482/usda.adc/1326639
title: U.S. National Fungus Collections
DOI: 10.6084/m9.figshare.24665571.v1
title: Adaptation of the European Fish Index (EFI+) to include the alien fish pressure

description: This dataset (CSV format) contains the data of 344 sites of the Mediterranean slope of the Iberian Peninsula (230 sites in Catalonia and 114 sites in the Jucar River Basin District) as described in "Adaptation of the European Fish Index (EFI+) to include the alien fish pressure". Fish data originated from samplings by electrofishing during low flow periods, following the CEN 14011 standard protocol.Contents: %_ALIEN_IND percentage of alien individuals%_ALIEN_SP percentage of alien speciesAFP Alien Fish PressureEFI+ indexIBICAT2010 indexIBI-JUCAR indexQBR Riparian vegetation quality indexIHF Fluvial habitat indexIPS Specific Pollution Sensitivity index based on diatomsIBMWP Macroinvertebrate-based indexARTIFICIAL % Land use as urbanized areasAGRICULTURE % agricultural areasFOREST % forested/natural areas
DOI: 10.6084/m9.figshare.13703407.v1
title: Cognitive Performance in Pain is Predicted by Effort, Not Goal Desire - Data

description: These data show that effort, and not financial rewards or motivation to achieve a goal, predict cognitive-task performance both in and out of pain. A lab-based study with small- and large-financial incentives and induced pain.
DOI: 10.6084/m9.figshare.14336594.v1
title: Excitatory and Inhibitory Inputs during Spontaneous activity

description: Whole- cell recording in voltage clamp, alternately held at the reversal potential for Na/K and Cl to isolate inhibitory and excitatory currents. Each file is a cell from an individual animal. <br><br>
DOI: 10.6084/m9.figshare.28540937.v1
title: Supplementary Material for: Weakly supervised deep learning can analyze focal liver lesions in contrast-enhanced ultrasound

description: Introduction
Assessing the malignancy of focal liver lesions is an important yet challenging aspect of routine patient care. Contrast-enhanced ultrasound (CEUS) has proved to be a highly reliable tool but is very dependent on the examiner’s expertise. The emergence of artificial intelligence has opened doors to algorithms that could potentially aid in the diagnostic process. In this study, we evaluate the performance of a weakly supervised deep learning model in classifying focal liver lesions (FLL) as malignant or benign.
Methods 
Our retrospective feasibility study was based on a cohort of patients from a tertiary care hospital in Germany undergoing routine CEUS examination to evaluate malignancy of FLL. We trained a weakly supervised attention-based multiple instance learning algorithm during 5-fold cross-validation to distinguish malignant from benign liver tumors, without using any manual annotations, only case labels. We aggregated the on-average best performing cross-validation cycle and tested this combined model on a held-out test set. We evaluated its performance using standard performance metrics and developed explainability methods to gain insight into the model's decisions.
Results
We enrolled 370 patients, comprising a total of 955,938 images extracted from CEUS videos or manually captured during the examination. Our combined model was able to identify malignant lesions with a mean area under the receiver operating curve of 0.844 in the cross-validation experiment and 0.94 (95% CI 0.89 - 0.99) in the held-out test set. The accuracy, sensitivity, specificity, and F1-Score of the combined model in finding malignant lesions in the held-out test, yielded 80.0%, 81.8%, 84.6%, and 0.81, respectively. Our exploratory analysis using visual explainability methods revealed that the model appears to prioritize information that is also highly relevant to expert clinicians in this task.
Conclusions
Weakly supervised deep learning can classify malignancy in CEUS examinations of FLLs and thus might one day be able to assist doctors’ decision-making in clinical routine.
DOI: 10.6084/m9.figshare.28726787.v1
title: data

description: Data for training and evaluation of the Transformer-based question generation model introduced in the following ECAI 2023 paper "Uniform training and marginal decoding for multi-reference question-answer generation" https://ebooks.iospress.nl/doi/10.3233/FAIA230539
DOI: 10.23645/epacomptox.19216932.v2
title: Performance Summary for Estrogen and Androgen Receptor Pathway Models and Associated Assay

description: Science Inventory, CCTE products: https://cfpub.epa.gov/si/si_public_search_results.cfm?advSearch=true&showCriteria=2&keyword=CCTE&TIMSType=&TIMSSubTypeID=&epaNumber=&ombCat=Any&dateBeginPublishedPresented=07/01/2017&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&DEID=&personName=&personID=&role=Any&journalName=&journalID=&publisherName=&publisherID=&sortBy=pubDate&count=25<br><br>The US EPA has developed batteries of in vitro assays to test chemicals for their potential to interact with the androgen and estrogen receptors (AR and ER). These assays have been combined using mathematical models to provide overall scores for chemicals, indicating level of agonist and antagonist activity. The combinations of assays and models are known as the AR and ER Pathway Models (Judson, Magpantay et al. 2015, Kleinstreuer, Ceger et al. 2017) because the method for combining assays makes use of the underlying biological pathways leading from the interaction of a chemical with either AR or ER through receptor dimerization and cofactor recruitment, binding to DNA, RNA and protein production and, in the case of ER, to cell proliferation. Approximately 1800 chemicals have been tested in the AR and ER assays as part of the ToxCast and Tox21 in vitro screening programs and have model scores. The AR and ER Pathway Models and associated in vitro assay data have been described in multiple peer reviewed publications (Browne, Judson et al. 2015, Judson, Magpantay et al. 2015, Browne, Judson et al. 2017, Judson, Houck et al. 2017, Kleinstreuer, Ceger et al. 2017, Browne, Kleinstreuer et al. 2018, OECD 2019, Judson, Houck et al. 2020) and FIFRA Scientific Advisory Panel (SAP) reviews (U.S. EPA 2013, U.S. EPA 2017, US EPA 2018). In these publications, the models have been evaluated against various sets of reference chemicals. This document provides a consolidated resource containing the performance metrics for each of the individual assays as well as the AR and ER Pathway Models themselves.
DOI: 10.6084/m9.figshare.28189199.v1
title: Select data.xlsx

description: With the rapid development of the cultural and creative industries, museum cultural and creative products (MCCPs) have become important mediums for preserving traditional culture and enhancing public cultural literacy. However, as a vital institution for the preservation and transmission of Qilu culture, Shandong Museum faces several challenges in developing and marketing MCCPs, including a lack of distinctive product features, weak brand awareness, and insufficient consumer purchase intentions (PIs). To explore the factors influencing tconsumer PIs for MCCPs, this study systematically reviewed relevant literature and constructed a theoretical model encompassing perceived quality, PI, perceived usefulness, perceived cultural value, perceived value, consumer satisfaction, and purchase intention. Empirical analysis was conducted using structural equation model. The findings indicate that perceived quality and perceived usefulness have significant positive effects on perceived value and purchase intention, while perceived value and consumer satisfaction are the core drivers of purchase intention. However, the direct effect of perceived cultural value on purchase intention was not significant. These results suggest that in the decision-making process, consumers focus more on the functionality and overall value of the product rather than on cultural attributes alone. This study offers important insights for the design and marketing of MCCPs at Shandong Province Museum: efforts should focus on improving product quality and functionality while achieving an organic integration of cultural connotations and practical value. By optimizing the consumer experience, this approach aims to achieve a harmonious development of market demand and cultural dissemination.
DOI: 10.4121/uuid:686925fd-017c-49df-a92b-3dc84138c513
title: Data accompanying the publication "Conductance through a helical state in an indium antimonide nanowire"

description: Raw data underlying the publication "Conductance through a helical state in an indium antimonide nanowire", published in nature communications Parent item: Data and scripts accompanying the publication "Conductance through a helical state in an indium antimonide nanowire" Data and scripts accompanying the publication "Conductance through a helical state in an indium antimonide nanowire" - published in Nature Communcations.
DOI: 10.6084/m9.figshare.14619273.v1
title: ReadMe

description: Description of the variables included in this dataset
DOI: 10.6084/m9.figshare.19721689.v1
title: Supplementary Material for: Putative Condition-Dependent Viability Selection in Wild-Type Stocks of <b><i>Drosophila pseudoobscura</i></b>

description: Meiotic recombination rates vary in response to intrinsic and extrinsic factors. Recently, heat stress has been shown to reveal plasticity in recombination rates in <i>Drosophila pseudoobscura.</i> Here, a combination of molecular genotyping and X-linked recessive phenotypic markers were used to investigate differences in recombination rates due to heat stress. In addition, haplotypes from the genetic crosses were compared to test if they deviated from equal proportions, which would indicate viability selection. To avoid this potential bias, SNP genotyping markers overlapping the regions assayed with mutant markers were used to further investigate recombination rate. Interestingly, skews in haplotype frequency were consistent with the fixation of alleles in the wild-type stocks used that are unfit at high temperature. Evidence of viability selection due to heat stress in the wild-type haplotypes was most apparent on days 7–9 when more mutant non-crossover haplotypes were recovered in comparison to wild type (<i>p</i> &lt; 0.0001). Recombination analysis using SNP markers showed days 9–10 as significantly different due to heat stress in 2 pairs of consecutive SNP markers (<i>p</i> = 0.018; <i>p</i> = 0.015), suggesting that during this time period the recombination rate is most sensitive to heat stress. This peak timing for recombination plasticity is consistent with <i>Drosophila melanogaster</i> based on a comparison of similarly timed key meiotic events, enabling future mechanistic work of temperature stress on recombination rate.
DOI: 10.6084/m9.figshare.7623671.v1
title: FCS and INI files

description: FCS data and INI files describing the experiments in the paper "Revisiting cell-particle association <i>in vitro</i>: a quantitative method to compare particle performance"
DOI: 10.6084/m9.figshare.7892411.v1
title: gVCF_HG03121

description: 1000 Genomes gVCF mapped to hs37d5 for HG03121. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.25034567.v1
title: Supplementary Material for: Age-period-cohort analysis of long-term trends in ischemic stroke mortality in China caused by specific risk factors from 1990 to 2019

description: Objective: To study the primary risk factors for the long-term trends of mortality rates in ischemic stroke (IS) in China.
Methods: Using the Global Burden of Disease Study 2019 (GBD 2019) database, research was conducted on the 11 primary risk factors for the mortality rates of IS in China from 1990 to 2019. This study employed Joinpoint regression software and the Age-Period-Cohort (APC) method to evaluate the trends of mortality rates divided by age, period, and cohort over time.
Results: From 1990 to 2019, the age-standardized mortality rate (ASMR) caused by a diet high in red meat and high body-mass index (BMI) in China showed an upward trend. ASMR increased first and then decreased due to smoking, diet high in sodium, particulate matter pollution, high fasting plasma glucose, and high systolic blood pressure. Low-density lipoprotein cholesterol (LDL-C), kidney dysfunction, low temperature, and lead exposure remained relatively stable during this period. In the 35-45 age group, the mortality rate of IS due to high LDL-C was up to about 60%, and smoking affected men more than women. Overall, high LDL-C, high systolic blood pressure, and particulate matter pollution were the most common risk factors in patients with IS. The risk of death rose with age. The period and cohort relative risks showed that metabolic risk factors had the greatest impact on the mortality of IS.
Conclusion: Metabolic risk factors have become the primary risk factors for the ASMR of IS in China. Relevant authorities should pay attention to their long-term effects on IS. Effective public health policies and interventions should be implemented to reduce the burden of IS.