Find research datasets worth reusing

opencc-by-4.0May 2023View details →

Source data for VALIS: Virtual Alignment of pathoLogy Image Series for multi-gigapixel whole slide images publication

Source data used to create figures in VALIS: Virtual Alignment of pathoLogy Image Series for multi-gigapixel whole slide images (Nature Communications, 2023)

opencc-by-4.0Jun 2022View details →

Code and source data for the paper: "Heat over heritability: increasing body size in response to global warming is not stabilized by genetic effects in Bechstein's bats"

The first two script include code for the model building testing different fixed effect strucutes. The next two script includes all code for the descriptive analysis, all figures, as well as the animal models that compare heritabilty between the different environments (Q1-Q4) as well as between the birth environments differentials of mothers and daughters. Data contain the pedigree ('pedigree_Model_cod.csv'), further information ('pedigree_information_cod.csv) and weather data ('Weather_summer.csv')

source data for NCOMMS-23-12375-T

NMR,CV data, you can get access to the original data such as origin file or Mnova file by double click the graph in the Word file.  Cartesian coordinates for the optimized structure was also included

Source code and data for aerosol emission and indirect feedback paper

A physics suite under development at NOAA’s Global System Laboratory (GSL) includes the aerosol-aware double moment Thompson-Eidhammer microphysics scheme (TH-E MP). This microphysics scheme uses two aerosol variables (water friendly (WFA) and ice friendly (IFA) aerosol number concentrations) to include interaction with some of the physical processes. In the original implementation, WFA and IFA depend on emissions derived from climatologies. In our approach, using the Common Community Physics Package (CCPP), we embedded sea-salt, dust, and biomass burning emission modules as well as anthropogenic aerosol emissions into the Unified Forecast System (UFS) to provide realistic aerosol emissions for these two variables. This represents a very simple approach with no additional tracer variables and therefore very limited additional computing cost. We then evaluate a comparison of simulations using the original TH-E MP approach, which derives the two aerosol variables using empirical emission formulas from climatologies (CTL) and simulations that use the online emissions (EXP). Aerosol Optical Depth (AOD) is derived from the 2 variables and appears quite realistic in the runs with online emissions when compared to analyzed fields. We find less resolved precipitation over Europe and North America from the EXP run, which represents an improvement compared to observations. Also interesting are moderately increased aerosol concentrations over Southern Ocean from the EXP run invigorating the development of cloud water and enhances the resolved precipitation in those areas. This study shows that a more realistic representation of aerosol emission may be useful when using double moment microphysics schemes.

Source data for the scientometric analysis of citizen science research publications

Source data for the scientometric comparison of citizen science research (n=5749 documents) and a semi-random sample of publications (n=5734) retrieved from the Web of Science Core Collection and published between 1997-2021. The data include information on: author(s) full name(s) ("AF"); year of publication ("PY"); title ("TI"); Digital Object Identifier ("DI"); abstract ("AB"); open access indicator ("OA"); author(s) affiliation(s) ("C1"); document type ("DT"); funding entity ("FU"); funding text ("FX"); total number of citations ("TC"); and identifier of the collection ("group"): CS for citizen science and SRS for the semi-random sample collection respectively.

opencc-zeroJun 2023View details →

Data for: Visualization of the hidden food sources of bass (Micropterus salmoides), crucian carp (Carassius carassius), and minnow (Zacco platypus) using 18S rRNA V9 primers on urban Singal Reservoir in Korea

Fish are the most important consumers in aquatic ecosystems, and the analysis of fish prey is very important for understanding their short-term feeding characteristics and the connectivity of food webs. In this study, DNA metabarcoding was used to identify the prey of the native fish species, Zacco platypus (the pale chub) and Carassius carassius, and an introduced species, Micropterus salmoides, in domestic lentic ecosystems. Prey community composition, selectivity index, prey diversity, and trophic level analyses were performed. The prey composition ratio analysis showed that in August 2020, 85.8% of M. salmoides' prey was fish from the orders Cypriniformes and Perciformes, and in July 2021, 100% of M. salmoides' prey was zooplankton from the orders Anomopoda and Calanoida. Zooplankton was the main prey of Z. platypus collected in August 2020 (69.5%) and C. carassius collected in July 2021 (88.9%). The selectivity index analysis showed that the preferred prey of M. salmoides was fish from the order Cypriniformes, the preferred prey of Z. platypus was phytoplankton from the division Bacillariophyta, and the preferred prey of C. carassius was zooplankton from the order Cladocera. For the prey width analysis, C. carassius had the highest BI index value (0.8), followed by Z. platypus (0.29), while M. salmoides had BI index values of 0.09, 0.19, and 0.001, indicating low prey width. These results provide fundamental data on the utility of DNA metabarcoding for dietary studies of major fish species in lentic ecosystems and for analyzing food web connectivity based on major prey items.

Source data of the study of semantic and syntactic relations

The data contain detailed answers of test participants to questions asked in accordance with the scenario of examining semantic and syntactic relations between tactile cartographic signs, planned to be placed on tactile maps of historic gardens in various garden design styles. The study was conducted as part of testing the legibility of cartographic tactile signs, realized within the research project No. Rzeczy są dla ludzi/0005/2020-00, titled “Technology for the development of tactile maps of historic parks”, financed by the National Centre for Research and Development, for the years 2021–2024, and realized at the Military University of Technology, Faculty of Civil Engineering, and Geodesy (Warsaw, Poland).

opencc-by-4.0Jul 2023View details →

Source code and data files for the fetal kick simulator developed in the Biomechatronics Lab at Imperial College London, UK

This repository holds the code for Fetal Kick Simulator Copyright (c) 2020, Imperial College London All rights reserved. Authors: Abhishek Kumar Ghosh, Ravi Vaidyanathan, Niamh C Nowlan. Imperial College London. This program is a free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. Acknowledgements: If this software is helpful, then Please consider acknowledging or referencing the authors. Publication: Link for the publication related to this repository is <a href="https://www.mdpi.com/1424-8220/20/21/6020">https://www.mdpi.com/1424-8220/20/21/6020</a>

opencc-zeroJul 2023View details →

Data from: Estimating potential global sources and secondary spread of freshwater invasions under historical and future climates

Aim: We employ a climate-matching method to evaluate potential source regions of freshwater invasive species to an introduced region and their potential secondary spread under historical and future climates. Location: Global source regions, with primary introductions to the Laurentian Great Lakes and secondary introductions throughout North America Methods: We conducted a climate-match analysis using the CLIMATE algorithm to estimate global source freshwater ecoregions under historical and future climates with an ensemble of general circulation models for climate change scenario SSP5-8.5. Given existing research, we use a climate match of ≥ 71.7% between ecoregions to indicate climatic conditions that will not inhibit the survival of introduced freshwater organisms. Further, we estimate the secondary spread of freshwater invaders to the ecoregions of North America under historical and future climates. Results: We identified 54 global freshwater ecoregions with a climate match ≥ 71.7% to the recipient Laurentian Great Lakes under historical climatic conditions and 11 additional ecoregions were predicted to exceed the threshold under climate change. Three of the 11 ecoregions were located in South America, a continent where no matches existed under historical climates and eight were located in the southern United States, southern Europe, Japan, and New Zealand. Further, we identify 34 North American ecoregions of potential secondary spread of freshwater invasions from the Great Lakes under historical climatic conditions, and five ecoregions were predicted to exceed the threshold under climate change. Main conclusion: We provide a climate-match method that can be employed to assess the sources and spread of freshwater invasions under historical and future climate scenarios. Our climate-match method predicted increases in climate match between the recipient region and several potential source regions, and changes in areas of potential spread under climate change. The identified ecoregions are candidates for detailed biosecurity risk assessments and related management actions. The identified ecoregions are candidates for detailed biosecurity risk assessments and related management actions.

Data included in "Canopy leaching rather than desorption of PM2.5 from leaves is the dominant source of throughfall dissolved organic carbon in forest"

Concentrations, optical properties, and carbon isotopic ratios of dissolved organic carbon in precipitation and throughfall, as well as concentrations and carbon isotopic ratios of total carbon in PM2.5, at the Taehwa Research Forest in South Korea

Lamian Paper Source Data

The compressed file includes: - Source_Data.xlsx: Source data in spreadsheet format. - SourceData.zip: Contains source data in `.rds` format, not available as spreadsheets.

Data for: Low mercury concentration in a Greenland glacial fjord attributed to oceanic sources

Total mercury (THg) and methyl mercury (MeHg) concentrations measured in southeast Greenland between 10 August and 20 August 2021. The majority of samples were collected in Sermilik Fjord and on the continental shelf to the west of the fjord mouth  (identified by CTD cast number; see below for corresponding data citation). A small number of samples were collected by hand from surface waters in Apuseeq Fjord, in a lake and river near the village of Tiilerilaaq (formerly known as Tiniteqilaq), and in a river near Tasiilaq. All samples are identified by the date, time, and lat/lon of collection. For further details about the sample collection and analysis, please see the methods section of the associated publication. Sermilik Fjord and continental shelf CTD data are available via the NSF Arctic Data Center (doi:10.18739/A2HD7NT9K).

Source Data for the publication: "How Orange Carotenoid Protein controls the excited state dynamics of Canthaxanthin"

This dataset contains the raw data for the results shown in the paper, in plain text format. The first line of each file describes the content of the columns. Contents: <ul> <li>ocp_adiabatic_energies.txt - Energies of the adiabatic states (A.U.) for all SH trajectories of CAN in OCP</li> <li>ocp_bla.txt - Values of the BLA coordinate (Angstrom) for all SH trajectories of CAN in OCP</li> <li>ocp_dihedrals.txt - Values of the CAN dihedrals ) degrees for all SH trajectories of CAN in OCP</li> <li>ocp_populations.txt - Calculated adiabatic populations of CAN in OCP</li> <li>vac_adiabatic_energies.txt - Energies of the adiabatic states (A.U.) for all SH trajectories of CAN in gas phase</li> <li>vac_bla.txt - Values of the BLA coordinate (Angstrom) for all SH trajectories of CAN in gas phase</li> <li>vac_dihedrals.txt - Values of the CAN dihedrals ) degrees for all SH trajectories of CAN in gas phase</li> <li>vac_populations.txt - Calculated adiabatic populations of CAN in gas phase</li> </ul>

opencc-by-4.0Nov 2023View details →

Spatial metatranscriptomics resolves host-bacteria-fungi interactomes, Source Data

Source Data for a publication: Spatial metatranscriptomics resolves host-bacteria-fungi interactomes.  Includes the data sets to generate the results.  Contains five different experiment types: - Pst  bacterial infiltration experiment - Enrichment experiment with different array types - Comparison between SmT vs. Amp-seq - Outdoor-grown leaf experiments - Sterile leaf experiment For each of the experiments are included (if generated, see the README file): - Gene count matrices - Microbial taxa count matrices - Bright field images - Alignment files (Spot files) - Putative microbial reads and related probe information - Data for enrichment analysis - Fluorescent images and corresponding fluorescent values

opencc-bySep 2023View details →

Source data figures Diverse Slip behaviour on Velocity-Weakening fault segments

txt data files for figures 3, 4 and 5 displayed on  manuscript Diverse Slip behaviour on Velocity-Weakening fault segments

opencc-zeroSep 2023View details →

Data from: Scoring thermal limits in small insects using open-source, computer assisted motion detection

Scoring large amounts of thermal tolerance traits live or with recorded video can be time consuming and susceptible to investigator bias, and as with many physiological measurements, there can be trade-offs between accuracy and throughput. Recent studies show that particle tracking is a viable alternative to manually scoring videos, although it may not detect subtle movements, and many of the software options are proprietary and costly. In this study, we present a novel strategy for automated scoring of thermal tolerance videos by inferring motor activity with motion detection using an open-source Python command line application called DIME (Detector of Insect Motion Endpoint). We apply our strategy to both dynamic and static thermal tolerance assays, and our results indicate that DIME can accurately measure thermal acclimation responses, generally agrees with visual estimates of thermal limits, and can significantly increase the throughput over manual methods.

opencc-by-4.0Sep 2023View details →

Data for: Sources, pathways and behaviour of cave air CO2 using carbon isotopes

Raw data for all figures in the manuscript by Krajnc et al. to be published by Geochimica et Cosmochimica Acta as "Sources, pathways and behaviour of cave air CO2 using carbon isotopes".

opencc-by-4.0Sep 2023View details →

Analyzing sources of error in TIRM experiments and data analysis.

The datasets contain the experimental and simulated intensity traces underlying the figures published in the paper "Analyzing sources of error in TIRM experiments and data analysis." by J. A. Rivera-Moran and P. R. Lang in the MDPI Polymers Special issue "Interaction and Dynamics of Polymers and Colloidal Particles Near Interfaces".

opencc-zeroOct 2023View details →

Source data for: Raman sideband cooling of molecules in an optical tweezer array

Ultracold molecules, because of their rich internal structures and interactions, have been proposed as a promising platform for quantum science and precision measurement. Direct laser-cooling promises to be a rapid and efficient way to bring molecules to ultracold temperatures. For trapped molecules, laser-cooling to the quantum motional ground state remains an outstanding challenge. A technique capable of reaching the motional ground state is Raman sideband cooling, first demonstrated in trapped ions and atoms. In this work, we demonstrate for the first time Raman sideband cooling of molecules. Specifically, we demonstrate 3D Raman cooling for single CaF molecules trapped in an optical tweezer array, achieving average radial (axial) motional occupation as low as $\bar{n}_r=0.27(7)$ ($\bar{n}_z=7.0(10)$). Notably, we measure a 1D ground state fraction as high as 0.79(4), and a motional entropy per particle of $s = 4.9(3)$, the lowest reported for laser-cooled molecules to date. These lower temperatures could enable longer coherence times and higher fidelity molecular qubit gates desirable for quantum information processing and quantum simulation. With further improvements, Raman cooling could also be a new route towards molecular quantum degeneracy applicable to many laser-coolable molecular species including polyatomic ones.