Find research datasets worth reusing

opencc-by-4.0Apr 2022View details →

An experimental data set for analysis of the thermophysical behavior of a single-story mechanically ventilated double-skin façade (DSF) in fixed boundary conditions corresponding to winter/mid-season and summer cases

Double-skin facades (DSFs) are dynamic and flexible building envelopes that employ a ventilated cavity to either prevent or reduce the solar-induced cooling load or exploit solar energy for passive solar heating. The mechanical ventilation of the cavity offers higher flexibility and control than natural ventilation, as the latter largely depends on stochastic and unpredictable external conditions. Furthermore, when mechanical ventilation rates are combined with the operation of a shading device, the possibilities for controlling the accumulated heat in the cavity of the DSF increase further. Therefore, this experimental campaign systematically investigates how these two important features interact in controlling the cavity's thermal load and airflow conditions. The measurement collected during the experiments constitutes a dataset that contains the results of a series of experimental runs where the different configurations of DSF, in terms of mechanical ventilation rate and venetian blinds, have been subjected to two representative boundary conditions through a climate simulator facility equipped with a solar simulator device. The full-scale DSF mock-up, which includes venetian blinds installed in a 200 mm ventilated cavity, is operated in this experiment in two modes: outdoor air curtain (OAC) and supply air (SA) mode. Tests were carried out under a steady-state regime with different boundary conditions. For the analysis of the utilization of the excess heat accumulated in the cavity and prevention of DSF overheating, boundary conditions corresponding to g-value calculations were selected. For the analysis of air preheating in the DSF cavity, the boundary conditions corresponding to late winter/mid-season weather (cold outdoor air and low-to-moderate solar irradiance) were chosen. The entire set of experimental data collected during the tests is made publicly available to enable the scientific community to access experimental data to further analyze this problem or for model validation purposes. The data set supplements the open-access paper entitled "Control of heat transfer in single-story mechanically ventilated facades" (<a href="https://doi.org/10.1016/j.enbuild.2022.112304">https://doi.org/10.1016/j.enbuild.2022.112304</a>), where additional information about the aims of the experiments, the detailed methods, and other data processing procedures can be found. The database is supported by a guide ("Guide.pdf"), where further explanations about how to read data and schematic drawings of the sensor layout are provided. The collection of experimental tests is divided into two files, according to two considered cases: <ul> <li>DSF operating in outdoor air curtain mode (24 steady-state measurements). The following factors were changed: mechanical ventilation rate (0, 10, 15, 20, 30, 40, 50, and 100 % of maximum fan power) and venetian blind configuration (closed θ=0 º, semi-open θ=45 º, and raised blinds). The outdoor and indoor temperatures, 30 ℃ and 25 ℃, and solar irradiance of 500 Wm-2 were replicated. [file name: "Summer.csv"],</li> <li>DSF operating in supply air mode (27 steady-state measurements). The following factors were changed: mechanical ventilation rate (0, 10, 15, 20, 30, 40, 50, 75, and 100 % of maximum fan power) and venetian blind configuration (closed θ=0 º, semi-open θ=45 º, and raised blinds). The outdoor and indoor temperatures, 10 ℃ and 25 ℃, and solar irradiance of 300 Wm-2 were replicated. [file name: " Winter_MidSeason.csv"]</li> </ul> Any inquiries about the experimental data can be sent to: <a href="mailto:aleksandar.jankovic@ntnu.no">aleksandar.jankovic@ntnu.no</a> The activities presented in this paper were carried out within the research project "REsponsive, INtegrated, VENTilated - REINVENT – windows," supported by the Research Council of Norway through the research grant 262198, and the partners SINTEF, Hydro Extruded Solutions, Politecnico di Torino and Aalto University.

opencc-by-4.0Sep 2021View details →

Radio-frequency C-V measurements with subattofarad sensitivity: data and analysis script

The attached files include: <ul> <li>QCoDeS database containing all of the raw data underlying the results presented in the publication "Radio-frequency CV measurements with subattofarad sensitivity" by F.K. Malinowski at al. published in Physical Review Applied in 2022</li> <li>Jupyter Notebook file with Python scripts, that processes the raw data and outputs the figures embedded in the publication (except for the schematics of the devices and the rf circuitry).</li> </ul>

opencc-by-4.0Jul 2022View details →

EPR data and analysis for Järsvall et al., Chem. Mater. 34:5673-5679, 2022

Released 2022-07-24 This directory contains both, raw data and analysis "recipes" used to analyse the EPR data for the following manuscript: <ul> <li>Emmy Järsvall, Till Biskup, Yadong Zhang, Renee Kroon, Stephen Barlow, Seth Marder, Christian Müller: Double doping of a low-ionization energy polythiophene with a molybdenum dithiolene complex. Chemistry of Materials, 34:5673-5679, 2022</li> </ul>

opencc-zeroJul 2022View details →

Data from: Controlled drainage and subirrigation suitability in the United States: A meta-analysis of crop yield and soil moisture effects

Controlled drainage and subirrigation (CDSI) is an important water management strategy in many regions, but the conditions under which CDSI is most likely to increase crop yield and soil moisture are not fully understood. A meta-analysis, consisting of 154 pairwise observations from replicated and randomized trials in 30 peer-reviewed primary research articles on CDSI (6 controlled drainage, 24 CDSI, analyzed together due to data scarcity), was conducted to study the responses of yield and soil moisture to CDSI, and investigate how crop type, soil texture, and cumulative growing season precipitation (PGS) influence these responses. Based on the yield response to these moderating factors, we used a fuzzy-logic approach to map potentially suitable locations for CDSI in the conterminous United States. On average, CDSI increased yield by 8.0% (95% CI = 1.8–14.7%) compared with conventional free drainage. The yield response to CDSI did not differ among crops. However, a greater yield response to CDSI was observed in medium-textured soils (19.4% increase; 95% CI = 12.4–27.0%) than in coarse- or fine-textured soils. The positive effect of CDSI on yield increased with decreasing PGS in coarse- and medium-textured soils. There was no clear effect of CDSI on soil moisture, nor did any moderators influence this relationship, though this may be attributed to the scarcity of studies on CDSI reporting soil moisture. The fuzzy-logic-based approach revealed that while potentially suitable areas are mostly concentrated in the well studied U. S. Midwest, these areas also exist in other regions where CDSI may warrant further study.

opencc-by-4.0Jul 2022View details →

Analysis of scholarly repositories' availability. Data and notebooks.

These datasets and companion Jupyter notebooks supplement the publication "Knock knock! Who's there?'' A study on scholarly repositories' availability" accepted at TPDL 2022, Padova, Italy.

opencc-by-4.0Dec 2021View details →

Secondary Data: Measuring Person-centred Care in German Nursing Homes – Exploring Construct Validity of the Dementia Policy Questionnaire using Adjusted Multiple Correspondence Analysis

This is the secondary data set and R-Code of R statistical software (version 4.0.4) to explore construct validity of the German Dementia Policy Questionnaire using Adjusted Multiple Correspondence Analysis.

Data for manuscript "rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data"

Output files generated by rMATS-turbo for the two example datasets described in the manuscript titled "rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data". <table> <tbody> <tr> <td>File</td> <td>Description</td> <td>Cell lines</td> <td>BioProject</td> </tr> <tr> <td>PC3E-GS689.tar.gz</td> <td>Compressed folder containing all 36 rMATS-turbo output files for Example 1 described in the manuscript</td> <td>PC3E and GS689 cell lines</td> <td>PRJNA438990</td> </tr> <tr> <td>CCLE.tar.gz</td> <td>Compressed folder containing all 36 rMATS-turbo output files for Example 2 described in the manuscript</td> <td>1,019 CCLE human cancer cell lines</td> <td>PRJNA523380</td> </tr> </tbody> </table> A detailed description of the output files is available in the manuscript and the rMATS-turbo software GitHub repository (https://github.com/Xinglab/rmats-turbo).

Raw data for "Fluorescence crosstalk reduction by modulated excitation-synchronous acquisition for multispectral analysis in high-throughput droplet microfluidics."

Raw data to quantify the crosstalk reduction and signal resolution improvement by MESA used in Figure 3 and 4.

Image data for bioRxiv article named: mtFociCounter - Reproducible, open source and quantitative single-cell analysis of mitochondrial nucleoids and other foci

Raw imaging data to reproduce and test the findings of the bioRxiv article: mtFociCounter - Reproducible, open source and quantitative single-cell analysis of mitochondrial nucleoids and other foci. It contains data from three imaging days and 2 or three technical replicates on each day.

opencc-by-4.0Sep 2020View details →

Supplementary data: Medicago transcriptomics DRMN analysis

Summary of DRMN per-gene module assignments, module motif enrichments, inferred network edge weights, and MTG-LASSO predictions, Supplementary data tables 1-4 of this submission, respectively.

opencc-zeroAug 2022View details →

Data from: Worldwide impacts of landscape anthropization on mosquito abundance and diversity: a meta-analysis

In recent decades, the emergence and resurgence of vector-borne diseases have been well documented worldwide, especially in tropical regions where protection and defence tools for human populations are still very limited. In this context, the dynamics of pathogens are influenced by landscape anthropization (i.e., urbanization, deforestation, and agricultural development), and one of the mechanisms through which this occurs is a change in the abundance and/or diversity of the vectors. An increasing number of empirical studies have described heterogeneous effects of landscape anthropization on vector communities; therefore, it is difficult to have an overall picture of these effects on a global scale. Here, we performed a meta-analysis to quantify the impacts of landscape anthropization on a global scale on the presence/abundance and diversity of mosquitoes, the most important arthropods affecting human health. We obtained 338 effect sizes on 132 mosquito species, compiled from 107 studies in 52 countries that covered almost every part of the world. The results of the meta-analysis showed an overall decline of mosquito presence/abundance and diversity in response to urbanization, deforestation, and agricultural development, except for a few mosquito species that have been able to exploit landscape anthropization well. Our results highlighted that these few favoured mosquito species are those of global concern. They thus provide a better understanding of the overall effect of landscape anthropization on vector communities and, more importantly, suggest a greater risk of emergence and transmission of vector-borne diseases in human-modified landscapes.

Data and analysis script to support "Multi-site analysis of sequence in leaf-out and flowering reveals evidence of local adaptation"

Data files and R script used to download and analyze plant leaf-out and flowering observations maintained by the USA National Phenology Network to evaluate the consistency of leaf-out and flowering among species pairs over multiple years.

[Demo Input Data] for SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells

This archive (input.tar.gz) contains the demo data for SCAFE v1.0.0 (on <a href="https://doi.org/10.5281/zenodo.7023163">Zenodo</a> or <a href="https://github.com/chung-lab/SCAFE/releases/tag/v1.0.0">Github</a>) SCAFE (Single Cell Analysis of Five-prime Ends) provides an end-to-end solution for processing of single cell 5’end RNA-seq data. It takes a read alignment file (*.bam) from single-cell RNA-5’end-sequencing (e.g. 10xGenomics Chromimum®), precisely maps the cDNA 5'ends (i.e. transcription start sites, TSS), filters for the artefacts and identifies genuine TSS clusters using logistic regression. Based on the TSS clusters, it defines transcribed cis-regulatory elements (tCRE) and annotated them to gene models. It then counts the UMI in tCRE in single cells and returns a tCRE UMI/cellbarcode matrix ready for downstream analyses, e.g. cell-type clustering, linking promoters to enhancers by co-activity etc. For details on installation, usage and test run on demo data, visit <a href="https://github.com/chung-lab/SCAFE">https://github.com/chung-lab/SCAFE</a>

opencc-by-4.0Sep 2022View details →

Quantitative analysis data of the laminae

The organic matter in the laminae was quantified using SVM. The data can be opened with ENVI software and ArcGIS software.

opencc-zeroAug 2022View details →

Matlab example for Local Enrichment Analysis (LEA) analysis with real data

Phenotypic plasticity is essential to the immune system, yet the factors that shape it are not fully understood. Here, we comprehensively analyze immune cell phenotypes including morphology across human cohorts by single-round multiplexed immunofluorescence, automated microscopy, and deep learning. Using the uncertainty of convolutional neural networks to cluster the phenotypes of 8 distinct immune cell subsets, we find that the resulting maps are influenced by donor age, gender, and blood pressure, revealing distinct polarization and activation-associated phenotypes across immune cell classes. We further associate T-cell morphology to transcriptional state based on their joint donor variability, and validate an inflammation-associated polarized T-cell morphology, and an age-associated loss of mitochondria in CD4+ T-cells. Taken together, we show that immune cell phenotypes reflect both molecular and personal health information, opening new perspectives into the deep immune phenotyping of individual people in health and disease.

opencc-by-4.0Sep 2022View details →

Excitation energy transfer and vibronic coherence in intact phycobilisomes — multidimensional electronic spectroscopy data set and MATLAB and Julia analysis code

Data sets used in the article "Excitation energy transfer and vibronic coherence in intact phycobilisomes" by Sil et al. The phycobilisomes were isolated from the short-filament mutant (SF33) of Fremyella diplosiphon UTEX 481 (also known as Tolypothrix sp. PCC 7601). Multidimensional electronic spectroscopy was performed with 6.7 fs mid-visible pulses (520–700 nm) using a pump–probe optical configuration using adaptive pulse shaping techniques. In addition to the full set of two-dimensional spectra and analysis files generated using global and target modeling and analysis of coherences (3DES oscillation maps), we provide here a linear absorption spectrum with phycobiliprotein component analysis as well as a set of 2D excitation–emission fluorescence spectra of intact and broken phycobilisome preparations.  Sil, S.; Tilluck, R. W.; Mohan TM, N.; Leslie, C. H.; Rose, J. B.; Domínguez-Martín, M. A.; Lou, W.; Kerfeld, C. A.; Beck, W. F. Excitation energy transfer and vibronic coherence in intact phycobilisomes. Nat. Chem. (2022), DOI: 10.1038/s41557-022-01026-8. <a href="https://urldefense.com/v3/__https://www.nature.com/articles/s41557-022-01026-8__;!!HXCxUKc!yaVwTZFk8T-j3ROhygpOGW5Xy_E2wQvf-QgNGr9FZZbp4oNpfp_ZmhkdWYLdg2mKSDP8yYrNAZs$">https://www.nature.com/articles/s41557-022-01026-8</a>

opencc-by-4.0Dec 2021View details →

Data presented in Multi-trial analysis of HIV-1 envelope gp41-reactive antibodies among global recipients of candidate HIV-1 vaccines.

This folder contains datasets analyzed in the manuscript: Multi-trial analysis of HIV-1 envelope gp41-reactive antibodies among global recipients of candidate HIV-1 vaccines. Frontiers in Immunology Sec. Vaccines and Molecular Therapeutics doi: 10.3389/fimmu.2022.983313

opencc-by-4.0May 2022View details →

Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey - Extended Data 4 - Analysis Data Sheet

This dataset is extended data to the manuscript "Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey" by Schmidt C., Hanne J, Moore J, Meesters C, Ferrando-May E, Weidtkamp-Peters S, and members of the NFDI4BIOIMAGE initiative. [version 1; peer review: awaiting peer review] F1000Research 2022, 11:638, https://doi.org/10.12688/f1000research.121714.1 This extended data includes: - Data Analysis Sheet and results table Note: The data is anonymized (i.e., all IP addresses as well as personal comments were deleted) The revised version was published after the peer-review process of the original article on zenodo.org

opencc-zeroSep 2022View details →

Raw RADseq data for: Population genomics analysis with RAD, reprised: Stacks 2

Restriction enzymes have been one of the primary tools in the population genetics toolkit for 50 years, being coupled with each new generation of technology to provide a more detailed view into the genetics of natural populations. Restriction site-Associated DNA protocols, which joined enzymes with short-read sequencing technology, have democratized the field of population genomics, providing a means to assay the underlying alleles in scores of populations. More than 10 years on, the technique has been widely applied across the tree of life and served as the basis for many different analysis techniques. Here, we provide a detailed protocol to conduct a RAD analysis from experimental design to de novo analysis—including parameter optimization—as well as reference-based analysis, all in Stacks version 2, which is designed to work with paired-end reads to assemble RAD loci up to 1000 nucleotides in length. The protocol focuses on major points of friction in the molecular approaches and downstream analysis, with special attention given to validating experimental analyses. Finally, the protocol provides several points of departure for further analysis.