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Data Repository for U of M (DRUM)

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Membraneless Compartmentalization of Cell-Free Transcription-Translation by Polymer-Assisted Liquid-Liquid Phase Separation
(2024-11-20) Izri, Ziane; Noireaux, Vincent; noireaux@umn.edu; Noireaux, Vincent; Noireaux Lab
Living cells use liquid-liquid phase separation (LLPS) to compartmentalize metabolic functions into mesoscopic-sized droplets. Deciphering the mechanisms at play in LLPS is therefore critical to understanding the structuration and functions of cells at the subcellular level. Although observed and achieved to a significant degree of control in vivo, the reconstitution of LLPS integrating advanced biological functions, such as gene expression, has been so far limited in vitro. LLPS of cell-free transcription-translation (TXTL) reactions requires multi-step experimental approaches that lack biomimetism and have relatively poor efficacy, thus limiting their usage in cell-free engineered systems such as synthetic cells. Here we report the polymer-assisted LLPS of TXTL reactions as the single-pot one-step compartmentalization of a model complex metabolic system obtained without using solvents or surfactants. LLPS occurs by adding the biocompatible polymers poly(ethylene glycol), poly(vinyl alcohol), and dextran to a TXTL reaction, that remains highly active. These polymers serve as partitioning agents that localize TXTL in mesoscopic-sized droplets rich in dextran. Cytoplasmic and membrane-interacting proteins are synthesized preferentially inside these droplets, and localize either uniformly or preferentially at the interface, depending on their nature. The LLPS-TXTL system presented in this work is a step toward the design of synthetic membraneless active organelles.
Wolf predation on white-tailed deer before, during, and after a historically-mild winter in northern Minnesota
(2024-11-15) Gable, Thomas D; Homkes, Austin T; Bump, Joseph K; gable079@umn.edu; Gable, Thomas D; Voyageurs Wolf Project
See Read me file
Transcriptomic data from RNA Sequencing of canine high grade glioma tumor samples
(2024-11-15) Arnold, Susan A; Pluhar, G. Elizabeth; Abrahante Llorens, Juan E; saarnold@umn.edu; Arnold, Susan; University of Minnesota Canine Brain Tumor Program
These files contain the raw data for bulk RNA sequencing performed on canine high grade glioma tumor samples. These samples were obtained from three breeds of dogs: French bulldogs, boxers, and Boston terriers. All dogs were enrolled in immunotherapy clinical trials within the University of Minnesota Canine Brain Tumor Program. They were obtained from two different time points relative to treatment: pre-treatment and post-treatment. Treatment consisted of surgical resection and immunotherapy. The purpose of these data are to provide a comprehensive profile of how canine high grade glioma transcriptomes change in response to immunotherapy treatment, and to determine if there are breed-associated changes in differential gene expression.
Data for Reexamination of the electronic phase diagram of doped NiS₂: Electronic, magnetic, and structural inhomogeneity across the Mott insulator-metal transition
(2024-11-04) Tao, Yu; Das, Bhaskar; Calder, Stuart; Day-Roberts, Ezra; Maiti, Moumita; Lee, Yeon; Komar, Caitlyn; Birol, Turan; Leighton, Chris; leighton@umn.edu; Leighton, Chris; Leighton Electronic and Magnetic Materials Lab; Chemical Engineering and Materials Science, University of Minnesota
Pyrite-structure NiS₂ is, in principle, a model antiferromagnetic Mott insulator that can be electron doped, hole doped, and bandwidth controlled. Despite decades of study, however, the electronic and magnetic behavior of NiS₂ have proven challenging to understand. Here, we build on recent advances establishing surface conduction in NiS₂ to completely reexamine the electronic phase behavior of electron- and hole-doped single-crystal Ni₁₋ⅹCuⅹS₂ and Ni₁₋ⅹCoⅹS₂. Magnetometry, heat capacity, neutron diffraction, and electronic transport measurements suggest that prior work missed vital details of the magnetic ordering in this system. While electron and hole doping rapidly increase the antiferromagnetic ordering temperature (by as much as 4-fold by x  0.1), signatures remain of antiferromagnetic and weak ferromagnetic ordering at the same temperatures as in undoped NiS₂. As these undoped ordering temperatures remain constant, the associated magnetic moments are diminished by doping, strongly implicating electronic/ magnetic phase coexistence across the Mott insulator-metal transition. Substantial structural changes and inhomogeneity accompany these evolutions, highlighting the importance of structural-chemical-electronic-magnetic coupling in NiS₂. The insulator-metal transition is also strongly electron/hole asymmetric, which we interpret with the aid of complementary dynamical mean-field theory results. These findings significantly revise and advance our understanding of the electronic phase behavior of this prototypical Mott insulator, highlighting the essential role of electronic, magnetic, structural, and chemical inhomogeneity across the Mott transition. This dataset contains all digital data in the published paper of the same name.
Supporting Data for Circular Dichroism of Distorted Double Gyroid Thin Film Metamaterials
(2024-11-04) McGuinness, Emily; Magruder, Benjamin; Dorfman, Kevin; Ellison, Chris; Ferry, Vivian; veferry@umn.edu; Ferry, Vivian; Department of Chemical Engineering and Materials Science, University of Minnesota
Strong circular dichroism (CD) has been reported in triply periodic, co-continuous gyroid thin films for certain orientations and surface terminations. However, processing of gyroid thin films introduces distortions experimentally, creating a mismatch between the structures created practically and those explored computationally. This work explores the impact of compression normal to the substrate (z-compression) with conserved volume in (110)-oriented plasmonic silver double gyroid thin films on CD using finite-difference time-domain (FDTD) simulations. As compression reaches fifteen percent and above, new features emerge including termination-dependent opposite-handed CD responses and, at larger compressions, shorter wavelength responses that span many surface terminations. The longest wavelength responses of the system red-shift with increasing compression. The top surface structure contributes strongly to the emerging opposite-handed features and red-shifting of wavelengths. However, the less surface termination dependent features arise from a mixture of contributions from the top surface and interior of the films. Interplay of these leads to CD-switching phenomena as a function of compression for certain terminations and wavelengths. When alternative methods are utilized to compress the system, such as compression with a Poisson’s ratio of 0.33 (comparable to polystyrene) or the generation of compressed equilibrium structures with non-affine strut changes via self-consistent field theory, similar optical responses persist. Overall, this study highlights the significant impact experimentally relevant distortions (especially compression and some non-affine structural shifts) can have on the CD response of block copolymer templated plasmonic double gyroid thin films, and provides mechanistic insight into the film interior versus surface contributions to the CD response during compression.
Complete data and code to generate datasets in: Occurrence and environmental data for aquatic plants of Minnesota from 1999-2018
(2024-07-15) Verhoeven, Michael; Larkin, Daniel J.; michael.verhoeven.mrv@gmail.com; Verhoeven, Michael; Minnesota Aquatic Invasive Species Research Center (MAISRC); Fisheries Systems Ecology Lab
A dataset (and multi-scale aggregations thereof) of point-level occurrences, relative abundances, and associated environmental data for macrophytes (freshwater plants) across Minnesota. The data encompass 3,194 surveys of 1,520 lakes and ponds performed over a 19-year timespan. A total of 372,091 points were sampled, across which 231 taxa were recorded. Macrophyte occurrence data and depth, as well as point-level relative-plant-abundance measures for a subset of surveys, were collated, cleaned, and joined to geospatial data and Secchi-depth measurements of water clarity, enabling light availability, a primary control on aquatic plant growth, to be estimated.
Eastern larch beetle reproductive success in western and subalpine larch
(2024-10-31) Picklo, Rose; Eidson, Erika; Steed, Brytten; Aukema, Brian; bhaukema@umn.edu; Aukema, Brian; University of Minnesota Forest Entomology Lab
Eastern larch beetle Dendroctonus simplex LeConte has been outbreaking for the past two decades in the Great Lakes region of North America, impacting approximately 400,000 hectares of eastern larch Larix laricina (tamarack) forest in Minnesota, United States, alone. Range expansions of some Dendroctonus species driven by climate change have occurred across North America as rising temperatures increase climatically suitable habitats across latitudes and elevations. The range of eastern larch beetle is currently sympatric to that of its host, eastern larch, but the insect could, in theory, eventually access ranges of other species of Larix native to North America. We compared host suitability of two potential novel hosts, western larch (Larix occidentalis Nutt.) and subalpine larch (Larix lyalli Parl.) against the beetle’s native host, eastern larch, using a reproductive success experiment conducted in cut bolts of all three species. We measured fertility, maternal gallery length, and offspring size and lipid content as metrics of reproductive success. We share data here upon publication of this work in the journal Frontiers in Forests and Global Change.
Data for Non-Local Spin Transport in the Light Intermetallic Alloy Al2Cu
(2024-10-24) Ramberger, Justin; Kaiser, Ben; Dutta, Paromita; Norum, Mikaela; Birol, Turan; Leighton, Chris; leighton@umn.edu; Leighton, Chris; Leighton Research Group
Data availability for the article titled Non-Local Spin Transport in the Light Intermetallic Alloy Al2Cu
Data, R Code, and Output Supporting: A “How-to” Guide for Estimating Animal Diel Activity Using Hierarchical Models
(2024-10-22) Iannarilli, Fabiola; Gerber, Brian D; Erb, John; Fieberg, John R; jfieberg@umn.edu; Fieberg, John; Fieberg lab
This repository contains data, code, and associated output supporting work presented in "Iannarilli F., Gerber B. D., Erb J., and Fieberg J. R. (2024). A “How-to” Guide for Estimating Animal Diel Activity Using Hierarchical Models. Journal of Animal Ecology". We provide a series of .Rmd files that can be compiled to form a step-by-step tutorial demonstrating how to quantify animal activity patterns from time-stamped data using trigonometric and cyclic cubic spline hierarchical models. These models can accommodate site-to-site variability in the frequency of site use and timing of activity, while accounting for sampling effort. The text is accompanied by a series of examples in which we address common ecological questions related to the study of animal diel activity, such as the shape of the underlying activity pattern (unimodal, bimodal, or cathemeral) and the effect of covariates or the co-occurrence of other species on activity patterns. An HTML version of this tutorial is available at https://hms-activity.netlify.app/.
Data for Response of a large, low porosity rock sample to hydromechanical loading
(2024-10-22) Asem, Pouyan; Detournay, Emmanuel; Voller, Vaughan; Labuz, Joseph; pasem@umn.edu; Asem, Pouyan; University of Minnesota
A unique laboratory framework is developed for measuring hydromechanical parameters in a 6025 mL confined specimen of Westerly blue granite. Tracking the water uptake in the sample shows that infiltration over a length scale of 230 mm is effectively modeled by assuming a sharp front separating saturated and dry regions. Through matching the movement of this front with the experimental data, an estimate of the sample permeability is obtained. In addition, following full saturation, Skempton coefficient B, drained bulk modulus K, unjacketed bulk modulus Ks′, and unjacketed pore modulus Ks'' are determined. Thus, we demonstrate that a single experimental framework for measuring the infiltration and saturation of a large, tight rock specimen provides a significant array of reliable parameters for use in modeling and characterizing critical hydrogeological processes.
Materials to re-create Direct Observations of Coastally-Generated Near-Inertial Waves During a Wind Event
(2024-10-22) Kelly, Samuel; smkelly@d.umn.edu; Kelly, Samuel; University of Minnesota Duluth, Large Lakes Observatory
A recent manuscript examined near inertial currents and internal waves in Lake Superior using shipboard observations. This submission includes the Matlab scripts and functions to analyze the observations and recreate the figures in the manuscript.
Access Across America: Auto 2022 Data
(2024-10-21) Owen, Andrew; Liu, Shirley Shiqin; Jain, Saumya; Hockert, Matthew; Lind, Eric; owenx148@umn.edu; Owen, Andrew; University of Minnesota Center for Transportation Studies, Accessibility Observatory
These data were created as part of a study that examined the accessibility to jobs by auto in the 50 largest (by population) metropolitan areas in the United States. The data include access at realistic observed driving speeds by time of day and road segment. The underlying speed data inputs restrict data sharing to participating sponsor states. The data available describe access to jobs by auto in the states/districts of California, Connecticut, District of Columbia, Florida, Illinois, Maryland, Massachusetts, Michigan, Minnesota, North Carolina, Texas, and Virginia; and the metropolitan areas within these states. These data are part of a longitudinal study. Auto data for additional years can be found in the Accessibility Observatory Data collection: http://hdl.handle.net/11299/200592
Access Across America: Walk 2022 Data
(2024-10-21) Owen, Andrew; Liu, Shirley Shiqin; Jain, Saumya; Hockert, Matthew; Lind, Eric; owenx148@umn.edu; Owen, Andrew; University of Minnesota Center for Transportation Studies, Accessibility Observatory
These data were created as part of a study that examines the accessibility to jobs by walking or rolling across the United States. It is the most detailed evaluation to date of access to jobs by walking, and it allows for a direct comparison of the walkability of America's metropolitan areas. These data are part of a longitudinal study. Walk/roll data for additional years can be found in the Accessibility Observatory Data collection: https://hdl.handle.net/11299/200592
Access Across America: Bike 2022 Data
(2024-10-21) Owen, Andrew; Liu, Shirley Shiqin; Jain, Saumya; Hockert, Matthew; Lind, Eric; owenx148@umn.edu; Owen, Andrew; University of Minnesota Center for Transportation Studies, Accessibility Observatory
These data were created as part of a study that examines the accessibility to jobs by biking across the United States. It is the most detailed evaluation to date of access to jobs by cycling, and it allows for a direct comparison of the bike accessibility performance of America's metropolitan areas. These data are part of a longitudinal study. Biking data for additional years can be found in the Accessibility Observatory Data collection: https://hdl.handle.net/11299/200592
Access Across America: Transit 2022 Data
(2024-10-21) Owen, Andrew; Liu, Shirley Shiqin; Jain, Saumya; Hockert, Matthew; Lind, Eric; owenx148@umn.edu; Owen, Andrew; University of Minnesota Center for Transportation Studies, Accessibility Observatory
These data were created as part of a study that examines the accessibility to jobs by transit across the United States. It is the most detailed evaluation to date of access to jobs by transit, and it allows for a direct comparison of the transit accessibility performance of America's metropolitan areas. These data are part of a longitudinal study. Transit data for additional years can be found in the Accessibility Observatory Data collection: https://hdl.handle.net/11299/200592
OrthoFusion: A Super-Resolution Algorithm to Fuse Orthogonal CT Volumes
(2024-10-21) Ellingson, Arin M; ellin224@umn.edu; Ellingson, Arin M
OrthoFusion, an intuitive super-resolution algorithm, is presented in this study to enhance the spatial resolution of clinical CT volumes. The efficacy of OrthoFusion is evaluated, relative to high-resolution CT volumes (ground truth), by assessing image volume and derived bone morphological similarity, as well as its performance in specific applications in 2D-3D registration tasks. Results demonstrate that OrthoFusion significantly reduced segmentation time, while improving structural similarity of bone images and relative accuracy of derived bone model geometries. Moreover, it proved beneficial in the context of biplane videoradiography, enhancing the similarity of digitally reconstructed radiographs to radiographic images and improving the accuracy of relative bony kinematics. OrthoFusion's simplicity, ease of implementation, and generalizability make it a valuable tool for researchers and clinicians seeking high spatial resolution from existing clinical CT data. This study opens new avenues for retrospectively utilizing clinical images for research and advanced clinical purposes, while reducing the need for additional scans, mitigating associated costs and radiation exposure.
Data for Catalytic Resonance Theory: Turnover Efficiency and the Resonance Frequency
(2024-10-14) Dauenhauer, Paul; Canavan, Jesse R; Hopkins, Justin A; Foley, Brandon R; Abdelrahman, Omar A; hauer@umn.edu; Dauenhauer, Paul
The data were collected via simulation in Matlab r2019 and used in the data Figures 1-4 of the manuscript, "Catalytic Resonance Theory: Turnover Efficiency and the Resonance Frequency"
Data for Evolving Mineralogy and Reactivity of Hematite-Coated Sands During Reduction by Fe(II) of 4-Chloronitrobenzene in Column Reactors
(2024-10-14) Harris, Celina M; Soroush, Adel; Hildebrandt, Alanna M; Amen, Kamilah Y; Corcoran, Louis G; Feinberg, Joshua M; Arnold, William A; Penn, R Lee; arnol032@umn.edu; Arnold, William; Arnold, Penn and Feinberg labs at the University of Minnesota
This study explores the reaction of contaminants mediated by iron oxide minerals in a column reactor that simulated iron reducing groundwater conditions. Reaction of the model nitroaromatic pollutant with hematite-coated sand in column reactors leads to growth of goethite and evolving reactivity due to changes in accessible surface area. Data collected include concentrations of the model pollutant (4-chloronitrobenzene) and its reaction product, the amount of new iron oxide mineral formed, and chloride concentrations in tracer studies.
Temperature Observations of the Twin Cities Canopy-Layer Urban Heat Island
(2024-10-10) Smoliak, Brian V; Snyder, Peter K; Twine, Tracy E; Mykleby, Phillip M; Hertel, William F; Liess, Stefan; liess@umn.edu; Liess, Stefan; Department of Soil, Water, and Climate
Data from a dense urban meteorological network (UMN) are analyzed, revealing the spatial heterogeneity and temporal variability of the Twin Cities (Minneapolis–St. Paul, Minnesota) canopy-layer urban heat island (UHI). Data from individual sensors represent surface air temperature (SAT) across a variety of local climate zones within a 5000-km2 area and span the 3-yr period from 1 August 2011 to 1 August 2014. Irregularly spaced data are interpolated to a uniform 1-km x 1-km grid using two statistical methods: 1) kriging and 2) cokriging with impervious surface area data. The cokriged SAT field exhibits lower bias and lower RMSE than does the kriged SAT field when evaluated against an independent set of observations. Maps, time series, and statistics that are based on the cokriged field are presented to describe the spatial structure and magnitude of the Twin Cities metropolitan area (TCMA) UHI on hourly, daily, and seasonal time scales. The average diurnal variation of the TCMA UHI exhibits distinct seasonal modulation wherein the daily maximum occurs by night during summer and by day during winter. Daily variations in the UHI magnitude are linked to changes in weather patterns. Seasonal variations in the UHI magnitude are discussed in terms of land-atmosphere interactions. To the extent that they more fully resolve the spatial structure of the UHI, dense UMNs are advantageous relative to limited collections of existing urban meteorological observations. Dense UMNs are thus capable of providing valuable information for UHI monitoring and for implementing and evaluating UHI mitigation efforts.
Microfluidic Experiments and Numerical Simulations of Inertia-induced Mixing and Reaction Maximization in Laminar Porous Media Flows
(2024-10-10) Chen, Michael; Lee, Sanghyun; Kang, Peter; pkkang@umn.edu; Kang, Peter; Kang Research Group
Solute transport and biogeochemical reactions in porous and fractured media flows are controlled by mixing, as are subsurface engineering operations such as contaminant remediation, geothermal energy production, and carbon sequestration. A porous media flow is generally regarded as slow, so the effects of fluid inertia on mixing and reaction are typically ignored. Here, we demonstrate through microfluidic experiments and numerical simulations of mixing-induced reaction, that inertial recirculating flows readily emerge in laminar porous media flows and dramatically alter mixing and reaction dynamics. An optimal Reynolds number that maximizes the reaction rate is observed for individual pore throats of different sizes. This reaction maximization is attributed to the effects of recirculation flows on reactant availability, mixing, and reaction completion, which depend on the topology of recirculation relative to the boundary of the reactants or mixing interface. Recirculation enhances mixing and reactant availability, but a further increase in flow velocity reduces the residence time in recirculation, leading to a decrease in reaction rate. The reaction maximization is also confirmed in a flow channel with grain inclusions and a randomized porous media. Interestingly, the domain-wide reaction rate shows a dramatic increase with increasing Re in the randomized porous media case. This is because fluid inertia induces complex three-dimensional flows in a randomized porous media, which significantly increases transverse spreading and mixing. This study shows how inertial flows control reaction dynamics at the pore scale and beyond, thus having major implications for a wide range of environmental systems.