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Simultaneous Detection of L-Lactate and D-Glucose Using DNA Aptamers in Human Blood Serum
Federated Research Data Repository / dépôt fédéré de données de recherche
Huang, Po-Jung Jimmy; Liu, Juewen — L-lactate is a key metabolite indicative of physiological states, glycolysis pathways, and various diseases such as sepsis, heart attack, lactate acidosis, and cancer. Detection of lactate has been relying on a few enzymes that need other substrates. In this work, DNA aptamers for L-lactate were obtained using a library-immobilization selection method and the highest affinity aptamer reached a Kd of 0.43 mM as determined using isothermal titration calorimetry. The aptamers showed up to 50-fold selectivity for L-lactate over D-lactate and had little responses to other closely related analogs such as pyruvate and 3-hydroxybutyrate. A fluorescent biosensor based on the strand displacement method showed a limit of detection of 0.55 mM L-lactate, and the sensor worked in 90% serum. Simultaneous detection of L-lactate and D-glucose in the same solution was achieved. This work has broadened the scope of aptamers to simple metabolites and provided a useful probe for continuous and multiplexed monitoring. https://creativecommons.org/publicdomain/zero/1.0/
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Atmospheric Chemistry Experiment SciSat Level 2 Processed Data, v4.0
Federated Research Data Repository / dépôt fédéré de données de recherche
Steffen, Johnathan; Crouse, Jeffrey; Bernath, Peter F.; Boone, Chris D. — ACE SciSat Level 2 Processed Data, v4.0. Temperature, Pressure and Volume Mixing Ratio (VMR) profiles as a function of altitude for many atmospherically relavent molecules: H2O, O3, N2O, CO, CH4, NO, NO2, HNO3, HF, HCl, OCS, N2O5, ClONO2, HCN, CH3Cl, CF4, CFC-12 (CCl2F2), CFC-11 (CCl3F), COF2, COCl2, COClF, C2H6, C2H2, HCFC-22 (CHClF2), HCOOH, SF6, HO2NO2, H2O2, H2CO, CH3OH, CCl4, N2, O2, CFC-113 (Cl2FC-CClF2), HCFC-141b (Cl2FC-CH3), HCFC-142b (ClF2C-CH3), HFC-134a (F3C-CFH2), PAN (CH3C(O)OONO2), CHF3, acetone (C3H6O), SO2, CH3CN, ClO, CO2, as well as isotopologues for some of these molecules. NOTE: under Global Attributes, version = 'Version 2.1' is incorrect. The software version for this package is Version 4.0. The version Global Attribute is an error. Please ignore. P. Bernath, et al. Sixteen-year trends in atmospheric trace gases from orbit. Journal of Quantitative Spectroscopy and Radiative Transfer, 107178, 2020; doi:10.1016/j.jqsrt.2020.107178. https://creativecommons.org/licenses/by/4.0/
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Expenditures of CARL member libraries for scholarly resource subscriptions licensed through CRKN for 2015 - 2016 / Dépenses des bibliothèques membres de l'ABRC pour les abonnements aux ressources savantes sous licence du RCDR pour l'année 2015 - 2016
Federated Research Data Repository / dépôt fédéré de données de recherche
Brin, Lise — Dataset and summary table of subscription expenditures of 29 member libraries of the Canadian Association of Research Libraries (CARL) for scholarly resources licensed through the Canadian Research Knowledge Network (CRKN) for the 2015 - 2016 fiscal year. / Ensemble de données et tableau sommaire des dépenses d'abonnement de 29 bibliothèques membres de l'Association des bibliothèques de recherche du Canada (ABRC) pour les ressources savantes sous license du Réseau canadien de documentation pour la recherche (RCDR) pour l'exercice financier 2015 - 2016. https://creativecommons.org/licenses/by/4.0/
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Atmospheric Chemistry Experiment Fourier Transform Spectrometer Level 2 Data v2.2
Federated Research Data Repository / dépôt fédéré de données de recherche
Boone, Chris D. — The Atmospheric Chemistry Experiment (ACE) is a Canadian satellite mission for remote sensing of the Earth's atmosphere that was launched into a high-inclination (74°), circular low-earth (650 km from the surface) orbit on August 12, 2003 (Bernath et al., 2006). This orbit gives SCISAT coverage of tropical, mid-latitude, and polar regions, ranging from latitudes 85N to 85S, allowing it to study a range of atmospheric processes. The main goal of ACE is to study the atmospheric chemistry and dynamics that affect stratospheric ozone depletion in the Arctic, but ACE measurements are also being used to study ozone depletion in the Antarctic, the relationship between chemistry and climate change, the atmospheric effects of biomass burning, the effects of aerosols and clouds on the global energy balance, and many other areas of atmospheric science. The primary instrument on ACE, a high-resolution Fourier Transform Spectrometer (FTS), is used in solar occultation mode to determine vertical profiles of trace gas volume mixing ratios (VMRs) and temperature. The ACE-FTS records a measurement every 2s, corresponding to a typical altitude spacing of 2-6 km. On the ground at the University of Waterloo, the retrieved results are interpolated onto a 1 km “grid” using a piecewise quadratic method. Included in this data set are ascii files for each "occultation", on both the "retrieval", or "measurement" grid ("tangrid") and the "scientific", 1 km grid, cataloged using the naming conventions "sr*****" and "ss*****" for sunrises and sunsets, respectively. Further, there is an additional pair of files for each occultation event for less abundant, subsidiary isotopologues (marked "sx*****iso.asc, etc.). All files contain a short header, followed by a series of columns with VMRs for each molecule. More detailed information can be accessed in the two attached documents, "ACEFTSPublicReleaseDocumentation.pdf", which includes background and supporting material to best make use of the data, and "ACE-SOC-0011-1D-ACE-FTS_ascii_fileformat_for_v2.2.pdf", with general comments on the file and data formatting itself. All retrieved molecules and their VMRs are presented in the ace_v2.2_asc.zip file, except for three species that were fixed and released shortly afterward. Data for ozone (O3), HDO, and N2O5 can be found in separate zip files, named according to the molecule they contain. Heavy water, HDO, is presented alongside all other isotopologues, while O3 and N2O5 are provided in a single, unique column. https://creativecommons.org/licenses/by-nc/4.0/
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5xFAD mice in their home-cage, the three-chamber sociability test and free social interaction task.
Federated Research Data Repository / dépôt fédéré de données de recherche
Kosel, Filip; Hamilton, Jacob; Harrison, Sarah; Godin, Victoria; Franklin, Tamara B. — Male transgenic and wild-type 5xFAD mice in their home-cage (aged 8-23 weeks), and male and female 5xFAD mice in the three-chamber sociability test and free social interaction task at 6 months of age. https://creativecommons.org/licenses/by-nc-sa/4.0/
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WETMETH: A new wetland methane model for implementation in Earth system models
Federated Research Data Repository / dépôt fédéré de données de recherche
Nzotungicimpaye, Claude-Michel — WETMETH is a new wetland methane model developed for implementation in Earth system models. It is currently embedded in the frozen ground version of the University of Victoria Earth System Climate Model (UVic ESCM), an Earth system model of intermediate complexity (EMIC). Here we provide model output files with all variables analyzed in the model description manuscript. These model outputs include results from a historical run from 1850 to 2019 and sensitivity runs over the 2000-2009 decade. https://creativecommons.org/licenses/by/4.0/
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The role of disulfide bonds in a Solanum tuberosum saposin-like protein explored using molecular dynamics
Federated Research Data Repository / dépôt fédéré de données de recherche
Wang, Shenlin; Song, Chen; Yada, Rickey Y.; Dupuis, John H. — The dataset contains simulation results for the associated publication on the role of disulfide bonds in the potato (Solanum tuberosum) plant specific insert protein. In addition, the files required to run the simulations (initial structures, topologies, and molecular dynamics parameter files) are included. https://creativecommons.org/licenses/by/4.0/
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Data and code for Bed and Bank Stress Partitioning in Bedrock Rivers
Federated Research Data Repository / dépôt fédéré de données de recherche
Nelson, Peter; Rennie, Colin D.; Li, Tingan; Venditti, Jeremy G. — The is the data and code for Bed and Bank Stress Partitioning in Bedrock Rivers submitted to Journal of Geophysical Research, Earth Surface. The data includes the velocity profiles, the topography, the width, and the shear stress distributions obaserved in the Fraser Canyons, the raw data is from the dataset https://doi.org/10.20383/101.0277; The data also includes the modelled ratio of wall to bed stress as a function of bank angles, bottom channel width and discharge, calculated from the Ray-Isovel Model; The Matlab code of the Ray-Isovel Model can be found from the file RIM, which was written by our coauther Peter Nelson. The main function of the model is fraser.m, you can run fraser.m using an example. If you want to change inputs, you can open getinput_fin1.m, and change varibles, for example ks, qw, bank angles. https://creativecommons.org/licenses/by/4.0/
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Gaseous HCl ambient intercomparison in Toronto Canada April 2019
Federated Research Data Repository / dépôt fédéré de données de recherche
Furlani, Teles; Veres, Patrick; Dawe, Kathryn; Neuman, J. Andrew; Brown, Steven; VandenBoer, Trevor; Cora, Young — Comparison of ambient gaseous HCl measurements made by Picarro cavity ring-down analyzer and denuders. Measurements made in Toronto, Ontario, Canada during April 2019. https://creativecommons.org/licenses/by/4.0/
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Organic barn dust inhibits surfactant protein D production and GPR116
Federated Research Data Repository / dépôt fédéré de données de recherche
Schneberger, David — Data sets for paper "Organic barn dust inhibits surfactant protein D production through protein kinase-c alpha dependent increase of GPR116" submitted to PLOS One. Data included covers response of mice to organic dust in relation to surfactant D production. A549 human cell line responses to organic dust with or without inhibition of protein kinase C-alpha are also shown in relation to surfactant D and GPR116 mRNA expression. https://creativecommons.org/licenses/by/4.0/
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Outdoor and indoor gaseous total chlorine measurement in Toronto Canada
Federated Research Data Repository / dépôt fédéré de données de recherche
Furlani, Teles C.; Ye, RenXi; Stewart, Jordan; Crilley, Leigh R.; Edwards, Peter M.; Kahan, Tara F.; Young, Cora J. — Outdoor and indoor measurements of gaseous total chlorine. Outdoor measurements made from York University rooftop in Toronto, Canada. Indoor measurements made after surface application of Cl-based cleaning product. Data accompanies paper: https://doi.org/10.5194/amt-2022-130 https://creativecommons.org/licenses/by/4.0/
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Sulfur stable isotopes as a tracer of insect migration and fish predation
Federated Research Data Repository / dépôt fédéré de données de recherche
Srayko, Stephen H.; Phillips, Iain D.; Chivers, Douglas P. — Here we examined the utility of the stable isotope ratio of sulfur, δ34S, as a tracer of the seasonal migration of water boatmen (Hemiptera: Corixidae) between wetlands and rivers and the use of these insects as a dietary subsidy by riverine fish. We found that both corixids and other invertebrate taxa originating from wetland ecosystems typically exhibited lower δ34S values, as opposed to riverine taxa. Specifically, riverine taxa from the South Saskatchewan River were more depleted in 34S than those from the North Saskatchewan River. spring and summer, δ34S values were more negative for corixid feeders in fall. We conclude that δ34S has the potential to trace insect movement and consumer use between isotopically distinct freshwater systems. https://creativecommons.org/licenses/by/4.0/
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Promotion of DNA Adsorption onto Microplastics by Transition Metal Ions
Federated Research Data Repository / dépôt fédéré de données de recherche
Wu, Lyuyuan; Patel, Kshiti; Zandieh, Mohamad; Liu, Juewen — Microplastics can adsorb and spread a variety of pollutants in the ecosystem posing a threat to human health. One of the common pollution sources of environmental waters is metal ions, which not only adsorb on microplastics but can also promote the adsorption of other invasive species such as environmental DNA. Recently, we showed that environmentally abundant metal ions (Na+, Mg2+ and Ca2+) can promote the adsorption of single-stranded DNA (ssDNA) onto micro-plastics. Herein, we investigated the effect of transition metal ions including Zn2+ and Mn2+ and compared them with Mg2+ for promoting DNA adsorption. To better mimic environmental DNA, we also used a salmon sperm double-stranded DNA (dsDNA) (~2000 bp). For both ssDNA and dsDNA, the transition metals induced a higher adsorption capacity compared to Mg2+, and that correlated with the higher binding affinity of transition metals to DNA. Although met-al-mediated interactions were vital for ssDNA adsorption, the dsDNA adsorbed on the micro-plastics even in the absence of metal ions, likely due to the abundance of binding sites of the 100-times longer dsDNA. Finally, desorption studies revealed that hydrophobic interactions were responsible for dsDNA adsorption in the absence of metal ions. https://creativecommons.org/licenses/by/4.0/
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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 — 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. https://creativecommons.org/licenses/by-nc/4.0/
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Meteorological data for three atmospheric river case studies and Python programs for calculating column relative humidity and primary condensation rate
Federated Research Data Repository / dépôt fédéré de données de recherche
Mo, Ruping — Atmospheric rivers (ARs) are long, narrow, and transient corridors of strong horizontal water vapor transport that frequently lead to heavy precipitation where they are forced upward. The presence and strength of ARs are often described using the integrated water vapor (IWV) and the integrated vapor transport (IVT). However, the associated precipitation is not directly correlated with these two variables. Instead, the intensity of precipitation is mainly determined by the net convergence of moisture flux and the initial degree of saturation of the air column. The column relative humidity (CRH) and primary condensation rate (PCR) are two supplements to the standard AR analysis to focus attention on the heavy precipitation potential. Datasets and two Python programs presented here can be used, for demonstration purposes, to calculate and verify the CRH and PCR in three case studies of the AR events in 2020. https://creativecommons.org/licenses/by/4.0/
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Aerosol Particle Mass and Chemical Composition Analysis Tuktoyaktuk 2018
Federated Research Data Repository / dépôt fédéré de données de recherche
Chang, Rachel — This file contains a summary of the total mass and chemical composition of coarse (10-2.5 μm) and fine (<2.5 μm) aerosol particles collected from Tuktoyaktuk, NWT during July-September 2018 using an AirPhoton Assembly, as described by Snider et al. (see related publication). Anions and cations were analyzed using ion chromatography with conductivity detection, and metals were analyzed by inductively coupled plasma-mass spectrometry (ICP-MS). An overview of method details is discussed by Snider et al. The system was mounted approximately 3.5 m above ground level at the Aurora College Community Learning Centre. Notes: the uncertainty of total mass is based on the error propagation associated with replicate filter weighing before and after sample collection. The mass of ions and metals in sample extracts was determined by multiplying extract concentrations (μg/mL or ng/mL) by the total extraction volume, which was 3 mL, and a factor of 2 to account for the mass on the entire filter. For the chemical composition analysis, the less-than sign is used to indicate when the masses of ions and metals are below their detection limit. Due to a file writing error during the study, the sample volume could not be determined and only the absolute mass collected on the filters is provided. https://creativecommons.org/publicdomain/zero/1.0/
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WRF-SFIRE LES Synthetic Wildfire Plume Dataset
Federated Research Data Repository / dépôt fédéré de données de recherche
Stull, Roland; Moisseeva, Nadya — The dataset consists of 147 large-eddy simulations of wildfire plumes produced with WRF-SFIRE LES, capturing a wide range of fire and atmospheric conditions. This synthetic dataset (147 NetCDF files) was produced using WRF-SFIRE model configured in idealized large-eddy resolving mode. Key parameters varied were ambient wind, fuel category, vertical potential temperature profile and fireline length, denoted as conditions W,F,R and L, respectively. Each 10 km x 20 km domain has 40 m horizontal grid spacing. Depending on the sounding R, the simulations were performed in either a shallow (3000 m) or a deep (5000 m) domain, with 51 or 71 hyperbolically stretched vertical levels, respectively. The files contained in this dataset were initialized from a restart file generated at the end of 1 h model spinup period. Each simulation is either 20 or 30 min in length, depending on initial conditions (see Data & File Overview in README.txt for further information). The fire was initialized over a one-minute interval using a straight line of length L. The ignition line was placed one kilometer downwind of the western edge of the domain (perpendicular to ambient wind) and centered in the north-south direction. With a refinement ratio of 10 in each horizontal direction, the fire was simulated on a 4 m sub-grid mesh. Full details of domain configuration are provided in: Moisseeva, Nadya, and Roland Stull. "Wildfire smoke-plume rise: a simple energy balance parameterization." Atmospheric Chemistry and Physics Discussions (2020): 1-20. https://doi.org/10.5194/acp-2020-827 https://creativecommons.org/licenses/by/4.0/
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Model output for Jarnikova et al. 2021 - Salish Sea coastal carbonate chemistry
Federated Research Data Repository / dépôt fédéré de données de recherche
Jarnikova, Tereza — The coupled physical-biogeochemical SalishSeaCast model reproduces observed seasonal and spatial variability in carbon concentrations. The model is the basis for an analysis of present and preindustrial carbonate chemistry conditions in the Strait of Georgia coastal system. Here we present the raw model output. https://creativecommons.org/licenses/by/4.0/
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Geochemical composition of groundwater, surface water, permafrost porewater, and active layer porewater in samples from the Coffee gold deposit, Dawson Range, Yukon, Canada
Federated Research Data Repository / dépôt fédéré de données de recherche
Skierszkan, Elliott K; Fellwock, Matt; Jackson, Scott I; Fraser, Colin; Lindsay, Matthew B.J. — This file contains aqueous geochemistry data for groundwater, surface water, permafrost porewater, and active layer porewater in samples collected around the Coffee gold deposit, Dawson Range, Yukon, Canada. The file also contains daily average streamflows for three hydrometric stations installed at the same field site. The data are associated with the article: “Stream metal(loid) signatures in discontinuous permafrost controlled by seasonal dynamics of groundwater discharge” by Skierszkan et al. (2023, in rev. with Water Resources Research). The data were used to investigate metal(loid) abundances and mobilization processes in water in a discontinuous permafrost region. (doi: XXXXXXX). The data consist of a compilation of analyses produced as part of baseline environmental monitoring at the proposed Coffee Gold Mine by its proponent, Newmont Corp, and supplemented with additional samples collected as part of a research project into geogenic metal(oid)s in permafrost regions led by Skierszkan et al. Additional useful references to understand the local geological and geochemical context are: Skierszkan, E. K., Dockrey, J. W., Helsen, J., Bataille, L.-L. F. C. P., de Laplante, G., McBeth, J. M., et al. (2021). Persistence of uranium in old and cold subpermafrost groundwater indicated by linking 234U-235U-238U, groundwater ages, and hydrogeochemistry. Earth and Space Chemistry, 5(12), 3474–3487. Skierszkan, E. K., Dockrey, J. W., Mayer, K. U., & Beckie, R. D. (2020). Release of geogenic uranium and arsenic results in water-quality impacts in a subarctic permafrost region of granitic and metamorphic geology. Journal of Geochemical Exploration, 217(October 2019), 106607. https://doi.org/10.1016/j.gexplo.2020.106607 Kidder, J. A., McClenaghan, M. B., Leybourne, M. I., McCurdy, M. W., Pelchat, P., Layton-Matthews, D., & Voinot, A. (2022). Hydrogeochemistry of porphyry-related solutes in ground and surface waters; an example from the Casino Cu–Au–Mo deposit, Yukon, Canada. Geochemistry: Exploration, Environment, Analysis, 22(2), geochem2021-058. https://doi.org/10.1144/geochem2021-058 https://creativecommons.org/licenses/by/4.0/
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FAST & the FRDR Reconciliation Data
Federated Research Data Repository / dépôt fédéré de données de recherche
Turp, Clara; Olson, Leanne; Stathis, Kelly; Bone, Christine — This dataset contains 8,000 English keyword terms harvested by the Federated Research Data Repository (FRDR) prior to 2019 and their mappings to the Faceted Application of Subject Terminology (FAST). This work was completed by the FAST & the FRDR working group (part of the Portage Network) using a combination of automated and manual reconciliation techniques. After 8,000 harvested English keywords from FRDR were loaded into the OpenRefine project, automatic reconciliation to FAST terms was then applied within OpenRefine. To confirm automatic reconciliation results and to complete reconciliation for terms that could not be matched automatically, members of the FAST & the FRDR working group applied the matching procedures. Further methodology details are available in: Turp C, Wilson L, Pascoe J, Garnett A. The FAST and the FRDR: Improving Metadata for Data Discovery in Canada. Publications. 2020; 8(2):25. https://doi.org/10.3390/publications8020025 https://creativecommons.org/licenses/by/4.0/

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