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Data Repository for U of M (DRUM)

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Anomalous Transport in Dissolving Porous Media: Transitions Between Fickian and Non-Fickian Regimes
(2025-02-17) Deng, Jingxuan; Sharma, Rishabh; Szymczak, Piotr; Kang, Peter K; pkkang@umn.edu; Kang, Peter K; University of Minnesota Kang Research Lab
Mineral dissolution is a key geologic process with broad impacts on natural processes and human activities. Depending on the interplay between advection, diffusion, and reaction rates, mineral dissolution can produce various dissolution patterns, such as wormholing and uniform dissolution. The resulting changes in pore structure directly influence the flow field, which in turn control solute transport behavior. In this study, we conducted numerical modeling of mineral dissolution and solute transport in pore networks to investigate how initial network heterogeneity and dissolution regimes affect transport dynamics. Our findings show that wormholing increases network heterogeneity by creating preferential flow paths and stagnation zones, resulting in a transition from Fickian to non-Fickian transport. Conversely, uniform dissolution extensively homogenizes the pore network and the flow field, leading to a transition from non-Fickian to Fickian transport, even in networks with high initial heterogeneity. Based on the initial heterogeneity and Damköhler number, transitions can be predicted.
Data for Unbiased Clustering of Residues Undergoing Synchronous Motions in Proteins using NMR Spin Relaxation Data
(2025-02-13) Veliparambil Subrahmanian, Manu; Veglia, Gianluigi; Melacini, Giuseppe; L Kovrigin, Evgenii; Loria, J Patrick; mvelipar@umn.edu; Veliparambil Subrahmanian, Manu; Veglia Lab
Carr-Purcell-Meiboom-Gill Relaxation Dispersion (CPMG-RD) experiments are highly effective for probing micro- to millisecond conformational exchange processes in proteins. By performing experiments at multiple magnetic field strengths , one can extract dynamic parameters such as exchange rates, population fractions, and chemical shift differences. PySyncDyn is a comprehensive Python-based toolkit that automates the entire workflow from raw data processing to the generation of Dynamic Correlation (SyncDyn) maps. The workflow includes the calculation of effective transverse relaxation rates , pairwise fitting using the Carver-Richards model, generation of correlation maps, and computation of a SyncDyn Score that quantifies the extent of correlated dynamics across the protein. In addition, the Score2Pymol.py script allows visualization of these scores on the three-dimensional structure of the protein in PyMOL.
Data for Reflection instructions influence 7- to 9-year-olds' metacognition and executive function at the levels of task performance and neural processing
(2025-02-13) Drexler, Colin; Zelazo, Philip David; cdrexler@umn.edu; Drexler, Colin; UMN Developmental Social Cognitive Neuroscience Lab
Though research on metacognitive development has historically remained independent from research on executive function (EF) skills, the two constructs share numerous theoretical similarities. Namely, the skill of reflection, or the ability to consciously reprocess information in real-time, may influence children’s awareness of their own use of EF skills. The present study examined the relations among implicit and explicit forms of metacognition in the Dimensional Change Card Sort (DCCS; Zelazo et al., 2012), while experimentally manipulating the propensity to reflect in 7- to 9-year-olds. Results showed that instructions to reflect led to improved task accuracy and better metacognitive control, but only younger children, as older children were likely reflecting spontaneously. Individual differences in trait mindfulness related to a similarly reflective mode of responding characterized by improved task accuracy and metacognitive control. In contrast, articulatory suppression impaired children’s task accuracy and metacognitive control. Additionally, simply asking children to make metacognitive judgments without extra instructions decreased the amplitude of neural indices of error monitoring, namely the error-related negativity (ERN) and N2 ERP components. Finally, individual differences in trait anxiety were related to larger Pe amplitudes. Taken together, the current findings reinforce theoretical frameworks integrating metacognition and EF, and highlight the shared influence of reflection across multiple levels of analysis.
Supporting data for "3D Printed Anisotropic Tissue Simulants with Embedded Fluid Capsules for Medical Simulation and Training"
(2025-02-10) Somayaji, Adarsh; Lawler, Matthew S; Gong, Alex T; Fuenning , Zachary M; Roach, Victoria A; S., Athira B; Traina, David J; Speich, Jason R; Wang, Ruikang K; Hackett, Matthew G; Hananel, David M; Sweet , Robert M; McAlpine, Michael C; mcalpine@umn.edu; McAlpine, Michael C.; McAlpine Research Group
Human tissues are primarily composed of collagen and elastin fiber networks that exhibit directional mechanical properties which are not replicable by conventional tissue simulants manufactured via casting. Here, we 3D print tissue simulants which incorporate anisotropic mechanical properties through the manipulation of infill voxel shape and dimensions. A mathematical model for predicting the anisotropy of single and multi-material structures with orthogonal infill patterns is developed. We apply this methodology to generate conformal printing toolpaths for replicating the structure and directional mechanics observed in native tissue within 3D printed tissue simulants. Further, a method to embed fluid-filled capsules within the infill structure of these tissue simulants to mimic blood is also presented. The improvements in simulation quality when using 3D printed anisotropic tissue simulants over conventional tissue simulants is demonstrated via a comparative acceptability study. These advances open new avenues for the manufacture of next-generation tissue simulants with high mechanical fidelity for enhanced medical simulation and training.
Supporting data for Renewable Lactam Monomer for Tunable and Processable Polyamides
(2025-02-06) Häkkinen, Satu; Krajovic, Daniel; Chamberlain, Kari; Shippee, Joshua; Biswas, Arpan; Zhang, Honghu; Felsenthal, Lillian; Dichtel, William; Hillmyer, Marc; hillmyer@umn.edu; Hillmyer, Marc; Hillmyer Group
This work aimed to improve the processability and application scope of polyamides by introducing a bio-derivable lactam co-monomer to controllably reduce the polyamides' crystallinity. Tuning the co-monomer composition modulated crystallinity, water uptake, and mechanical properties while achieving newfound solubilities, 3D printability, and structural adhesion properties.
Data for Detection of Exchangeable Protons in NMR Metabolomic Analysis using AI-Designed Water Irradiation Devoid Pulses
(2025-02-06) Veliparambil Subrahmanian, Manu; Veglia, Gianluigi; Vuckovic, Ivan; Macura, Slobodan; mvelipar@umn.edu; Manu, Veliparambil Subrahmanian; Veglia Lab
1H NMR spectroscopy has enabled the quantitative profiling of metabolites in various biofluids, emerging as a possible di-agnostic tool for metabolic disorders and other diseases. To boost the signal-to-noise ratio and detect proton resonances near the water signal, current 1H NMR experiments require solvent suppression schemes (e.g., presaturation, jump-and-return, WATERGATE, excitation sculpting, etc.). Unfortunately, these techniques affect the quantitative assessment of analytes containing exchangeable protons. To address this issue, we introduce two new1D 1H NMR techniques that eliminates the water signal, preserving the intensities of exchangeable protons. Using GENETICS-AI, a software that combines an evolutionary algorithm and artificial intelligence, we tailored new WAter irradiation DEvoid (WADE) pulses and optimized 1D 1H NOESY sequence for metabolomics analysis. When applied to human urine samples, kidney tissue extract, and plasma, the WADE technique allowed for accurate measurement of typical metabolites and direct quantification of urea, which is usually challenging to measure using standard NMR experiments. We anticipate that these new NMR techniques will significantly improve the accuracy and reliability of metabolite quantitative assessment for a wide range of biological fluids.
Zebra Mussel Safari: A Participatory Science Program to Guide Management Decisions
(2025-02-06) Lorentz, Sawyer; Bajcz, Alex; Weber, Megan; Duhr, Meg; Phelps, Nicholas B D; phelp083@umn.edu; Phelps, Nicholas; Minnesota Aquatic Invasive Species Research Center (MAISRC)
The Zebra Mussel Safari program is a participatory science initiative aimed at monitoring zebra mussel (Dreissena polymorpha) populations within Minnesota lakes. This dataset includes materials designed to support and ease volunteers' participation in the program. Additionally, the dataset includes zebra mussel abundance data collected from the seven Minnesota lakes involved in the 2023 program.
COVID-OUT: Early Outpatient Treatment for SARS-CoV-2 Infection. Comprehensive Datasets
(2025-02-03) Bramante, Carolyn; covidout@umn.edu; Bramante, Carolyn
The COVID-OUT clinical trial was a decentralized, randomized, placebo controlled clinical trial of early outpatient treatment of SARS-CoV-2 infection. The trial used a 2x3 factorial design to test metformin versus placebo, ivermectin versus placebo, and fluvoxamine versus placebo.
Supporting Data for Mesoscopic Morphologies in Frustrated ABC Bottlebrush Block Terpolymers
(2025-02-03) Cui, Shuquan; Murphy, Elizabeth A; Santra, Subrata; Bates, Frank S; Lodge, Timothy P; lodge@umn.edu; Lodge, Timothy P; University of Minnesota Department of Chemistry
Bottlebrush block polymers, characterized by densely grafted side chains extending from a backbone, have recently garnered significant attention. A particularly attractive feature is the accessibility of ordered morphologies with domain spacings exceeding several hundred nanometers, a capability that is challenging to achieve with linear polymers. These large morphologies make bottlebrush block polymers promising for various applications, such as photonic crystals. However, the structures observed in AB diblock bottlebrushes are generally limited to simple lamellae and cylindrical phases, which restricts their use in many applications. In this study, we synthesized a large library of 50 ABC bottlebrush triblock terpolymers, poly(DL-lactide)-b-poly(ethylene-alt-propylene)-b-polystyrene (PLA-PEP-PS), spanning a wide range of compositions using ring-opening metathesis polymerization (ROMP) of norbornene-functionalized macromonomers. This constitutes a frustrated system, in that the mandatory internal interfaces (PLA/PEP) have larger interfacial energies than PLA/PS. We systematically explored phase behavior using small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM). Morphological characterization revealed a series of intriguing mesoscopic structures, including layered microstructures, core-shell hexagonally packed cylinders (CSHEX, plane group p6mm), alternating tetragonally packed cylinders (ATET, plane group p4mm), and an unprecedented morphology, rectangular centered cylinders-in-undulating-lamellae (RCCUL, plane group c2mm). Adjustments in molecular weight resulted in a wide range of unit cell dimensions (exemplified by RCCUL), from 40 nm to over 130 nm. This work demonstrates that multiblock bottlebrushes offer promising opportunities for developing materials with novel diverse structures and a broad range of domain dimensions.
An Oxymetazoline-based Nasal Solution Removes Bacteria-Blood Debris on Dental Surfaces and Has Antimicrobial Activity toward Streptococcus mutans Data Sharing Archive
(2025-01-30) Jones, Robert S; Kumar, Dhiraj; Pride, Morgan; rsjones@umn.edu; Jones, Robert; B-A-M (Biofilm-Apatite-Microbiome) Lab
Data used in the manuscript An Oxymetazoline-based Nasal Solution Removes Bacteria-Blood Debris on Dental Surfaces and Has Antimicrobial Activity toward Streptococcus mutans Background: An over-the-counter vasoconstrictive nasal solution with oxymetazoline (NS-OXY, 0.05%) has potential to be used as a dental pulpal hemostatic medicament. A molecular engineering approach examined NS-OXY and its molecular constituent’s an-timicrobial and blood biomass removal efficacy. Methods: An ex vivo cavity model was developed where standardized prepared teeth were exposed overnight to a model dentinal caries pathogen, S. mutans, and then exposed to Sheep’s blood for 10 minutes, which sim-ulated a pulpal exposure. Cavity preparations were rinsed with OXY (0.05%), ben-zalkonium chloride (BKC-0.025%), NS-OXY (with OXY-0.05% and BKC), ferric sulfate (20%;ViscoStat, FS), and distilled water (DI). For examining the bactericidal effect of NS-OXY, a disc diffusion antimicrobial assay was used where S. mutans was grown (20-hrs) on brain-heart infusion (BHI) w/0.5% glucose agar plates and exposed to the treatment groups. Results: NS-OXY treated samples had a lower residual bacterial or blood biomass than FS (P=.003). The diffusion test showed that NS-OXY, BKC, and FS had zones of inhibition greater than 10 mm, with NS-OXY having higher activity against S. mutans than FS (P=.0002) but lower than BKC (P=0.0082). Conclusions: NS-OXY may con-sidered as a dental hemostatic agent after traumatic and carious pulpal exposure owing to NS-OXY’s antimicrobial and vasoconstrictive properties.
Thermodynamic Free Energy Data for Ge/GeO2 Phase Stability
(2025-01-30) Szymanski, Nathan J; Noordhoek, Kyle; Liu, Fengdeng; Shin, Ho-sung; Kim, Donghwan; Bartel, Christopher J; Jalan, Bharat; nszymans@umn.edu; Szymanski, Nathan; DMC Lab
This dataset includes thermodynamic free energy calculations for GeO2 reactions involving GeO and O2. The data provides insights into phase stability and reaction kinetics under varying conditions, supporting experimental findings in GeO2 thin-film synthesis via molecular beam epitaxy (MBE).
Data Repository for Effects of Fluid Flow and Fracture Aperture on Solute Exchange in Triple Porosity Carbonates: Etched Rock Core Experiments and Numerical Modeling
(2025-01-30) Soucey, Charles E; Sutton, Collin R; Zahasky, Christopher; Yang, Weipeng; Kang, Peter K; pkkang@umn.edu; Kang, Peter K; Kang Research Lab
The data contained in this repository is related to the results and figures shown in the manuscript "Effects of Fluid Flow and Fracture Aperture on Solute Exchange in Triple Porosity Carbonates: Etched Rock Core Experiments and Numerical Modeling." The data encompasses multiple different data types and covers all of the major experiments used in the manuscript, including PET scan data extracted from core flooding experiments in our etched rock cores, COMSOL numerical model files, image data from digital photographs and HSV thresholding of cores, and breakthrough curve data with model files for MFIT curve fitting. The files included here are the necessary files for replicating the primary results outlined in the paper. This data is now released for the purpose of allowing open access to data and information for the purpose of replicating our results in future studies.
New Materials to re-create Synoptic Observations of Near-Inertial Motions in an Enclosed Basin
(2025-01-30) Green, Erica L; Kelly, Samuel M; smkelly@d.umn.edu; Kelly, Samuel
A recent manuscript examined near inertial currents and internal waves in Lake Superior using mooring observations. This submission includes the Matlab scripts and functions to analyze the observations and recreate the figures in the manuscript.
Supplementary raw data for α‐N‐Methyltransferase regiospecificity is mediated by proximal, redundant enzyme–substrate interactions
(2025-01-27) Crone, Kathryn K; Labonte, Jason W; Elias, Mikael H; Freeman, Michael F; mffreema@umn.edu; Freeman, Michael F; Freeman Lab University of Minnesota
The data deposited here are raw mass spectrometry files associated with the results presented in the paper, "α‐N‐Methyltransferase regiospecificity is mediated by proximal, redundant enzyme–substrate interactions." These data have been made publicly available in keeping with our lab's data availability policy.
Data from: How do trees outside forests contribute to human wellbeing? A systematic review from South Asia
(2025-01-21) Choksi, Pooja; Lalai, Dhwani; Menon, Anamika; Joglekar, Abha; Roy, Anirban; Ramprasad, Vijay; Thapa, Mahendra Singh; Gudasalamani, Ravikanth; Dhyani, Shalini; Bunyan, Milind; Shastri, Seema; Plieninger, Tobias; Adhikari, Binod; Fischer, Harry; Lahiri, Sutirtha; Djenontin, Ida N. S.; Elias, Faisal; Kocher, Megan; Ortiz Cuadra, Juan; Fleischman, Forrest; choks027@umn.edu; Choksi, Pooja
Trees outside forests (ToF) can provide several ecosystem services or benefits such as carbon sequestration, biodiversity conservation and soil enrichment. These benefits, largely focused on agri-silvipastoral systems, have been well studied and documented. Human wellbeing outcomes of ToF, on the other hand, are relatively less understood. South Asia, in particular, is an important region to study given the cultural norm of trees outside forests. This region is home to millions of small-scale farmers, with often less than 4 hectares each, where trees are an important source of fodder, nutrition, and livelihoods. Moreover, countries in South Asia such as India have large land restoration targets such as restoring 26 million hectares of degraded land by 2030, and recent studies have indicated that ToF may be an important aspect of meeting this pledge. Multiple papers based on this data from a systematic review will help understand the reported benefits and drawbacks for human wellbeing of ToF and the circumstances under which these outcomes are perceived by people. Our data will help understand the institutional, geographic, managerial and population characteristics that mediate the human wellbeing outcomes directly measured by a study or perceived by the population considered in a particular study. In the context of this review, we broadly use the term human wellbeing, to include the following components: material and living standards, health, education, work and leisure, agency and political voice, social relationships, physical and economic security.
Data for the flume experiments and numerical simulations of the surface and subsurface flows in an emergent vegetation canopy at St. Anthony Falls Laboratory in 2024.
(2025-01-21) Huang, Shih-Hsun; Nuli, Rohit; Yang, Judy Q; judyyang@umn.edu; Yang, Judy Q; University of Minnesota Environmental Transport Lab
We combined laboratory experiments and coupled numerical simulations to study the hyporheic exchange process within an emergent vegetation canopy in a channel with a permeable bed.
R Code and Output Supporting: Oviposition substrate preferences of two endangered prairie butterflies in an ex situ conservation environment
(2025-01-21) Thomas, Amaya; Fieberg, John R; Runquist, Erik; Nordmeyer, Cale; Stapleton, Seth; Jfieberg@umn.edu; Fieberg, John; Fieberg Lab
This repository contains the data, supplementary material, and R code and associated output supporting the results reported in: Thomas, A., Fieberg, J., Runquist, E., Nordmeyer, C., & Stapleton, S. Oviposition substrate preferences of two endangered prairie butterflies in an ex situ conservation environment.
Fish abundance training data in support of: Climate-driven declines in abundance across thermal guilds in fish communities of 11,000 temperate lakes
(2025-01-13) Link, Denver J; Verhoeven, Michael R; Masui, Holly K; Nelson, Jenna KR; Hansen, Gretchen JA; ghansen@umn.edu; Hansen, Gretchen; University of Minnesota Department of Fisheries, Wildlife, Conservation Biology
Anticipating and planning for changes in biological communities due to climate warming presents numerous challenges, particularly in projecting how species abundance relationships will respond to future thermal conditions. In this study, we use regional fisheries-independent catch data to train a novel physiologically guided model that predicts fish abundances under warming scenarios in over 11,000 lakes across the Midwestern U.S. The dataset includes catch-per-effort data for eight sport fish species (cisco, northern pike, walleye, black crappie, yellow perch, smallmouth bass, largemouth bass, and bluegill sunfish) from 6,805 lakes, 46,287 surveys, and spanning 81 years (1940–2023) across seven states. We selected survey gear types for each state and species based on agency recommendations and survey documentation to ensure accurate representation of relative abundance. Rigorous data screening was performed to eliminate anomalies that could bias abundance estimates. Each survey location is linked to National Hydrography Dataset (NHD) identifiers, enabling integration with landscape-level environmental covariates. These data were used in a companion study to inform a joint species physiologically guided abundance model to project future species abundances across the region.
The use of Oxymetazoline-based Nasal Solutions to remove Bacteria-Blood Debris and Eradicate Rothia dentocariosa: an ex vivo cavity model study - Data Sharing Archive
(2025-01-06) Kumar, Dhiraj; Pride, Morgan; Mukherjee, Kaushik; Jain, Gaurav; Mutreja, Isha; Jones, Robert S.; kumard@umn.edu; Kumar, Dhiraj
solution with oxymetazoline (NS-OXY, 0.05%), against a dentinal caries pathogen. Methods: Using a disc diffusion susceptibility test (n=6), Rothia dentocariosa was grown on brain-heart infusion (BHI) agar plates and exposed to OXY (0.05%), benzalkonium chloride (BKC-0.025%), OXY-NS (with OXY-0.05% and BKC), ferric sulfate (20%; ViscoStat), and distilled water (DI). This was followed by exposure of an ex vivo dental caries model with sheep blood to simulate the clinical pulpotomy procedure. An antibacterial broth inhibition test was conducted by adding the test samples in BHI broth at 37±0.5 °C in an aerobic chamber. Results: In the disc diffusion test, NS-OXY and BKC had the largest zone of inhibition (ZOI) measuring 14.42 mm (±1.62) and 18.92 mm (±4.14) respectively, indicating antibacterial activity. Ferric sulfate demonstrated a smaller ZOI, while OXY alone had no ZOI. The antibacterial broth test showed antibacterial effects with stable OD and pH levels for test samples containing BKC (0.025%) and diluted NS-OXY (0.01%) for up to 20 h. DI- and OXY-treated samples showed an increase in OD, indicating an increase in bacterial count and a concurrent drop in pH. BKC treatment statistically (P<0.05) reduced polyP extracts, which may contribute to blood clot formation. NS-OXY demonstrated antibacterial properties, likely due to the addition of BKC to Rothia dentocariosa. NS-OXY showed concentration dependent biocompatibility with dental pulp stem cells while FS was cytotoxic at the same dilution. Conclusion: These antimicrobial properties, together with OXY’s hemostatic effects, suggest the potential off-label use of NS-OXY during a pulpotomy procedure in primary and permanent teeth. This study provides support for potential future clinical trials of repurposing FDA-approved drugs consisting of oxymetazoline and benzalkonium chloride for dental and other similar applications. Featured Application: An over-the-counter nasal solution containing oxymetazoline has the potential to be used off-label to manage surgical bleeding from dental pulp exposures and provide antimicrobial properties against Rothia dentocariosa, a model gram-positive bacteria associated with deep dentinal caries.
Supporting Information for Engineering Aliphatic Polyester Block Copolymer Blends for Hydrolytically Degradable Pressure Sensitive Adhesives
(2025-01-06) Shuang, Liang; Krajovic, Daniel M; Hoehn, Brenden D; Ellison, Chris J; Hillmyer, Marc A; hillmyer@umn.edu; Hillmyer, Marc; Hillmyer and Ellison groups
This work aimed to explore aliphatic polyester triblock copolymers of poly(L–lactide)–block–poly(γ–methyl–ε–caprolactone)–block–poly(L–lactide) (LML) and associated blends with renewable tackifier in pressure-sensitive adhesive (PSA) formulations and investigate effects of tackifier, composition, and processing history on microstructural, thermal, mechanical, and adhesive properties of the PSAs. After solvent casting and two–step annealing at 170 °C for 60 min and 100 °C for 5 min, LML–based PSAs showed stable and competitive adhesion properties when compared to commercial PSAs, which we attribute to both microphase separation and crystallinity in the poly(L–lactide) end blocks. Moreover, theses LML–based PSA formulations are hydrolytically degradable into water soluble or dispersible compounds at 45 ℃ under basic conditions within 30 days, offering the possibility of sustainable end–of–life scenarios for example through industrial composting.