84 Works

Minnesota Solvation Database (MNSOL) version 2012

Aleksandr V Marenich, Casey P Kelly, Jason D Thompson, Gregory D Hawkins, Candy C Chambers, David J Giesen, Paul Winget, Christopher J Cramer & Donald G Truhlar
The Minnesota Solvation Database consists of a collection of 3037 experimental free energies of solvation or transfer free energies for 790 unique solutes in 92 solvents (including water) and gas-phase M06-2X/MG3S optimized molecular geometries in Cartesian coordinates for the corresponding solutes. All of the 790 solutes in this database (541 neutrals and 249 singly-charged ions) contain at most the following elements: H, C, N, O, F, Si, P, S, Cl, Br, and I.

R Code and Output Supporting: Resampling-Based Methods for Biologists

John Fieberg, Kelsy Vitense & Douglas H. Johnson
This repository contains data, R code, and associated output from running R code supporting results reported in: Fieberg, J., K. Vitense, and D. H. Johnson 2020. Resampling-Based Methods for Biologists. PeerJ [In Revision]

Habitat fragmentation influences genetic diversity and differentiation: Fine-scale population structure of Cercis canadensis (eastern redbud)

Meher Ony, Marcin Nowicki, Sarah Boggess, William Klingeman, John Zobel, Robert Trigiano & Denita Hadziabdic
Forest fragmentation may negatively affect plants through reduced genetic diversity and increased population structure due to habitat isolation, decreased population size, and disturbance of pollen-seed dispersal mechanisms. However, in the case of tree species, effective pollen-seed dispersal, mating system, and ecological dynamics may help the species overcome the negative effect of forest fragmentation. A fine-scale population genetics study can shed light on the postfragmentation genetic diversity and structure of a species. Here, we present the...

Exploring whole-genome duplicate gene retention with complex genetic interaction analysis

Elena Kuzmin, Benjamin VanderSluis, Alex N. Nguyen Ba, Wen Wang, Elizabeth N. Koch, Matej Usaj, Anton Khmelinskii, Mojca Mattiazzi Usaj, Jolanda Van Leeuwen, Oren Kraus, Amy Tresenrider, Michael Pryszlak, Ming-Che Hu, Brenda Varriano, Michael Costanzo, Michael Knop, Alan Moses, Chad L. Myers, Brenda J. Andrews & Charles Boone
Whole-genome duplication has played a central role in genome evolution of many organisms, including the human genome. Most duplicated genes are eliminated and factors that influence the retention of persisting duplicates remain poorly understood. Here, we describe a systematic complex genetic interaction analysis with yeast paralogs derived from the whole-genome duplication event. Mapping digenic interactions for a deletion mutant of each paralog and trigenic interactions for the double mutant provides insight into their roles and...

Assessing zinc tolerance in two butterfly species: consequences for conservation in polluted environments

Alexander Shephard
1. Zinc is a widespread pollutant released from industrial combustion, auto- mobile residue, and mining. Zinc accumulates in soils and mobilises into plant tissue where it may be consumed to potentially toxic levels by leaf feeding insects, including developing pollinators. 2. While zinc tolerance thresholds have been previously assessed in insect pollinators, most observations are limited to model organisms and pest species. We lack understand- ing of zinc tolerance in insects of conservation concern. 3....

Long-term evidence shows crop-rotation diversification increases agricultural resilience to adverse growing conditions in North America

Timothy Bowles, Maria Mooshammer, Yvonne Socolar, Franciso Calderón, Michel Cavigelli, Steve Culman, William Dean, Axel Garcia Y Garcia, Amélie Gaudin, W Scott Harkom, Michael Lehman, Shannon Osborne, G Philip Robertson, Jonathan Salerno, Marty Schmer, Jeffrey Strock, A Stuart Grandy & Craig Drury
A grand challenge facing humanity is how to produce food for a growing population in the face of a changing climate and environmental degradation. Though empirical evidence remains sparse, management strategies that increase environmental sustainability, like increasing agroecosystem diversity through crop rotations, may also increase resilience to weather extremes without sacrificing yields. We used multilevel regression analyses of long-term crop yield datasets across a continental precipitation gradient to assess how temporal crop diversification affects maize...

Diversification or collapse of self-incompatibility haplotypes as a rescue process

Alexander Harkness, Emma Goldberg & Yaniv Brandvain
In angiosperm self-incompatibility systems, pollen with an allele matching the pollen recipient at the self-incompatibility locus is rejected. Extreme allelic polymorphism is maintained by frequency-dependent selection favoring rare alleles. However, two challenges result in a "chicken-egg"problem for the spread of a new allele (a tightly linked haplotype in this case) under the widespread "collaborative non-self recognition" mechanism. A novel pollen-function mutation alone would merely grant compatibility with a nonexistent style-function allele: a neutral change at...

Variation in mouse pelvic morphology maps to locations enriched in Sox9 Class II and Pitx1 regulatory features

Charles Roseman, Terrence Capellini, Evelyn Jagoda, Scott Williams, Mark Grabowski, Christine O'Connor, John Polk & James Cheverud
Variation in pelvic morphology has a complex genetic basis and its patterning and specification is governed by conserved developmental pathways. Whether the mechanisms underlying the differentiation and specification of the pelvis also produce the morphological covariation on which natural selection may act is still an open question in evolutionary developmental biology. We use high-resolution Quantitative Trait Locus (QTL) mapping in the F34 generation of an advanced intercross experiment (LG,SM-G34) to characterize the genetic architecture of...

Data from: Temporal scale-dependence of plant-pollinator networks

Benjamin Schwarz, Diego Vázquez, Paul CaraDonna, Tiffany Knight, Gita Benadi, Carsten Dormann, Benoit Gauzens, Elena Motivans, Julian Resasco, Nico Blüthgen, Laura Burkle, Qiang Fang, Christopher Kaiser-Bunbury, Ruben Alarcón, Justin Bain, Natacha Chacoff, Shuang-Quan Huang, Gretchen LeBuhn, Molly MacLeod, Theodora Petanidou, Claus Rasmussen, Michael Simanonok, Amibeth Thompson, Daniel Cariveau, Michael Roswell … & Jochen Fründ
The study of mutualistic interaction networks has led to valuable insights into ecological and evolutionary processes. However, our understanding of network structure may depend upon the temporal scale at which we sample and analyze network data. To date, we lack a comprehensive assessment of the temporal scale-dependence of network structure across a wide range of temporal scales and geographic locations. If network structure is temporally scale-dependent, networks constructed over different temporal scales may provide very...

Data from: Zooming in on mechanistic predator-prey ecology: integrating camera traps with experimental methods to reveal the drivers of ecological interactions

Justine Smith, Justin Suraci, Jennifer Hunter, Kaitlyn Gaynor, Carson Keller, Meredith Palmer, Justine Atkins, Irene Castañeda, Michael Cherry, Patrick Garvey, Sarah Huebner, Dana Morin, Lisa Teckentrup, Martijn Weterings & Lydia Beaudrot
1. Camera trap technology has galvanized the study of predator-prey ecology in wild animal communities by expanding the scale and diversity of predator-prey interactions that can be analyzed. While observational data from systematic camera arrays have informed inferences on the spatiotemporal outcomes of predator-prey interactions, the capacity for observational studies to identify mechanistic drivers of species interactions is limited. 2. Experimental study designs that utilize camera traps uniquely allow for testing hypothesized mechanisms that drive...

Ictal source imaging in epilepsy patients - Supplementary Data

Shuai Ye, Lin Yang, Yunfeng Lu, Michal Kucewicz, Benjamin Brinkmann, Cindy Nelson, Abbas Sohrabpour, Gregory Worrell & Bin He
Objective Localization of seizure onset zone in focal epilepsy patients is a crucial step prior to surgical planning. Noninvasively achieving this goal would have a tremendous impact on clinical management of intractable seizure. Methods In a total of 39 focal epilepsy patients, we recorded and extracted 138 seizures and 1,325 interictal epileptic discharges using high-density EEG. We have investigated a novel approach for directly imaging sources of seizures and interictal spikes from high density EEG...

Data from: Surf and Turf Vision: Patterns and predictors of visual acuity in compound eye evolution

Kathryn Feller, Lorian Schweikert, Camilla Sharkey, Alyssa McDuffee-Altekruse, Heather Bracken-Grissom, Nathan Lord & Megan Porter
Eyes have the flexibility to evolve to meet the ecological demands of their users. Relative to camera-type eyes, the fundamental limits of optical diffraction in arthropod compound eyes restricts the ability to resolve fine detail (visual acuity) to much lower degrees. We tested the capacity of several ecological factors to predict arthropod visual acuity, while simultaneously controlling for shared phylogenetic history. In this study, we have generated the most comprehensive review of compound eye visual...

Parasite intensity and the evolution of migratory behavior

Laurinne Balstad, Sandra Binning, Meggan Craft, Marlene Zuk & Allison Shaw
Migration can allow individuals to escape parasite infection, which can lead to a lower infection probability (prevalence) in a population and/or fewer parasites per individual (intensity). Since individuals with more parasites often have lower survival and/or fecundity, infection intensity shapes the life-history tradeoffs determining when migration is favored as a strategy to escape infection. Yet, most theory relies on susceptible-infected (SI) modeling frameworks, defining individuals as either healthy or infected, ignoring details of infection intensity....

Identifying the fitness consequences of sex in complex natural environments

Catherine Rushworth, Yaniv Brandvain & Thomas Mitchell-Olds
In the natural world, sex prevails, despite its costs. While much effort has been dedicated to identifying the intrinsic costs of sex (e.g. the cost of males), few studies have identified the ecological fitness consequences of sex. Furthermore, correlated biological traits that differ between sexuals and asexuals may alter these costs, or even render the typical costs of sex irrelevant. We conducted a large-scale multi-site reciprocal transplant using multiple sexual and asexual genotypes of a...

Data and R Markdown files for: Estimating the capacity of Chamaecrista fasciculata for adaptation to change in precipitation

Anna Peschel, Emma Boehm & Ruth Shaw
Adaptation through natural selection may be the only means by which small and fragmented plant populations will persist through present day environmental change. A population’s additive genetic variance for fitness (VA(W)) represents its immediate capacity to adapt to the environment in which it exists. We evaluated this property for a population of the annual legume Chamaecrista fasciculata through a quantitative genetic experiment in the tallgrass prairie region of the Midwest USA, where changing climate is...

Data for \"Simulation of natural alteration of iron oxides in soil: conversion of synthetic ferrihydrite to hematite without artificial dopants, observed with magnetic methods\" collected at the University of Minnesota between 2016 and 2020

Dario Bilardello, Subir K. Banerjee, Michael Volk & R Lee Penn
Magnetic, pXRD and Mössbauer metadata used in the cited study on alteration of synthetic ferrihydrite. All magnetic data was collected at the Institute for Rock Magnetism on a Quantum Design MPMS and comprises magnetic susceptibility (in-phase and out-of-phase) as a function of temperature (10-300K) and frequency (1-1000 Hz), hysteresis loops measured at 5K and 300 K, and magnetic remanence data (pTRM, temperature and AF demagnetized, the "goethetite test") collected between 400 and 10 K.

D2D 2016 Food Study

Hikaru H Peterson
The data contains responses to an interactive survey at the 2016 Minnesota State Fair (N=333), which was used to obtain measurements on food-related behavior and sociodemographic factors. The survey included a conjoint task to elicit food discard tendencies to construct the food waste proxy. The study considered cosmetic deterioration, date labels, implied shelf life, package size, and prices paid, in fresh, packaged spinach and ground beef products.

Validation of an automated shape-matching algorithm for biplane radiographic spine osteokinematics and radiostereometric analysis error quantification

Arin M Ellingson & Craig C Kage
Biplane radiography and associated shape-matching provides non-invasive, dynamic, 3D osteo- and arthrokinematic analysis. Due to the complexity of data acquisition, each system should be validated for the anatomy of interest. The purpose of this study was to assess our system’s acquisition methods and validate a custom, automated 2D/3D shape-matching algorithm relative to radiostereometric analysis (RSA) for the cervical and lumbar spine. Additionally, two sources of RSA error were examined via a Monte Carlo simulation: 1)...

Data from: Honeybee microbiome is stabilized in the presence of propolis

Perot Saelao, Renata S. Borba, Vincent Ricigliano, Marla Spivak & Michael Simone-Finstrom
Honey bees have developed many unique mechanisms to help ensure the proper maintenance of homeostasis within the hive. One specific method includes the collection of antimicrobial plant resins and wax to form propolis, which is deposited throughout the hive. Propolis is believed to play a significant role in reducing disease load in the colony due to its antimicrobial and antiseptic properties. However, little is known on how propolis may be interacting with the commensal bacteria...

Mitochondrial genomes and thousands of ultraconserved elements resolve the taxonomy and historical biogeography of the Euphonia and Chlorophonia finches (Passeriformes: Fringillidae)

Tyler Imfeld, Keith Barker & Robb Brumfield
Relationships of the Neotropical finches in the genera Euphonia and Chlorophonia (Fringillidae: Euphoniinae) have been clarified by recent molecular studies, but species-level relationships within this group have not been thoroughly addressed. In this study, we sampled specimens representing every recognized species of these genera, in addition to 2 outgroup taxa, and used target enrichment to sequence thousands of ultraconserved element (UCE) loci, as well as mitochondrial DNA reconstructed from off-target reads, from each specimen to...

A catastrophic tropical drought kills hydraulically vulnerable tree species

Jennifer Powers, German Vargas-G, Timothy Brodribb, Naomi Schwartz, Daniel Perez-Aviles, Chris Smith-Martin, Justin Becknell, Filippo Aureli, Roger Blanco, Erick Calderón-Morales, Julio César Calvo-Alvarado, Ana Julieta Calvo-Obando, María Marta Chavarría, Dorian Carvajal-Vanegas, César Dionisio Jiménez-Rodríguez, Evin Murillo Chacon, Colleen Schaffner, Leland Werden, Xiangtao Xu & David Medvigy
Drought-related tree mortality is now a widespread phenomenon predicted to increase in magnitude with climate change. However, the patterns of which species and trees are most vulnerable to drought, and the underlying mechanisms have remained elusive, in part due to the lack of relevant data and difficulty of predicting the location of catastrophic drought years in advance. We used long‐term demographic records and extensive databases of functional traits and distribution patterns to understand the responses...

Supplement to: Hippocampal neurochemical profile and glucose transport kinetics in patients with type 1 diabetes

Petr Bednařík, Pierre Gilles Henry, Ameer Khowaja, Nathan Rubin, Anjali Kumar, Dinesh Deelchand, Lynn Eberly, Elizabeth Seaquist, Gülin Öz & Moheet Amir
Context Longstanding type 1 diabetes (T1D) may lead to alterations in hippocampal neurochemical profile. Upregulation of hippocampal glucose transport as a result of recurrent exposure to hypoglycemia may preserve cognitive function during future hypoglycemia in subjects with T1D and impaired awareness of hypoglycemia (IAH). The effect of T1D on hippocampal neurochemical profile and glucose transport is unknown. Objective To test the hypothesis that hippocampal neurochemical composition is altered in T1D and glucose transport is upregulated...

Weights of gaur (Bos gaurus) and banteng (Bos javanicus) killed by tigers in Thailand

Supawat Khaewphakdee, Achara Simcharoen, Somphot Duangchantrasiri, Vijak Chimchome, Saksit Simcharoen & James Smith
The primary prey of tigers across much of Southeast Asia has been depleted, reducing the ability of already limited habitat to support tigers. To better understand the extent to which two of the largest prey species, gaur (Bos gaurus) and banteng (Bos javanicus), contribute to the tiger’s diet, we estimated the average size of these species killed by tigers. This information is needed to more accurately calculate biomass of these species in the tiger’s diet...

Data from: Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations

Alexandra Kaye Fraik, Mark Margres, Brendan Epstein, Soraia Barbosa, Menna Jones, Sarah Hendricks, Barbara Schonfeld, Amanda R. Stahlke, Anne Veillet, Rodrigo Hamede, Hamish McCallum, Elisa Lopez-Contreras, Samantha J Kallinen, Paul A Hohenlohe, Joanna Kelley & Andrew Storfer
Landscape genomics studies focus on identifying candidate genes under selection via spatial variation in abiotic environmental variables, but rarely by biotic factors such as disease. The Tasmanian devil (Sarcophilus harrisii) is found only on the environmentally heterogeneous island of Tasmania and is threatened with extinction by a nearly 100% fatal, transmissible cancer, devil facial tumor disease (DFTD). Devils persist in regions of long-term infection despite epidemiological model predictions of species’ extinction, suggesting possible adaptation to...

Nitrate removal and N2O production from upflow and downflow column woodchip bioreactors

Gary Feyereisen, Kurt Spokas, Jeffrey Strock, David Mulla, Andry Ranaivoson & Jeffrey Coulter
Woodchip denitrifying bioreactors (WDBR) reduce off-field tile drainage nitrogen (N) losses from agricultural fields. Limited evaluation exists regarding the influence of flow direction through WDBRs. Changing flow direction could reduce short circuiting. This study evaluated the dependency of nitrate-nitrogen removal and dissolved nitrous oxide (dN2O) production rates on vertical flow direction in triplicate column bioreactors at 12-h (without carbon dosing) and 2-h (with carbon dosing) hydraulic residence times. Results presented demonstrate that there was no...

Registration Year

  • 2020
    84

Resource Types

  • Dataset
    84

Affiliations

  • University of Minnesota
    84
  • University of California, Berkeley
    5
  • University of Guelph
    4
  • Agricultural Research Service
    4
  • University of Michigan-Ann Arbor
    3
  • Field Museum of Natural History
    3
  • United States Geological Survey
    3
  • University of California, Davis
    3
  • University of Washington
    2
  • Stanford University
    2