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Simulation Files for Zebrafish Spinal Circuit for Swimming Model
Federated Research Data Repository / dépôt fédéré de données de recherche
Bui, Tuan — 2021-08-31 Simulation files for zebrafish spinal circuit for swimming model. Many spinal circuits dedicated to locomotor control have been identified in the developing zebrafish. We have built models of developing zebrafish spinal circuits coupled to simplified musculoskeletal models that reproduce coiling and swimming movements (beat and glide movement, double coiling and single coiling). We simulated intact spinal circuits as well as circuits with silenced neurons or altered synaptic transmission. The output of the simulations is found in this dataset. Models were built and simulated using the Python programming language. The code for the models can be found at https://github.com/Bui-lab/Code/tree/master/Zebrafish%20spinal%20locomotor%20circuit . These models and the simulations are described in Roussel et al. (2021). https://doi.org/10.1101/2021.02.10.430671 . The data used to generate the figures are found in this dataset.
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Dataset for Automated Discovery of Noncovalent Inhibitors of SARS-CoV-2 Main Protease by Consensus Deep Docking of 40 Billion Small Molecules
Federated Research Data Repository / dépôt fédéré de données de recherche
Gentile, Francesco; Fernandez, Michael; Ban, Fuqiang; Ton, Anh-Tien; Mslati, Hazem; Perez, Carl F.; Leblanc, Eric; Yaacoub, Jean Charle; Gleave, James; Stern, Abraham; Wong, Bill; Jean, Francois; Strynadka, Natalie; Cherkasov, Artem — 2021-11-19 Repository for computational and experimental data resulting for a deep learning-accelerated, structure-based virtual screening campaign of 40 billion small molecules against the SARS-CoV-2 main protease (Mpro). The repository contains ligand structures used for pharmacophore generation, docking poses of experimentally confirmed active inhibitors and docking grid, raw experimental data for determination of half-maximal inhibitory concentration (IC50), and computational data from the virtual screening and filtering procedure as well as related analysis scripts. Refer to the article "Automated Discovery of Noncovalent Inhibitors of SARS-CoV-2 Main Protease by Consensus Deep Docking of 40 Billion Small Molecules" published in Chemical Science for more information.
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SLiM 3 outputs of in silico local adaptation with conditonally deleterious mutations and antagonistic pleiotropy in a two-deme model
Federated Research Data Repository / dépôt fédéré de données de recherche
Carson, Bryce — 2022-06-28 Evolution model output data simulating the impact of custom mutations upon local adaptation. Dataset also includes an SQLite3 database containing analyzed results of the evolutionary model. Methodological information is in the `README.md` file in the dataset, and usage instructions and workflow information for the code can be found at <https://github.com/bryce-carson/APCD10Cr_Carson_2022>. Model data was derived using SLiM v3.3.2. See Haller and Messer (2019) https://doi.org/10.1093/molbev/msy228 for additional information.
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Maps of Major Land Use - Land Cover Categories and Respective E. coli Contamination Potential Classes for Groundwater Wells in Ontario
Federated Research Data Repository / dépôt fédéré de données de recherche
White, Katie; Dickson-Anderson, Sarah; Schuster-Wallace, Corinne — 2024-04-09 These maps contain data of 11 major Land Use - Land Cover (LULC) categories and their E. coli contamination potential for groundwater wells. The LULC categories included in this dataset include agricultural/pastural land, urban, open/barelands, aggregate mines, scrubland, disturbance, bedrock, forest, grasslands, wetlands, and water. The LULC impact on E. coli contamination potential for wells is classified as very high, high, moderate, and low.
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Inventory of Canadian Repository Platforms - Inventaire de plateformes de dépôt canadiennes
Federated Research Data Repository / dépôt fédéré de données de recherche
CARL Open Repositories Working Group; Groupe de travail sur les dépôts ouverts de l'ABRC — 2022-02-11 The CARL Open Repositories Working Group (ORWG) oversees the collection of data on repository platforms in use across Canada. This dataset reflects updates collected from repository managers at the end of the year. More information on this ongoing initiative: https://www.carl-abrc.ca/advancing-research/institutional-repositories/inventory-of-canadian-repository-platforms/ Le Groupe de travail sur les dépôts ouverts (GTDO) de l'ABRC est responsable d'un inventaire des plateformes de dépôts utilisées au Canada. Ces données reflètent des mises à jour contribuées par la communauté de dépôt canadienne de fin d'année. Détails supplémentaires sur cette initiative en cours : https://www.carl-abrc.ca/fr/faire-avancer-la-recherche/depots-institutionnels/inventaire-plateformes-depot-canadiennes/
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Seasonal mass migration of water boatmen (Hemiptera: Corixidae) as a wetland-river linkage and dietary subsidy to riverine fish
Federated Research Data Repository / dépôt fédéré de données de recherche
Srayko, Stephen H.; Jardine, Timothy D.; Phillips, Iain D.; Chivers, Douglas P. — 2022-01-12 We investigated the magnitude and implications of a little understood ecosystem linkage in the form of migrating aquatic insects, corixids (Hemiptera: Corixidae), that fly from geographically isolated wetlands into large rivers in the Prairie Pothole Region (PPR) of North America every fall, to overwinter. These migrations can lead to greatly increased riverine corixid densities and a shift in the species assemblage to one dominated by wetland-breeding species. Once in the rivers, these migratory insects act as an important dietary subsidy to several species of riverine fish. The following dataset contains files from our study with information on (1) study sites, (2) corixid abundances and (3) species composition in wetland and river habitats, (4) fish stomach content data, (5) data from passive samplers used to estimate migratory corixid inputs into rivers, and (6) a simulation used to estimate the magnitude of the corixid flux between wetlands and rivers over a larger scale. This study has demonstrated an extensive cross-boundary flux that occurs between spatially separated wetland and river ecosystems, highlighting a need for conservation to ensure that this connection is maintained.
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SalishSeaCast hourly surface along-axis wind velocity, temperature and nitrate summary 2015-2019
Federated Research Data Repository / dépôt fédéré de données de recherche
Moore-Maley, Ben; Allen, Susan E. — 2022-01-28 Aggregated hourly surface along-axis wind velocity, temperature and nitrate results for 2015-2019 from the SalishSeaCast hourly hindcast archive (https://salishsea.eos.ubc.ca/erddap/). This file is a companion asset to the following publication: B. Moore-Maley and S. E. Allen: Wind-driven upwelling and surface nutrient delivery in a semi-enclosed coastal sea, Ocean Sci., 2022. SalishSeaCast is a NEMO 3.6 configuration for the Salish Sea (https://salishsea-meopar-docs.readthedocs.io/). Along-axis wind velocity and wind stress are calculated from the Environment and Climate Change Canada HRDPS model (https://weather.gc.ca/grib/grib2_HRDPS_HR_e.html). This file has a companion software repository, which includes scripts to recreate the file (https://github.com/SalishSeaCast/SoG_upwelling_EOF_paper).
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Estimating the likelihood of GHG concentration scenarios from probabilistic IAM simulations
Federated Research Data Repository / dépôt fédéré de données de recherche
Huard, David — 2022-02-01 Dataset holding analysis-ready data, results and scripts for the paper "Estimating the likelihood of GHG concentration scenarios from probabilistic IAM simulations". Includes compatible CO2 emissions diagnosed from CMIP5 and CMIP6 carbon fluxes, probabilistic CO2 emissions from IAM simulations, observed historical carbon dioxide (CO2) emissions, CMIP5 and CMIP6 scenario emissions (RCPs, SSPs), and the estimated scenario (RCPs, SSPs) likelihoods for each IAM simulation. All datasets are stored in netCDF format and strive to comply with the CF convention. Also includes the graphics and tables from the paper, as well as the Python code to generate them from the data above. Details on the directory content can be found in READMEs for each directory, and file-specific information found in the global attributes of each netCDF file.
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Precipitation gauge and supplemental weather station data for three Oldman River headwater locations in SW Alberta
Federated Research Data Repository / dépôt fédéré de données de recherche
Hopkinson, Christopher D.; Barnes, Celeste — 2022-06-09 Geonor totalising precipitation gauge and supporting meteorological variable data collected by the University of Lethbridge, ARTeMiS Laboratory for the 2018 to 2021 hydrological years are provided for three valley to ridge weather stations in headwater locations of the Canadian Rockies in SW Alberta.
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Data for: Evaluation of Fresh, Frozen, and Lyophilized Fecal Samples by SPME and Derivatization Methods using GC×GC-TOFMS
Federated Research Data Repository / dépôt fédéré de données de recherche
Nam, Seo Lin; Tarazona Carrillo, Kieran; de la Mata, A. Paulina; de Bruin, Olle M.; Doukhanine, Evgueni; Harynuk, James — 2022-04-25 This collection contains the raw data files and aligned peak tables from the fresh, frozen, and lyophilized fecal samples analyzed for the manuscript https://doi.org/10.1007/s11306-022-01881-z. The raw files are in .peg format collected on a LECO Pegasus 4D system (LECO Instruments, St. Joseph, MI, USA), with an Agilent Technologies 7890 gas chromatograph (Palo Alto, CA, USA). The .CSV files contain the aligned peak tables obtained using the Statistical Compare function on ChromaTOF® (v.4.72; LECO Instruments, St. Joseph, MI, USA).
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On the Transferability of Pre-trained Language Models for Low-Resource Programming Languages
Federated Research Data Repository / dépôt fédéré de données de recherche
Chen, Fuxiang — 2022-03-23 Pre-trained Language Models (PLM) such as CodeBERT and GraphCodeBERT, when trained on a large corpus of code, have recently displayed promising results in Software Engineering (SE) down-stream tasks. A PLM is most useful if it can be leveraged to improve the performance on code corpora written in low-resource programming languages, where training data is limited. In this work, our focus is on studying the impact of PLMs on a low-resource programming language corpus — specifically, we choose Ruby as the study subject. A recent study by Ahmed and Devanbu reported that using a corpus of code written in multilingual datasets to fine-tune multilingual PLMs achieves higher performance as opposed to using a corpus of code written in just one programming language. However, no analysis was made with respect to monolingual PLMs. Furthermore, some programming languages are inherently different and code written in one language usually cannot be interchanged with the others, i.e., Ruby and Java code possess very different structure. To better understand how monolingual and multilingual PLM affects different programming languages, we investigate 1) the performance of PLMs on Ruby for two popular SE tasks: Code Summarization and Code Search, 2) the strategy (to select programming languages) that works well on fine-tuning multilingual PLMs for Ruby, and 3) the performance of the fine-tuned PLMs on Ruby given different code lengths — here, we bin the Ruby code based on its number of tokens; understanding the performance on different code lengths will enable developers to make more informed decision on the use of PLMs based on their code. This dataset, containing the PLMs and their fine-tuned models (there are over a hundred trained and fine-tuned models), was generated by the researchers at the University of British Columbia, Singapore Management University and JetBrains.
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Annual frequencies of freezing rain diagnosed from the fifth-generation Canadian Regional Climate Model (CRCM5) for the past and future climates
Federated Research Data Repository / dépôt fédéré de données de recherche
McCray, Christopher D.; Paquin, Dominique; Thériault, Julie M.; Bresson, Émilie — 2022-06-09 This dataset contains output of yearly frequencies (hours) of freezing rain identified using four precipitation-type algorithms applied to output of the fifth-generation Canadian Regional Climate Model (CRCM5) run at Ouranos. Algorithms are applied to three-hourly output of eight simulations of four dynamically-downscaled global climate models (GCMs) on a 0.22° horizontal grid over the North American domain. Simulations for 1980-2005 are forced with observed greenhouse gas concentrations, with data for 2006-2099 using the RCP 8.5 greenhouse gas concentration trajectory. Each occurrence of freezing rain identified in the model output is multiplied by 3 for comparison with hourly observations. These data are associated with the article "A multi-algorithm analysis of projected changes to freezing rain over North America in an ensemble of regional climate model simulations" by McCray et al., submitted in 2022 to the Journal of Geophysical Research: Atmospheres.
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Repartitioning of co-precipitated Mo(VI) during Fe(II) and S(-II) driven ferrihydrite transformation: Datasets and Supplementary Materials
Federated Research Data Repository / dépôt fédéré de données de recherche
Schoepfer, Valerie A.; Lindsay, Matthew B.J. — 2022-05-03 This file contains aqueous and solid phase geochemical data resulting from a set of experiments documenting the repartitioning of initially co-precipitated molybdenum(VI) during electron transfer and atom exchange of ferrihydrite. Data include aqueous Fe, S, and Mo concentrations, as well as pH and Eh. Solid phase data consists of spectra from K- and LIII- edge X-ray absorption spectroscopy, X-ray diffraction patterns, and d-spacings associated with transmission electron microscopy-selected area electron diffraction. These data are associated with the article "Repartitioning of co-precipitated Mo(VI) during Fe(II) and S(-II) driven ferrihydrite transformation" by Schoepfer and Lindsay (In preparation).
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Data for: Assessing Red Blood Cell Deformability from Microscopy Images Using Deep Learning
Federated Research Data Repository / dépôt fédéré de données de recherche
Lamoureux, Erik S.; Islamzada, Emel; Wiens, Matthew V. J.; Matthews, Kerryn; Duffy, Simon P.; Ma, Hongshen — 2022-06-16 Abstract: Red blood cell (RBC) deformability is a key biophysical property that enables their navigation through small spaces in the microvasculature. The loss of RBC deformability can be due to pathology, natural ageing, or storage, and can impede proper cell function. Established methods to assess RBC deformability require specialized equipment, long measurement time, and skilled personnel. To address this, we used a deep learning image classification approach to differentiate between softer and harder RBCs. Ground truth deformability assessment was conducted using a microfluidic ratchet sorting device. After microfluidic deformability sorting, cells were imaged in brightfield at 40X magnification. Our model predicted individual RBC deformability with 81 ± 11% accuracy averaged across ten donors. This produced RBC deformability assessments within 10.4 ± 6.8% of the value obtained using the microfluidic device. Measuring RBC deformability using imaging is desirable as it only requires a standard imaging microscope, expanding its accessibility to clinics or research groups where this evaluation would otherwise not be feasible. Technical Information: 40X brightfield microscopy images of red blood cells in a 96-well imaging plate. Full well image scans were conducted using a DS-Qi2 camera on a Nikon Ti-2E inverted microscope, capturing images of 2424 x 2424 pixels.
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A longitudinal microstructural MRI dataset in healthy C57Bl/6 mice at 9.4 Tesla
Federated Research Data Repository / dépôt fédéré de données de recherche
Rahman, Naila; Xu, Kathy; Budde, Matthew D.; Brown, Arthur; Baron, Corey A. — 2022-07-07 Multimodal microstructural MRI has shown increased sensitivity and specificity to changes in various brain disease and injury models in the preclinical setting. Here, we present an in vivo longitudinal dataset, acquired as control data and to investigate microstructural changes in the healthy mouse brain. The dataset consists of structural T2-weighted imaging, magnetization transfer ratio and saturation imaging, and advanced quantitative diffusion MRI (dMRI) methods. The dMRI methods include oscillating gradient spin echo (OGSE) dMRI and microscopic anisotropy (μA) dMRI, which provide additional insight by increasing sensitivity to smaller spatial scales and disentangling fiber orientation dispersion from true microstructural changes, respectively. The technical skills required to analyze microstructural MRI data are complex and include MRI sequence development, acquisition, and computational neuroimaging expertise. Here, we share unprocessed and preprocessed data, and scalar maps of quantitative MRI metrics. We envision utility of this dataset in the microstructural MRI field to develop and test biophysical models, methods that model temporal brain dynamics, and different registration and preprocessing pipelines.
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Fragmentation of hunting bullets observed with synchrotron radiation: Lighting up the source of a lesser-known lead exposure pathway
Federated Research Data Repository / dépôt fédéré de données de recherche
Leontowich, Adam — 2022-06-23 Bullet fragments have been previously observed in the remains and edible portions of big game animals that were harvested using rifles. The fragmentation issue has attracted attention because traditional hunting bullets are more than 70% lead, which is toxic to humans and scavengers in the ecosystem. We prepared gunshot wounds in ballistic gelatin blocks, and then applied synchrotron X-ray imaging technology to the bullet fragmentation process for the first time. The K edge subtraction (KES) imaging method allowed a clear separation of lead in an image from false positives, including the other major bullet component, copper, and non-lead objects such as bone fragments. The superior brightness of synchrotron radiation was also harnessed to resolve thousands of embedded sub-10 µm fragments, a size range not previously observed using commonly applied X-ray imaging modalities. The results challenge the current understanding of the maximum extent that fragments may be distributed, and the effectiveness of imaging methods used to screen wild game donations at food banks for lead bullet fragments. This dataset contains all of the raw data files associated with our 2022 publication of the same title.

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