cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/rkw6tvtngy
title: Enabling particle transport on CAD-based geometries for radiation simulations with penRed

description: Geometry construction is a fundamental aspect of any radiation transport simulation, regardless of the Monte Carlo code being used. Typically, this process is tedious, time-consuming, and error-prone. The conventional approach involves defining geometries using mathematical objects or surfaces. However, this method comes with several limitations, especially when dealing with complex models, particularly those with organic shapes. Furthermore, since each code employs its own format and methodology for defining geometries, sharing and reproducing simulations among researchers becomes a challenging task. Consequently, many codes have implemented support for simulating over geometries constructed via Computer-Aided Design (CAD) tools. Unfortunately, this feature is lacking in penRed and other PENELOPE physics-based codes. Therefore, the objective of this work is to implement such support within the penRed framework.
DOI: 10.6084/m9.figshare.20290923.v2
title: data.csv

description: <strong>Dataset for evaluating global yield advantage and its drivers of legume-based rotations</strong>
DOI: 10.17632/7ncthkxw26
title: L-BAIBA Synergizes with Sub-optimal Mechanical Loading to Promote New Bone Formation

description: To investigate potential mechanisms for the synergism of L-BAIBA and mechanical loading on bone formation, RNA Seq was performed on osteocyte-enriched cortical bone from mice treated with L-BAIBA and sub-optimal mechanical loading (8.25N) for either long-term (2 weeks L-BAIBA and loading) or short-term (5 days L-BAIBA and a single bout of mechanical loading). These supplementary data contain the differentially expressed genes and full GO pathway analysis used to create Figures 5-9 in the manuscript. A description for each supplemental file can be found in the 'Supplemental File Legends' document.
DOI: 10.6084/m9.figshare.11886891.v2
title: Processed naive T cell single-cell RNA-seq, Seurat object

description: Processed naive CD4 and CD8 T cell single-cell RNAseq data from human samples. The file contains a Seurat object stored as an .rds file which can be read into R with the readRDS() function. It was generated using the raw data of similar name in this project, as well as the code stored here: https://github.com/dtm2451/ProgressiveHematopoiesis
DOI: 10.6084/m9.figshare.20936143.v2
title: fMRI Data

description: Smoothed normalised images, condition onsets and motion parameters for 15 subjects
DOI: 10.6084/m9.figshare.22787477.v2
title: First order controls of avulsion in river deltas

description: This dataset (Table S1) accompanies manuscript submitted by the same authors to the JGR Earth Surface.
DOI: 10.6084/m9.figshare.24409453.v1
title: Raw datebase

description: The file contains the raw results of the determination of biogenic amines and amino acids.
DOI: 10.6084/m9.figshare.25793967.v3
title: Transcriptional Signatures of Domestication Revealed by Meta-Analysis of Pig, Chicken, Wild Boar, and Red Junglefowl Gene Expression Data

description: Domesticated animals have undergone significant changes in their behavior, morphology, and physiological functions during domestication. To identify the changes in gene expression associated with domestication, we collected RNA-seq data of pigs, chickens, wild boars, and red junglefowl from public databases and performed a meta-analysis. Gene expression was quantified and the expression ratio between domesticated animals and their wild ancestors (DW-ratio) was calculated. Genes were classified as “upregulated,” “downregulated,” or “unchanged” based on their DW-ratio, and DW-score was calculated for each gene. Gene set enrichment analysis revealed that genes upregulated in pigs were related to defense from viral infection, whereas those upregulated in chickens were associated with aminoglycan and carbohydrate derivative catabolic processes. Genes commonly upregulated in pigs and chickens are involved in the immune response, olfactory learning, epigenetic regulation, cell division, and extracellular matrix. In contrast, genes upregulated in wild boar and red junglefowl are related to stress response, cell proliferation, cardiovascular function, neural regulation, and energy metabolism. These findings provide valuable insights into the genetic basis of the domestication process and highlight potential candidate genes for breeding applications.<br><b>Supplementary Table1 - Pig and Wild Boar Sample metadata</b><b>Supplementary Table2 - Chicken and Red Junglefowl sample metadata</b><b>Supplementary Table3 - TPM Data of Pig and Wild Boar</b><b>Supplementary Table4 - TPM Data of Chicken and Red Junglefowl</b><b>Supplementary Table5 - DW-Score Data for Gene Expression of Pig and Wild Boar</b><b>Supplementary Table6 - DW-Score Data for Gene Expression of Chicken and Red Junglefowl</b><b>Supplementary Table7 - Lists of upregulated genes in Pig</b><b>Supplementary Table8 - Lists of upregulated genes in Wild Boar</b><b>Supplementary Table9 - Result and lists of enrichment analysis of Pig</b><b>Supplementary Table10 - Result and lists of enrichment analysis of Wild Boar</b><b>Supplementary Table11 - Lists of upregulated genes in Chicken</b><b>Supplementary Table12 - Lists of upregulated genes in Red Junglefowl</b><b>Supplementary Table13 - Result and lists of enrichment analysis of chicken</b><b>Supplementary Table14 - Result and lists of enrichment analysis of Red Junglefowl</b><b>Supplementary Table15 - DW-Score data for pig and wild boar converted to human gene IDs</b><b>Supplementary Table16 - Lists of upregulated genes in Pig converted to human gene IDs</b><b>Supplementary Table17 - </b><b>Lists of upregulated genes in Wild Boar converted to human gene IDs</b>
DOI: 10.6084/m9.figshare.9820139.v1
title: flights.csv

description: Sourced from Kaggle (https://www.kaggle.com/usdot/flight-delays)
DOI: 10.6084/m9.figshare.14156801.v1
title: Tree Swallow Nest Box Productivity Dataset from Long-Point, Ontario, Canada (1977-2014)

description: The Tree Swallow (<i>Tachycineta bicolor</i>) is one of the most common birds in eastern North America that normally nests in tree cavities excavated by other species like woodpeckers, but also readily accepts human made nest’ boxes. Based on this quality and their abundance, Birds Canada has monitored nest boxes of tree swallows around the Long Point Biosphere Reserve, Ontario, from 1974 onwards. Each year, May through June, volunteer research assistants check nest box contents daily, and band the adults and their young. Nest-box records are available from about 300 boxes from 3-4 sites during this period. Data collected includes nest box observations, clutch initiation dates, clutch size and egg weight, nest success, weather, insect abundance, and banding data. This data set includes all data entry related to eggs, nests, nestlings, nest check observations, and banding data from 1977 to 2014. This dataset is designed to be open access and used directly with R (version R 4.0.3) and can be complimented with large scale weather data from nearby weather station. Additionally, this dataset will be updated to include insect and weather data collected at the study site. The goal organizing this dataset is to be used for studies focusing on, but not limited to: egg weight shifts over time and with respect to weather and diet, effects of wintering grounds on egg mass and nest success, nestling provisioning rates, and nest success trends with respect to rainfall.<br><br>** All relevant metadata can be found within the dataset **<br>
DOI: 10.6084/m9.figshare.21365133.v1
title: covid19_vaccine_research_foundation_data

description: These are bibliometric data used to analyzed results in COVID-19 vaccine research foundation project conducted in 2022. There are three datasets: (1) COVID-19 vaccine publications inluding pmid, title, and abstracts; (2) Author publication history showing the past 10 years publications record of authors contributing to COVID-19 vaccine manuscripts; (3) Cited publications of COVID-19 vaccine papers.
DOI: 10.17632/7jw7b2fmnt
title: Modeling Travel Choice

description: Data were obtained from the government of the Republic of Korea via a R&D and service project programs.
1. National Household Travel Survey
2. Vehicle Navigation Data
3. Smartcard Data
4. Bike-sharing Data
5. Geographic Information System (GIS) Data
DOI: 10.17632/hd5y556xht
title: SPSS Dataset: Assessment of the High Performance Cycle with U.S. Workers

description: Data collected from U.S. workers. Survey delivered and sample obtained using Prolific (https://www.prolific.co/), with a sample representative of the U.S. population across age, gender and ethnicity. The high performance cycle questionnaire was developed by Borgogni and Dello Russo (2012). A self-report questionnaire developed by Onwezen, van Veldhoven and Biron (2014) was used to assess job performance. Data was transferred to SPSS AMOS for structural equation modeling analysis.
DOI: 10.17632/pmbm24cf54
title: Supplementary material for 'Case Studies in Mathematical Modeling for Medical Devices' , John Crowe

description: This site contains supplementary material for this textbook including worked solutions to problems, code used to generate figures and additional material. The book was published in January 2025 and the supplementary material will be added to this site in the order that ties in with the book's content.

If there is any material that is not available that is particularly required then contact me.
DOI: 10.17632/t7n3ghty5w
title: STD DTI-CV

description: Data from 50 surveys to local government tourism officers of the network of intelligent tourist destinations of the Comunitat Valenciana (Spain).U
DOI: 10.6084/m9.figshare.28824248.v1
title: <b>Oviposition site selection in the giant water bug</b><i> </i><b><i>Kirkaldyia deyrolli</i></b>

description: Oviposition site selection determines fitness in the giant water bug <i>Kirkaldyia deyrolli</i>
DOI: 10.60893/figshare.apb.28466282.v1
title: supplementary materials

description: supplementary figures and tables
DOI: 10.6084/m9.figshare.19619853.v1
title: Variations of the intensity of the Siberian High during the Last Glacial revealed by the sorting coefficient of loess-paleosol deposits in Eastern Central Asia

description: This dataset is from a 14-m loess section in Tacheng Basin, Xinjiang, China. The dataset contains five sheets, such as Raw grain size, Bulk grain size, GSD of amphibole, GSD of epidote, and Ratio between amphibole and epidote.
DOI: 10.6084/m9.figshare.22147283.v3
title: Dataset for paper "Overestimated nitrogen loss from denitrification for natural terrestrial ecosystems in CMIP6 Earth System Models" authored by Feng et al.

description: This is the dataset for paper "Overestimated nitrogen loss from denitrification for natural terrestrial ecosystems in CMIP6 Earth System Models" authored by Feng et al. <br> The dataset contains six .nc files, and each file contains soil_N15, fgas, and N loss and their quantiles derived with different combinations of N weathering, N depostion and BNF. <br> Figure1_data.nc is the data for Figure 1 in the main.
DOI: 10.6084/m9.figshare.27142647.v1
title: Raw Data

description: This research aims to investigate the factors influencing land rental rates and selling prices. It also intends to develop a forecast model and predictors of land yield. Based on variables influencing the rent and property prices along the indicated road within a 500-meter radius, we collected data on 100 parcels of land. It was announced that the land lots would be available for sale or rental in January through March of 2024. The aforementioned factors include the following: the width of the land parcel; the width of the road; the surface of the road; the distance from the major road; the distance from the MRT station; the distance from the community; the distance from retail centres, and the distance from convenience stores. The remaining samples, which consisted of 88 plots after the outliers were subtracted, were used to formulate a forecast model, which was then grounded and examined using multiple regression analysis. The study's findings revealed that, at a significant level of 0.05, the distance from the MRT station is a predictor of the yield rate of land for rent along Nakhon-In Road, explaining its influence. This distance was found to be 5.60%. Log (yield rate of land d per year) = -0.370 + 0.217 Log (distance from the MRT station) is the regression equation that can be created using the Log – Log format, which is the best forecast model for land yield rate.
DOI: 10.6084/m9.figshare.29145539.v1
title: Figure source data_.xlsx

description: In this study, we fabricated the first room temperature silicon (Si)-based optical detectors for propylene (C3H6) and methane (CH4)
DOI: 10.6084/m9.figshare.13490262.v3
title: Supplemental file_placental proteomeV2_SM20201227.docx

description: This file consists of supplemental data from the manuscript titled "Pre-existing hypertension and pregnancy induced hypertension reveal molecular differences in placental proteome in rodents"<br>Authored by Sheon Mary<sup>1</sup>, Heather Small<sup>1</sup>, Florian Herse<sup>2</sup>, Emma Carrick<sup>1</sup>, Arun Flynn<sup>1</sup>, William Mullen<sup>1</sup>, Ralf Dechend<sup>2,3</sup>, Christian Delles<sup>1</sup> <sup>1</sup>BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Scotland, UK <sup>2</sup>Experimental and Clinical Research Center, a joint cooperation between Max-Delbrück-Center for Molecular Medicine and Charité - Universitätsmedizin Berlin, Germany <sup>3</sup>HELIOS Clinic, Department of Cardiology and Nephrology, Berlin, Germany<b></b>
DOI: 10.6084/m9.figshare.29106236.v3
title: Septal LYVE1+ macrophages control adipocyte stem cell adipogenic potential

description: Tissue macrophages are a heterogeneous cell population residing in diverse subtissular niches dictating their tissue-specific functions. Here, we assessed the heterogeneity of adipose tissue macrophages (ATM) in regard to their subtissular localization and functional specializations. We identified 3 ATM populations residing in  subtissular niche with distinct turnover, phenotypes and functions: CD209b–LYVE1–CD16.2+ parenchymal ATM, CD209b–LYVE1+CD16.2– capsular ATM and CD209b+LYVE1+CD16.2– septal ATM, the latter specifically localized in white adipose tissue septum in contact with CD26+ adipocyte stem cells (ASC). Septal ATM depletion or their deficiency in transforming growth factor β1 (TGFβ1) expression in the context of HFD changed ASC adipogenic potential promoting a beiging process, thus preventing diet-induced obesity. Our findings highlight the role played by a discrete anatomically-defined macrophage population and their crosstalk with ASC, controlling their fate and ultimately tissue expansion.
DOI: 10.6084/m9.figshare.5124502.v1
title: Supplementary Material for: The Relation of Uric Acid to Brain Atrophy and Cognition: The Rotterdam Scan Study

description: <b><i>Background:</i></b> Uric acid has been associated with focal vascular brain disease. However, it is unknown whether uric acid also relates to global brain changes such as brain atrophy. We therefore studied the relation of uric acid to brain atrophy and whether this is accompanied by worse cognitive function. <b><i>Methods:</i></b> In 814 persons of the population-based Rotterdam Study (mean age 62.0 years), we studied the relation of uric acid levels to brain tissue atrophy and cognition using linear regression models adjusted for age, sex and putative confounders. Brain atrophy was assessed using automated processing of magnetic resonance imaging. Cognition was assessed using a validated neuropsychological test battery and we computed compound scores of cognitive domains. <b><i>Results:</i></b> Higher uric acid levels were associated with white matter atrophy [difference in Z-score of white matter volume per standard deviation increase in uric acid: -0.07 (95% CI: -0.12; -0.01)], but not with gray matter atrophy. This was particularly marked when comparing hyperuricemic to normouricemic persons [Z-score difference: -0.27 (-0.43; -0.11)]. Worse cognition was primarily found in persons with hyperuricemia [-0.28 (-0.48; -0.08)]. <b><i>Conclusions:</i></b> Hyperuricemia is related to white matter atrophy and worse cognition.
DOI: 10.6084/m9.figshare.6157445.v1
title: WCNPruning input set

description: Wikipedia Category network Sept 17. <br>Input files for: https://github.com/epfl-dlab/WCNPruning<br>Input files:<i>article_types_dbpedia.tsv.gz<br></i><i>category_graph_sept17.tsv.gz<br></i><i>article_categories_sept17.tsv.gz</i><br><br>Output file:articles_scores_gini_coefficient0.966.json.gz<br>
DOI: 10.11583/dtu.28531154.v1
title: NEB and band structure calculations for APbI<sub>3</sub> (A=Cs, Rb, K) perovskite memristive devices

description: This database contains the input and output files related to the publication: "Engineering of A-Site Cations in APbI₃ (A = Cs, Rb, K) Perovskites for Resistive Switching Control and Self-Rectifying Memristors for Next-Generation Computing Applications"Using Density Functional Theory (DFT) and the VASP software, structural relaxations using the PBEsol functional and spin orbit coupling correction are performed on APbI₃ (A = Cs, Rb, K) perovskites. The band structure is calculated using the HSE06 functional to obtain accurate bandgaps. To investigate the migration barrier of vacancy-assisted I-hopping and A-hopping, climbing image nudged elastic band calculations are performed. This database contains the input files (INCAR, POSCAR, POTCAR and KPOINTS) to reproduce the results of this studies. Output files (CONTCAR, OUTCAR) are also present, showing the results obtained.
DOI: 10.17632/829ph4nkny
title: Dataset for Chemical Kinetics Bayesian Inference Toolbox (CKBIT)

description: The robust estimation of chemical kinetic parameters and their associated uncertainty is essential in the field of chemistry and catalysis. The Chemical Kinetics Bayesian Inference Toolbox (CKBIT) is a Python software library introduced to enable users to implement advanced Bayesian inference techniques for kinetic parameter estimation and uncertainty quantification. Leveraging functionalities of other open source Python packages and offering simplified implementation through minimal user-required coding and straightforward Excel input files, CKBIT aspires to make the inference method easily accessible for chemical kinetics. CKBIT provides maximum a posteriori, Markov chain Monte Carlo, and variational inference estimation options. Users may apply these functionalities to estimate activation energies, reaction orders, and pre-exponential terms from chemical reaction data from batch reactors, continuous stirred-tank reactors, and plug flow reactors. The availability of prior distribution specification and the implementation of hierarchical modeling in CKBIT provide a heightened level of accuracy in estimates of kinetic parameters and their uncertainties.
DOI: 10.17632/ffzjcnfmcg
title: Suppl. material "Checkpoint Inhibitor-induced lichen planus differs from spontaneous lichen planus on the clinical, histological and gene expression level"

description: Suppl. Figure 1. Gene expression analysis of lichen planus subtypes reveals notable differences in the gene expression profiles of immune-related Lichen planus, spontaneous Lichen planus and non-disease controls. (A) Heatmap showing the hierarchical clustering of 730 analyzed genes using NanoString. Volcanoplots of showing log2 fold change on x axis (cutoff at fold change =1.5 and -1.5); log10 (padj) with cutoff at p adj. = 0.05 on y axis; up- (green) and downregulated (purple) genes in irLP vs NDC (B), LP vs NDC (C) and irLP vs LP (D); irLP: immune-related lichen planus; LP: lichen planus; NDC: non-disease controls.
Suppl. Figure 2. Cell distribution in immune-related lichen planus, spontaneous lichen planus and healthy skin. Algorithms from meta-analysis databases (PanglaoDB and Cell Atlas) were applied and the cell compositions were calculated according to the expression of defined genes per cell type. irLP: immune-related lichen planus; LP: lichen planus; NDC: non-disease controls; n.s. = not significant
Suppl. Figure 3. Significantly upregulated pathways in immune-related lichen planus compared to non-disease controls. Heatmap showing gene expression of genes involved in IL-12 mediated signaling events demonstrating upregulation of involved genes in irLP lesional skin compared to NDC. irLP: immune-related lichen planus; NDC: non-disease controls.


Suppl. Table 1 : Patient’s characteristics under immune checkpoint inhibition (ICI) ; n=14
Suppl. Table 2 : Duration and response to therapy in irLP ; irLP : immune-related lichen planus
Suppl. Table 3: Top 20 upregulated genes in irLP compared to NDC; irLP : immune-related lichen planus ; NDC: non-diseased controls
Suppl. Table 4: Important biological functions in irLP compared to NDC (Gene Set Analysis Significance Scores); irLP : immune-related lichen planus ; NDC: non-diseased controls
Suppl. Table 5: Top 20 upregulated genes in LP compared to NDC ; LP: lichen planus ; NDC: non-diseased controls
Suppl. Table 6: Top 20 upregulated genes in irLP compared to LP ; irLP : immune-related lichen planus; LP: lichen planus
Suppl. Table 7: Top 13 downregulated genes in irLP compared to LP; irLP : immune-related lichen planus; LP: lichen planus
Suppl. Table 8: Important pathways in irLP compared to LP (Gene Set Analysis Significance Scores) irLP : immune-related lichen planus ; LP: lichen planus
DOI: 10.17632/fzwt6b2bh3
title: infosys_news_dataset

description: This data set useful for study to shows the effect of emotion classification of financial news(10 years) in prediction of stock market prices.
DOI: 10.6084/m9.figshare.11917770.v2
title: An investigation of irreproducibility in maximum likelihood phylogenetic inference

description: All gene alignments, gene trees, log files, and command lines, as well as summary and statistics of the runs, are available on the figshare repository.
DOI: 10.6084/m9.figshare.5480896.v1
title: Tree from Do extra-group fertilizations increase the potential for sexual selection in male mammals?

description: Tree used to construct evolutionary relationships for species in our comparative analyses
DOI: 10.6084/m9.figshare.7637951.v1
title: Hyperdiverse mtDNA dataset A

description: DNA sequence alignment of 399 concatenated sequences of the partial gene fragments of the 16S, COI and Cytb genes. 1775 base pairs. From 399 specimens collected in the Azores archipelago, Spain, Portugal, Scotland and Rhodes.<br>
DOI: 10.17632/2956vk52jz
title: Data for: Large-Eddy Simulation of Sand Transport Under Unsteady Wind
DOI: 10.6084/m9.figshare.12356750.v2
title: Dataset

description: Dataset <br>
DOI: 10.6084/m9.figshare.19690621.v1
title: Size of the shadow economy in Nigeria.xlsx

description: The dataset is the outcome of our research on the size and determinants of the shadow eocnomy in Nigeria. We estimated and provide the size and growth of the shadow economy in Nigeria from 2019 quarter 1 to 2019 quarter 4.
DOI: 10.6084/m9.figshare.26491009.v1
title: de novo design of tmfap

description: PDB validation reports and design scripts.
DOI: 10.6084/m9.figshare.26507083.v2
title: A First Look at Conventional Commits Classification

description: Data and scripts for the ICSE 2025 paper "A First Look at Conventional Commits Classification".Refer to our GitHub repository for more details: https://github.com/0x404/conventional-commit-classification
DOI: 10.17632/brrx42bjvg
title: The olfactory basis of orchid pollination

description: Data for Lahondere et al. 2020