cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25378/janelia.25934782.v1
title: WHaloCaMP data

description: Raw data for figures present in the manuscript linked in Related Materials. Each tab of the spreadsheet corresponds to a main figure panel in the linked manuscript. Details of the methodology used to acquire the data are described in the methods section of the manuscript linked in Related Materials. The manuscript, "A modular chemigenetic calcium indicator enables in vivo functional imaging with near-infrared light", describes engineering and validation of the chemigenetic calcium indicator WHaloCaMP, which can be used for sensing calcium ion concentration changes in the neurons of model organisms using fluorescence microscopy.Abstract: Genetically encoded fluorescent calcium indicators have revolutionized neuroscience and other biological fields by allowing cellular-resolution recording of physiology during behavior. However, we currently lack bright, genetically targetable indicators in the near infrared that can be used in animals. Here, we describe WHaloCaMP, a modular chemigenetic calcium indicator built from bright dye-ligands and protein sensor domains that can be genetically targeted to specific cell populations. Fluorescence change in WHaloCaMP results from reversible quenching of the bound dye via a strategically placed tryptophan. WHaloCaMP is compatible with rhodamine dye-ligands that fluoresce from green to near-infrared, including several dye-ligands that efficiently label the central nervous system in animals. When bound to a near-infrared dye-ligand, WHaloCaMP1a is more than twice as bright as jGCaMP8s, and shows a 7× increase in fluorescence intensity and a 2.1 ns increase in fluorescence lifetime upon calcium binding. We use WHaloCaMP1a with near-infrared fluorescence emission to image Ca<sup>2+</sup> responses in flies and mice, to perform three-color multiplexed functional imaging of hundreds of neurons and astrocytes in zebrafish larvae, and to quantitate calcium concentration using fluorescence lifetime imaging microscopy (FLIM).
DOI: 10.4121/uuid:2ac74fbd-2276-44ad-aff1-2f68972b7b51
title: Public Benchmark Dataset for Testing rPPG Algorithm Performance

description: The current needs in remote photoplethysmography (rPPG) research were investigated and it was concluded there is a lack of reproducibility and comparability in the current rPPG research. Three main challenges for rPPG algorithms were defined and incorporated in the dataset; lighting & skin tone, motion robustness and high heart rates & pulse-rate change robustness. Videos accompanied by ECG measurements were recorded to create test material for these challenges.
DOI: 10.6084/m9.figshare.19078235.v1
title: drag-data.csv

description: The dataset that underlies my PhD dissertation, and that can be explored visually through my Observable account: https://observablehq.com/collection/@kallewesterling/dissertation-data.
DOI: 10.6084/m9.figshare.20496240.v1
title: PPGBP dataset

description: PPGBP dataset: The short-recorded PPG dataset collected and shared by Liang et al. [4]. It contains 219 subjects, with one BP reading followed by three PPG segments with a duration of 2.1 seconds each. Thus, it is the smallest set in the number of segments (613) but with a relatively high number of subjects. The original sampling frequency of 1000 Hz was resampled at 125 Hz. We conducted a 5-fold CV to partition the data once it was preprocessed. [4] Liang, Y., Chen, Z., Liu, G. & Elgendi, M. PPG-BP database (2018). Figshare https://doi.org/10.6084/m9.figshare.5459299.
DOI: 10.6084/m9.figshare.22559526.v1
title: Choline and trimethylamine N-oxide supplementation in normal chow diet and western diet promotes the development of atherosclerosis in Apoe –/– mice through different mechanisms

description: Trimethylamine N-oxide (TMAO), a gut microbiota-dependent metabolite, has been shown to aggravate cardiovascular disease. However, the mechanisms of TMAO in the setting of cardiovascular disease progress remain unclear. Here, we aim to investigate the effects of TMAO on atherosclerosis (AS) development and the underlying mechanisms. Apoe –/– mice received choline or TMAO supplementation in a normal diet and a western diet for 12 weeks. Choline or TMAO supplementation in both normal diet and western diet significantly promoted plaque progression in Apoe–/– mice. Besides, serum lipids levels and inflammation response in the aortic root were enhanced by choline or TMAO supplementation. In particular, choline or TMAO supplementation in the western diet changed intestinal microbiota composition and bile acid metabolism. Therefore, choline or TMAO supplementation may promote AS by modulating gut microbiota in mice fed with a western diet and by other mechanisms in mice given a normal diet, even choline or TMAO supplementation in a normal diet can promote AS.
DOI: 10.6084/m9.figshare.25772685.v2
title: Collections of Icons and Workflows for Robotic and Generative AI Agent-oriented Research for Health and Sustainability Sciences

description: The advent of large language models (LLMs) and other modern AI systems with reasoning capabilities enables the creation of agent-oriented research, where AI agents perform various tasks, including running and supervising domain-specific research systems. Here, we release a collection of icons, workflows, and example cases for the design of agent-oriented workflows used at Insilico Medicine. This collection of useful icons can be utilized to construct these workflows. In the future, we envision this collection being used for automated instructional workflow generation.<br>Distributed under CC BY-NC-SA. Version 21052024.
DOI: 10.6084/m9.figshare.7258382.v1
title: Selection of the optimal trading model for stock investment in different industries

description: <b>we will provide software codes and data of the paper" Selection of the optimal trading models for stock investment in different industries" on this website.<br></b>
DOI: 10.6084/m9.figshare.865669.v1
title: Blind Champagne Tasting

description: The article relating to this dataset was published in the journal Flavour 2013, 2:25 doi:10.1186/2044-7248-2-25 <strong>Participants</strong> Fifteen participants gave their informed consent prior to taking part in the tasting. Their median age was 30 years (ranging from 21 to over 60) and 11 were male. The studies have been approved by the Central University Research Ethics Committee of the University of Oxford and are therefore in compliance with the Helsinki Declaration. The whole sample had been involved in professional activities related to wine or spirits. To assess Champagne expertise, in particular, the participants were given the following questions: ‘How would you rate your experience with Champagne? Novice, intermediate, or expert’ and ‘Is your professional activity related to Champagne? Yes, no, please specify’. We chose to avoid mixing kinds of expertise because perceptions of wine are known to differ among different kinds of experts. For instance, experts included critics but importantly did not include any wine-makers or sommeliers. As such, there were four expert Champagne tasters who included wine merchants, well-known Champagne critics/journalists/writers specializing in champagne, and trade ambassadors for a Champagne house. There were six intermediate Champagne tasters, which included wine and spirit trade retailers, writers/journalists for food and wine columns, and sales representatives for Champagne houses. Finally, there were five self-assessed novice Champagne tasters, who included wine brand owners, people who worked for a Champagne house, wine trade, and spirit ambassadors who generally drank Champagne monthly. <strong>Stimuli</strong> The seven sparkling wines used in the present study consisted of six Champagnes: Mumm de Verzenay, Mumm Rosé, Mumm Vintage 2004, Perrier-Jouët Blason Rosé, Perrier-Jouët Belle Epoque 2004, Perrier-Jouët Belle Epoque Blanc de Blancs 2002, and a Ridgeview Bloomsbury Non-Vintage Sparkling wine from Sussex (UK) - the only sparkling wine not made in Champagne but made of the same grape varieties and using the same method. These wines were chosen to provide a range from 0 to 100% Chardonnay grapes.
DOI: 10.17632/ddt338rh9n
title: University students’ scores for the subject of electrical engineering in 2013-2019

description: The database was created to store food engineering bachelor (BSc) students’ scores in the subject of electrical engineering. Data were collected in the years of 2013 – 2019.

Students could freely choose one group to participate practicals. Groups were offered on Thursday (08 – 10 h, 10 – 12 h, 12 – 14 h, 14 – 16 h, 16 – 18 h) and Friday (08 – 10 h, 10 – 12 h) with maximum capacity of 25 students per group. Semester activity was awarded with bonus points, what was added to the summary points of the written test during calculation of the grade. Students had optional written test, which could result an offered grade without oral exam. The test was not mandatory, students missing the test participated the standard exam procedure. All written tests included calculations and questions were composed with combination of the sitting position. Students had to substitute their row and column position into the questions, such as “resistance R1 = {ROW} + 10 Ω”. Tests were solely composed of calculations until 2016. After that, in the years 2017 – 2019, theory questions were also prepared as free choice test. For those written tests, theory and calculations contributed to the summary with 30% and 70%, respectively.

The database is provided as Microsoft® Excel™ XML format (XLSX) and SQLite 3 database. Database indexes were created for faster search on potential grouping parameters and students’ position (row and column) during written test. Data is structured into fields as:
- Year in the range of 2013 – 2019
- Text field to distinguish student groups within a year
- Text field with the name of the day (Thursday, Friday)
- Start time of the group: 8 h, 10 h, 12 h, 14 h, 16 h
- Text field indicating gender based on given name
- Student’s row position in the room during written test
- Student’s column position in the room during written test
- Practical test result in the range 1 – 5
- Bonus points collected during the year
- Theory points relative to the possible maximum
- Calculation points relative to the possible maximum
- Summary test points relative to the possible maximum 

See description file (PDF) for more information about database format and how to import data into R.
DOI: 10.6084/m9.figshare.25037582.v1
title: Genome and annotation of Mimosa bimucronata

description: We use PacBio HiFi and Hi-C data to assemble a chromosome-level genome for Mimosa bimucronata
DOI: 10.6084/m9.figshare.29060586.v1
title: Additional file 2 of Deciphering the role of RNA in regulating CTCF’s DNA binding affinity in leukemia cells

description: Additional file 2. Table S1 Statistical overview of ChIP-seq data analysis.
DOI: 10.21954/ou.rd.21222089.v1
title: Carbon Monoxide Oxidation Protein HMMs

description: Data relating to the thesis: Constraining Microbial Community Composition, Structure, and Function Within Acidic Geothermal Springs on São Miguel Island <br> This contains the latest version of each of the HMMs constructed to detect the different proteins associated with carbon monoxide oxidation
DOI: 10.6084/m9.figshare.21901842.v4
title: Supplimentary Information.docx

description: Data from : A Global Meta-analysis of Cover Crop Response on Soil Carbon Storage Within a Corn Production System
DOI: 10.6084/m9.figshare.29146283.v3
title: Cryosphere Lake Greenhouse Gases Database 2025

description: This is an expanded cryosphere lake greenhouse gas dataset based on the Cryosphere Inland Water Greenhouse Gases Database (https://doi.org/10.5281/zenodo.11054180). To compile the dataset, we searched various sources, including peer-reviewed papers, dissertations, theses, and public data repositories. The searches were conducted using platforms such as Web of Science, Google Scholar, ProQuest Dissertations & Theses Global, China National Knowledge Infrastructure, Arctic Data Center, Zenodo, Environmental Data Initiative, and PANGAEA. The search string is: (methane OR CH4 OR carbon dioxide OR CO2 OR nitrous oxide OR N2O OR greenhouse*) AND (lake OR pond OR reservoir) AND (Arctic* OR Tibet* OR Greenland OR Antarctic OR glacier* OR permafrost). We ensured completeness by conducting multiple searches before April 2025.The R code file is used to analyze the temperature dependence of CH4 emissions in cryosphere lakes.
DOI: 10.6084/m9.figshare.1194579.v1
title: Moving Stimuli Are Less Effectively Masked Using Traditional Continuous Flash Suppression (CFS) Compared to a Moving Mondrian Mask (MMM): A Test Case for Feature-Selective Suppression and Retinotopic Adaptation

description: These are the data reported in: Moors P, Wagemans J, de-Wit L (2014) Moving Stimuli Are Less Effectively Masked Using Traditional Continuous Flash Suppression (CFS) Compared to a Moving Mondrian Mask (MMM): A Test Case for Feature-Selective Suppression and Retinotopic Adaptation. PLoS ONE 9(5): e98298. doi:10.1371/journal.pone.0098298 Two files contain the experimental data, one the simulation data, and the last one the explanation of all the variables in the three data files.
DOI: 10.6084/m9.figshare.26832166.v2
title: Monthly streaflow from 15 hydrological stations in Central Asia

description: Monthly streamflow from 15 hydrological stations in Central Asia.m
DOI: 10.17632/ppj493vx4j
title: Garcia-Cicco and Garcia-Schmidt: "Revisiting the Exchange Rate Pass Through: A General Equilibrium Perspective"

description: Repliction codes for Garcia-Cicco and Garcia-Schmidt (2020) "Revisiting the Exchange Rate Pass Through: A General Equilibrium Perspective"
DOI: 10.17632/t43tv8wwc4
title: Dicount & CEA

description: This dataset accompanies a study that presents a Mixed-Integer Linear Programming (MILP) model for optimizing the total cost of a Closed-Loop Supply Chain (CLSC) network in the electronics sector. The model considers two products, two manufacturers, two distribution centers, two collection centers, and two customer zones over two time periods. It incorporates behavioral factors such as discount incentives and consumer environmental awareness to estimate product return rates and optimize cost components across the supply chain.
DOI: 10.17632/xznv43bvjp
title: Replication package for: "Global and local technical changes: A new decomposition of the Malmquist Productivity Index using virtual units"

description: This replication package contains the files required for replicating the results presented in the paper “Global and local technical changes: A new decomposition of the Malmquist Productivity Index using virtual units” co-authored by Juan Aparicio and Daniel Santín and accepted for publication by January 2024 in Economic Modelling. 
The package contains: 
- The well-known database of 42 Swedish pharmacies between 1980 and 1989 previously analyzed in the seminal paper of Färe et al. (1992). They showed how to implement and decompose the Malmquist productivity index (MPI) using data envelopment analysis (DEA). This decomposition of total factor productivity changes consists of two terms; the catching-up effect or efficiency change and the frontier-shift effect or technical change (TC). This dataset was also used in other seminal papers as in Balk and Althin (1996), and Althin (2001).
- R code with the data in Table 1 and the steps for doing the numerical analysis and achieving the results showed in Table 2 and Fig. 4. It also allows to obtain results in Table 3 changing K.
- R code with the steps for doing the numerical analysis and obtaining GTC and LTC reproducing Tables 4 and 5 and Fig. 5. 
- A README file basic instructions for running the R scripts and the definition of variables (for more details see the papers above).

References:
Althin, R. (2001). Measurement of productivity changes: Two Malmquist index approaches. Journal of Productivity Analysis, 16(2), 107-128.
Balk, B. M., & Althin, R. (1996). A new, transitive productivity index. Journal of Productivity Analysis, 7(1), 19-27.
Färe, R., Grosskopf, S., Lindgren, B., & Roos, P. (1992). Productivity changes in Swedish pharmacies 1980-1989: A non-parametric Malmquist approach. Journal of Productivity Analysis, 3(1), 85-101.
DOI: 10.6084/m9.figshare.23943198.v2
title: Table S3: HN-ratio (Expression Ratio) Data for All Human Genes

description: HN-ratios (expression ratios) are calculated for data collected for pairs of heat stress and non-treatment conditions in human.A script was used to calculate the HN-ratio (https://github.com/no85j/hypoxia_code/blob/master/CodingGene/HN-ratio_log2.ipynb).
DOI: 10.6084/m9.figshare.25295566.v1
title: Data_for_SMCI_paper

description: This study defines a new detecting framework for dry and wet abrupt alternation and assesses the temporal concentration of soil moisture and the frequency of dry and wet abrupt alternation in China from 1979-2100. All raw data are available in the public domain.
DOI: 10.6084/m9.figshare.25679952.v1
title: Refined AI-predicted Models with Ligands

description: This data record contains the energy minimized (relaxed) ligand-containing structures which are included in the relaxed AI-predicted models with ligands, but their refined version. Refinement includes, as described in the Methods section, the removal of low confidence regions with a pLDDT score below 70, and filtering for models with 10 or more amino-acid residues remaining. After refinement, ligands which are no longer within 5 Å of any atom in the model were removed. The included subfolders contain, as individual PDB files, 14,973 ligand-containing relaxed and refined AlphaFold 2 models, 15,070 ligand-containing relaxed and refined OpenFold models, and 12,855 ligand-containing relaxed and refined ESMFold models.
DOI: 10.6084/m9.figshare.29117657.v1
title: Datasets for Hisano et al. "<b>Shelterbelts </b><b>s</b><b>upport </b><b>e</b><b>dge </b><b>b</b><b>irds but </b><b>l</b><b>imit </b><b>g</b><b>rassland and </b><b>w</b><b>etland </b><b>s</b><b>pecialists in </b><b>agricultural landscape</b>"

description: Data sets for Hisano et al.: Shelterbelts support edge birds but limit grassland and wetland specialists in agricultural landscapeData Key.xlsx: data keys for the materialsGroup_dat.csv: Habitat group data for GLMMMajor_SPEC_dat.csv: Major species data for GLMMMinor_spec_dat.csv: Minor species data for Fisher's exact testSPEC_List_Kahokugata.csv: A list of species names (Japanese, English, Latin)
DOI: 10.6084/m9.figshare.3528722.v1
title: Appendix C. Statistical tables and additional results.

description: Statistical tables and additional results.
DOI: 10.6084/m9.figshare.978509.v3
title: HypnOBE

description: Materials related to the paper "Out of Body Experience induced by hypnotic suggestion. Part 1: phenomenology and perceptual characteristics" available at http://papers.ssrn.com/sol3/papers.cfm?abstract_id=2443719
DOI: 10.17632/2jd6y5c7k4
title: Data for "Durability behavior of concrete incorporating reclaimed asphalt pavement as aggregates: a comprehensive review" paper

description: data used in the paper named: Durability behavior of concrete incorporating reclaimed asphalt pavement as aggregates: a comprehensive review
DOI: 10.17632/xxxfxrwkg3
title: Local skin reactions and the onset of influenza-like signs and symptoms induced by imiquimod 3.75% cream

description: Supplemental figures for article for JAAD International
DOI: 10.6084/m9.figshare.10296338.v1
title: The forgotten dimension of the housing policy: reflections on the case of the metropolitan area of Curitiba (State of Paraná)

description: Abstract In Brazil, the housing policy regained importance over the last fifteen years, with the construction of an institutional framework and the massive production of affordable houses. Several studies were developed, mainly related to the housing program Minha Casa Minha Vida. In this scenario, this article is part of a deeper and latent discussion: it aims to investigate the dynamics involved in the overlap between housing issues and metropolitan areas, spaces of special interest, as they concentrate more than half of the housing deficit and about 80% of informal settlements in Brazil. Through a study of the Metropolitan Area of Curitiba, we seek to discuss the “forgotten dimension”, without which the undertaken efforts may not produce the expected effects.
DOI: 10.6084/m9.figshare.1204727.v1
title: Analysis of Feature Intervisibility and Cumulative Visibility Using GIS, Bayesian and Spatial Statistics: A Case Study from the Mandara Mountains, Northern Cameroon

description: All data from the paper "Analysis of Feature Intervisibility and Cumulative Visibility Using GIS, Bayesian and Spatial Statistics: A Case Study from the Mandara Mountains, Northern Cameroon" published in PLOS ONE are included in this fileset.
DOI: 10.17632/ysk4trkgpt
title: Building energy simulation calibration accuracy and modelling complexity: implications for energy performance improvement

description: Data that support the findings relating to the manuscript: L. Peinturier, D. Wallom. "Building energy simulation calibration accuracy and modelling complexity: implications for energy performance improvement" (submitted for review). The data includes detailed model results alongside DesignBuilder models created as part of the study.
DOI: 10.6084/m9.figshare.17079170.v1
title: Additional file 9 of miR-30b-5p inhibits proliferation, invasion, and migration of papillary thyroid cancer by targeting GALNT7 via the EGFR/PI3K/AKT pathway

description: Additional file 9. The GSEA analysis on the signaling pathways.
DOI: 10.6084/m9.figshare.24784497.v3
title: S6_Table:Final 30-day experiment complete dataset

description: This has the daily spectral readings along with the predicted mL and the daily EC readings. Tank 1 was control Tank 2 was the treatment. S0 corresponds with Sensor 1 in the paper and S3 corresponds with Sensor 4.
DOI: 10.6084/m9.figshare.25563693.v1
title: mp_20

description: https://github.com/txie-93/cdvae/tree/main/data/mp_20