Find research datasets worth reusing

opencc-by-4.0Apr 2024View details →

A Case-Control Study to Measure Behavioral Risks of Malware Encounters in Organizations

The behavior of enterprise users (e.g. browsing at night or visiting gambling sites) is a potential factor that might increase the chances of malware encounters (e.g. coinminers vs ransomware) on the field. This dataset report the aggregated results of a case-control study on telemetry data collected by Trend Micro, a global cybersecurity vendor, to identify users’ behavioral characteristics that can be used to differentiate cybersecurity risks profiles.

opencc-by-4.0Jul 2024View details →

Dataset for KIOS CoE Sandboxing use-case SUC5 corresponding to cyber attacks affecting the control of active distribution grids and microgrids

These datasets  illustrate two primary scenarios (S1-S2) concerning the operation of the sandboxing use case SUC5 corresponding to cyber attacks affecting the control of active distribution grids and microgrids. These scenarios examine the functioning of an active distribution grid and microgrid system, along with the effects of certain cyber-attacks in this context. The demonstration of each scenario is detailed in selected time-series plots which were described in detail in Section 1.3 of the supporting document of SUC5 (accompanied by an in-depth analysis of the processes and an impact assessment). All data captured during the execution of each scenario was collected, including electrical measurements, reference and set-point signals.  <ul> <li>SUC5/S1 datasets/MITM with FDI cyber-attack in an active distribution grid (grid-connected): This dataset is related to the operation of the fifth sandboxing use case (SUC5) of the KIOS CoE Sandboxing environment for cyber-physical analysis of EPES, which examines the operation of an active distribution grid, when the distribution grid is interconnected with the main grid. Specifically, this dataset corresponds to the first scenario (S1) of SUC5, where a MITM with FDI cyber-attack is virtually conducted within the sandboxing environment to introduce an offset deviation to the active power set-point allocated to BSS inverter controller from the secondary controller. More details about the scenario related to this dataset can be found in Section 1.3 of the supporting document. The dataset includes electrical measurements of the active power generated by the BSS inverter (connected at bus 2), and the active power set-point before and after the attack. The dataset is provided in the form of time-series measurements available as MATLAB (.mat) and CSV (.csv) files. The measurements were recorded from the real time simulator using the “OpWrite” block of the RT-LAB, with 1-millisecond time resolution.   </li> <li>SUC5/S2 datasets/MITM with FDI cyber-attack in a microgrid (islanding mode): This dataset is related to the operation of the fifth sandboxing use case (SUC5) which investigates the operation of a microgrid during islanding mode. This dataset corresponds to the second scenario (S2) of SUC5, where a MITM with FDI cyber-attack is virtually conducted within the sandboxing environment to introduce an offset deviation to the frequency reference signal, exchanged between the higher-level controller (tertiary controller) and the microgrid local controller (secondary V-f controller). More details about the scenario related to this dataset can be found in Section 1.3 of this supporting document. The dataset includes electrical measurements of the microgrid frequency, the reference frequency value generated by the tertiary controller, as well as the attacked frequency reference value. The dataset is provided in the form of time-series measurements available as MATLAB (.mat) and CSV (.csv) files. The measurements were recorded from the real time simulator using the “OpWrite” block of the RT-LAB, with 1-millisecond time resolution.   </li> </ul>

opencc-by-4.0Feb 2021View details →

Supplementary material for "Learning Boolean controls in regulated metabolic networks: a case-study"

This record contains notebooks and Docker image for reproducing the learning of Boolean controls in regulated metabolic networks, and the case study presented in the CMSB 2021 conference proceeding article "Learning Boolean controls in regulated metabolic networks: a case-study". Visualize notebooks online: <ul> <li><a href="https://nbviewer.jupyter.org/urls/zenodo.org/record/5060985/files/CaseStudy-Simulations.ipynb">CaseStudy-Simulations.ipynb</a></li> <li><a href="https://nbviewer.jupyter.org/urls/zenodo.org/record/5060985/files/CaseStudy-SearchSpace.ipynb">CaseStudy-SearchSpace.ipynb</a></li> <li><a href="https://nbviewer.jupyter.org/urls/zenodo.org/record/5060985/files/CaseStudy-Inference.ipynb">CaseStudy-Inference.ipynb</a></li> </ul> Notebooks can be executed interactively within the Docker image <code>bioasp/boolean-caspo-flux:cmsb2021 </code>which extends the <a href="http://colomoto.org/notebook">CoLoMoTo Docker</a> version <code>2021-02-01.</code> Alternatively, they can be executed without any installation at <a href="https://mybinder.org/v2/zenodo/10.5281/zenodo.5070151/">https://mybinder.org/v2/zenodo/10.5281/zenodo.5070151/</a>. The Docker image can be executed as follows: <pre><code class="language-bash">docker pull bioasp/boolean-caspo-flux:cmsb2021 docker run -it --rm -p 8888:8888 bioasp/boolean-caspo-flux:cmsb2021 </code></pre> then point your browser to <a href="http://127.0.0.1:8888">http://127.0.0.1:8888</a>. The image can be imported using the command <code>docker load</code> with the image file provided in this record: <pre><code>docker load -i image.tar.gz</code></pre> or with the <code>donodo</code> command available at <a href="https://github.com/pauleve/donodo">https://github.com/pauleve/donodo</a>: <pre><code>pip install -U donodo donodo pull 10.5281/zenodo.5070151</code></pre>

opencc-by-4.0Dec 2022View details →

Multiplexed histology of COVID-19 post-mortem lung samples - CONTROL CASE 1 FOV1

Image-based data set of a post-mortem lung sample from a non-COVID-related pneumonia donor (CONTROL CASE 1, FOV1) Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.

Multiplexed histology of COVID-19 post-mortem lung samples - CONTROL CASE 2 FOV2

Image-based data set of a post-mortem lung sample from a non-COVID-19-related pneumonia donor (CONTROL CASE 2 FOV2) Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.

Multiplexed histology of COVID-19 post-mortem lung samples - CONTROL CASE 2 FOV1

Image-based data set of a post-mortem lung sample from a non-COVID-19-related pneumonia donor (CONTROL CASE 2 FOV1) Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.

Multiplexed histology of COVID-19 post-mortem lung samples - CONTROL CASE 3 FOV2

Image-based data set of a post-mortem lung sample from a non-COVID-19-related pneumonia donor (CONTROL CASE 3 FOV2) Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.

Multiplexed histology of COVID-19 post-mortem lung samples - CONTROL CASE 1 FOV3

Image-based data set of a post-mortem lung sample from a non-COVID-related pneumonia donor (CONTROL CASE 1 FOV3) Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.

opencc-by-4.0Feb 2024View details →

Prospective with historical control, case-matched cohort study of the tertiary survey beneficial in critically severe trauma patients.

Raw data, Tertiary survey record form, and STROBE checklist of "Prospective with historical control, case-matched cohort study of the tertiary survey beneficial in critically severe trauma patients" study.

opencc-by-4.0May 2022View details →

Data in support of "An exploration of linkage fine-mapping on sequences from case-control studies"

These data were simulated for an exploration of linkage fine-mapping on sequences from case-control studies. The code to generate and analyze the data is available on GitHub in the scripts at <a href="https://github.com/SFUStatgen/PBJ0">https://github.com/SFUStatgen/PBJ0</a>. Queries may be directed to Payman Nickchi at <a href="mailto:pnickchi@sfu.ca">pnickchi@sfu.ca</a> or Charith (Bhagya) Karunarathna at <a href="mailto:ch757276@dal.ca">ch757276@dal.ca</a>.

opencc-by-4.0Jun 2022View details →

Hyperglycemia and steroid use increase the risk of rhino-orbito-cerebral mucormycosis regardless of COVID-19 hospitalization: Case-control study, India

Abstract BACKGROUND In the context of the ongoing COVID-19 pandemic increased incidence of ROCM was noted in India, among those infected with COVID. We determined risk factors for rhino-orbito-cerebral mucormycosis (ROCM) post Coronavirus disease 2019 (COVID-19) among those never and ever hospitalized for COVID-19 separately through a multi-centric, hospital-based, unmatched case-control study across India. METHODS We defined cases and controls as those with and without post-COVID ROCM, respectively. We compared their socio-demographics, comorbidities, steroid use, glycaemic status, and practices. We calculated crude and adjusted odds ratio (AOR) with 95% confidence intervals (CI) through logistic regression. The covariates with p-value for crude OR of less 0·20 were considered for the regression model. RESULTS Among hospitalised, we recruited 267 cases and 256 controls and 116 cases and 231 controls among never hospitalised. Risk factors (AOR; 95% CI) for post-COVID ROCM among the hospitalised were age 45-59 years (2·1; 1·4 to 3·1), having diabetes mellitus (4·9; 3·4 to 7·1), elevated plasma glucose (6·4; 2·4 to 17·2), steroid use (3·2; 2 to 5·2) and frequent nasal washing (4·8; 1·4 to 17). Among those never hospitalised, age ≥ 60 years (6·6; 3·3 to 13·3), having diabetes mellitus (6·7; 3·8 to 11·6), elevated plasma glucose (13·7; 2·2 to 84), steroid use (9·8; 5·8 to 16·6), and cloth facemask use (2·6; 1·5 to 4·5) were associated with increased risk of post-COVID ROCM. CONCLUSIONS Hyperglycemia irrespective of having diabetes mellitus and steroid use was associated with increased risk of ROCM independent of COVID-19 hospitalisation. Rational steroid usage and glucose monitoring may reduce the risk of post-COVID.

opencc-by-4.0May 2022View details →

Data in support of "An exploration of linkage fine-mapping on sequences from case-control studies"

These data were simulated for an exploration of linkage fine-mapping on sequences from case-control studies. The scripts to generate and analyze the data are available at <a href="https://github.com/SFUStatgen/PBJ0">https://github.com/SFUStatgen/PBJ0</a>. Queries may be directed to Payman Nickchi at <a href="mailto:pnickchi@sfu.ca">pnickchi@sfu.ca</a> or Charith (Bhagya) Karunarathna at <a href="mailto:ch757276@dal.ca">ch757276@dal.ca</a>. README file for All_data directory Directory structure The All_data directory consists of this README file and 500 sub-directories named DatasetX, for X=1 to 500. Within each DatasetX sub-directory are further sub-directories named alt and null containing files named pop_data.RData and sample_data.RData. alt versus null directories The files in the alt and null directories contain the same variant data but different phenotype data. In particular, under the null hypothesis, disease status is simulated at random according to a 5% prevalence in the population, whereas under the alternative hypothesis disease status is simulated according to a penetrance model that depends on causal SNVs. The R script to simulate data under the alternative hypothesis is in the file 1_SimulateData.R in the Github repository <a href="https://github.com/SFUStatgen/PBJ0">https://github.com/SFUStatgen/PBJ0</a>. pop_data.RData and sample_data.RData files The data structures contained in the pop_data.RData and sample_data.RData files are described below. The structure is the same under both the null and alternative hypothesis. pop_data.RData From R, load("pop_data.RData") loads a list named pop_data whose elements describe the population’s haplotype and phenotype data. The list elements are as follows. <ul> <li>Variants: a matrix of variants for the population of 6200 haplotypes <ul> <li>rows are SNVs,</li> <li>columns are sequences</li> </ul> </li> <li>Positions: a data frame of SNV positions <ul> <li>rows are SNVs,</li> <li>column 1 is the SNV name and column 2 is the SNV position in base pairs</li> </ul> </li> <li>Population.Mapping: a data frame telling us how the sequences are paired into individuals <ul> <li>rows are individuals</li> <li>First column 1 is an individual ID from 1,…,3100; columns 2 and 3 are the sequence IDs of the first and second sequence for that individual where the sequence IDs are the column names of the Variants matrix.</li> </ul> </li> <li>Genotype.Matrix: a matrix of genotypes (i.e. variant counts) for the 3100 individuals <ul> <li>rows are SNVs</li> <li>columns are the individuals</li> </ul> </li> <li>causal_region: a vector containing the lower- and upper-limit of the causal region in base pairs.</li> <li>cSNV: a vector containing the IDs of the causal SNVs, where the SNV IDs are the row names of the Variants matrix.</li> <li>DISCRETE: a list with the following elements. <ul> <li>CaseIndividuals: vector of IDs of the affected individuals in the population.</li> <li>ControlIndividuals: vector of IDs of the unaffected in the population.</li> <li>BinaryTrait: a vector of trait status (0=unaffected, 1=affected) for each individual.</li> </ul> </li> </ul> Note: Within the same DatasetX directory, the only difference between the pop_data data structures under the null and alternative hypothesis is the phenotype information contained in their respective DISCRETE list elements. Both the null and alternative pop_data data structure share list elements: Variants, Positions, Population.Mapping, Genotype.Matrix, causal_region and cSNV. sample_data.RData From R, load("sample_data.RData") loads a list whose elements describe the sequences and phenotypes of the sample of 50 affected individuals (cases) and 50 unaffected individuals (controls) from the population. <ul> <li>Haps: a list with two elements. <ul> <li>sample_haps: a matrix of 200 sequences for the 50 cases and 50 controls. Rows are SNVs and columns are sequences, with the sequences of sampled cases appearing first (i.e. first 100 columns), followed by the sequences of sampled controls (i.e. last 100 columns). Sequences include only those SNVs that are polymorphic in the sample.</li> <li>ccStatus: a vector indicating the case/control status of the individual to which the sequence belongs, with case=1 and control=0.</li> </ul> </li> <li>Genos: a list with two elements. <ul> <li>sample_genos: a matrix of 100 genotypes for the 50 cases and 50 controls. Rows are SNVs and columns are genotypes, with genotypes of cases appearing first, followed by genotypes of controls.</li> <li>ccStatus: a vector indicating the case/control status of each individual, with case=1 and control=0.</li> </ul> </li> <li>Posn: a data frame of SNV positions for each SNV that is polymorphic in the sample. The first column is the SNV name and the second is the SNV position in base pairs. Posn is a subset of pop_data$Positions.</li> <li>poly_cSNV: a vector of IDs for causal SNVs that are polymorphic in the sample.</li> <li>CaseIND: a vector of individual IDs for the case individuals (see pop_data$Population.Mapping).</li> <li>ControlIND: a vector of individual IDs for the control individuals (see pop_data$Population.Mapping).</li> <li>CaseHapID: a vector of IDs for the sequences that belong to cases (see the sequence IDs in the column names of the matrix pop_data$Variants).</li> <li>ControlHapID: a vector of IDs for the sequences that belong to controls (see the sequence IDs in the column names of the matrix pop_data$Variants).</li> </ul>

opencc-by-4.0Dec 2021View details →

Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and East Asian ancestries

Colorectal cancer (CRC) is a leading cause of mortality worldwide. We conducted a genome-wide association study meta-analysis of 100,204 CRC cases and 154,587 controls of European and Asian ancestry, identifying 205 independent risk associations, of which 50 were unreported. We performed integrative genomic, transcriptomic and methylomic analyses across large bowel mucosa and other tissues. Transcriptome- and methylome-wide association studies revealed an additional 53 risk associations. We identified 155 high confidence effector genes functionally linked to CRC risk, many of which had no previously established role in CRC. These have multiple different functions, and specifically indicate that variation in normal colorectal homeostasis, proliferation, cell adhesion, migration, immunity and microbial interactions determines CRC risk. Cross-tissue analyses indicated that over a third of effector genes most likely act outside the colonic mucosa. Our findings provide insights into colorectal oncogenesis, and highlight potential targets across tissues for new CRC treatment and chemoprevention strategies. The data submitted here are expression and methylation models with LD reference data for the transcriptome-wide (TWAS), methylome-wide (MWAS) and transcript isoform-wide association study (TIsWAS) as described in the manuscript "Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and East Asian ancestries". Details of the methods are presented in the method section and supplementary information file.  TWAS analysis  Gene expression models for the six in-house expression datasets were generated using the PredictDB v7 pipeline for a total of 1,077 participants. Elastic net model building with 10-fold cross-validation was performed independently for each dataset. The elastic net models for GTEx v8 Colon Transverse were obtained from the PredictDB data repository (<a href="http://predictdb.org/">http://predictdb.org/</a>) and had been generated using the same pipeline. Models were computed using HapMap2 SNPs ±1Mb from each gene, together with covariate factors estimated using PEER32, clinical covariates when appropriate (age, sex and, where appropriate, case-control status, type of polyp and anatomic location in the colorectum), and three PCs from the individual dataset’s SNP genotype data. Transcript-based TWAS analyses (TIsWAS) were likewise performed by using transcript-level data from the SOCCS, BarcUVa-Seq and GTEx Colon Transverse datasets. MWAS analysis  Methylation beta values were calculated based on the manufacturer’s standard, ranging from 0 to 1. Quality control and data normalization were performed in R using the ChAMP software pipeline for the EPIC and 450K arrays. Briefly, we filtered out failed probes with detection P > 0.02 in >5% of samples, probes with <3 reads in >5% of samples per probe and all non-CpG probes. Samples with failed probes >0.1 were also excluded from downstream analyses. We discarded all probes with SNPs within 10bp of the interrogated CpG (from 1,000 Genomes Project, CEU population)34, and probes that ambiguously mapped to multiple locations in the human genome with up to two mismatches33. We only considered probes mapping to autosomes and those overlapping between the EPIC and the 450K arrays. Normalization was achieved using the Beta MIxture Quantile (BMIQ) method. Per probe methylation models were created using the PredictDB pipeline on the normalized methylation matrix and the genotypes as per TWAS eQTL analysis. To optimize power, we restricted our analysis to 263,341-238,443 (for the 450K array) and 377,678 (for the EPIC array) probes annotated to Islands, Shores and Shelves, and discarded “Open Sea” regions.

opencc-by-4.0Jun 2024View details →

Dataset from: "Assessment of depression, anxiety, and psychological symptoms in parents of pediatric palliative care patients: A single-center case-control study"

The dataset comprises raw data from a case-control study that compared levels of depression, anxiety, and general psychological symptoms between parents of pediatric palliative care (PPC) patients and parents of healthy controls. Beck Depression Inventory (BDI), Beck Anxiety Inventory (BAI), and Symptom Checklist-90 Revised (SCL-90-R) were employed to provide a comprehensive and nuanced understanding of the mental health challenges faced by parents. The designation "case" in the first column (A) represents the parents of PPC patients, while the designation "control" represents the control group.  The columns labeled B to S present demographic characteristics data, while columns T to AR present inventory scores. Columns BB to GC, in turn, present the responses to the inventory items.

opencc-by-4.0Mar 2018View details →

Data Set Used in Combinatorial Modeling and Test Case Generation for Industrial Control Software using ACTS

This document contains the data set used for the study Combinatorial Modeling and Test Case Generation for Industrial Control Software using ACTS that is currently in submission.

opencc-by-4.0Dec 2022View details →

Multiplexed histology of COVID-19 post-mortem lung samples - CONTROL CASE 1 FOV2

Image-based data set of a post-mortem lung sample from a non-COVID-related pneumonia donor (CONTROL CASE 1, FOV2) Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.