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  • Equilibrium configurations of hard polygons near the melting transition

    Work
    Creator: Sharon C. Glotzer, James Antonaglia, Michael Engel, Joshua A. Anderson, and Jaime A. Millan
    Description: This dataset was generated for our work "Shape and symmetry determine two-dimensional melting transitions of hard regular polygons". The dataset includes simulation results for 13 different polygons (equilateral triangles through regular tetradecagons and the 4-fold pentille) at a variety of packing fractions near the isotropic fluid to solid phase transition. Each trajectory contains the final 4 frames of each simulation run we conducted at system sizes of over one million particles. For each shape, there is a JSON file that describes the vertices of the polygon and a number of simulation trajectory files in GSD (https://bitbucket.org/glotzer/gsd) format. The trajectory files contain the positions and orientations of all the polygons at each frame, along with the simulation box size. The trajectory file names identify the packing fraction of that simulation run.
  • Regional Climate Model Simulations

    Work
    Creator: Steiner, A.L.
    Description: Land and water body surfaces play a critical role in hydroclimate by driving the transfer of moisture from the surface reservoir into the atmosphere. At the same time, atmospheric circulation transports moisture into and out of regions. To date, the hydroclimate impacts of the surface relative to large-scale transport and the variability over land and lake surfaces have not been quantified for the Great Lakes region despite known impacts of the lakes on the local climate. Using a Regional Climate Model (RegCM4) driven by three different boundary conditions, we simulate the hydroclimate of the Great Lakes region for a 23-year historical period. Observations and reanalysis products define land-lake-atmosphere feedbacks and are compared with the model. Reanalyses estimate up to 85% of the local precipitation is transported into the region from external sources. Seasonal RegCM4 precipitation biases reflect the biases in advective moisture flux, which depend on synoptic weather patterns such as the placement of troughs and ridges. In contrast with external sources, the land and lake surfaces account for over 30% of summer precipitation. However, RegCM4 underestimates the contribution of the land by 40% due to low evaporation rates as compared to the reanalyses. Observations at three flux towers indicate that evaporation and its drivers vary strongly by vegetation species, yet the lumped land cover description prescribed in the model neglects secondary species. Such species in the Great Lakes region have high evaporation potentials, and their absence in the model may account for the evaporation discrepancies. This highlights the need for greater complexity in the land cover classifications used in regional climate models to better capture land-atmosphere hydroclimate feedbacks. Over the lakes, one model member overestimates convective precipitation caused by enhanced evaporation under warm lake surface temperatures, highlighting the need for accurate representation of lake temperatures in the surface boundary condition. While external moisture sources dominate precipitation patterns, we conclude that the surface plays a substantial role in modifying regional hydroclimate.
  • Semantic-Based Document Retrieval Using Spatial Distributions of Concepts

    Work
    Creator: Ruas, Terry L. and Grosky, William I.
    Description: This dataset was used for a proof-of-concept of fixed lexical chain approach for semantic information retrieval.
  • Three-Dimensional Body Shape Manikins of Young Children for Child Restraint Design

    Work
    Creator: Jones, Monica L.H.
    Description: These manikins represent body shape models for children weighing 9 to 23 kg in a seated posture relevant to child restraint design. The design of child restraints is guided in part by anthropometric data describing the distributions of body dimensions of children. However, three-dimensional body shape data have not been available for children younger than three years of age. These manikins will be useful for assessing child accommodation in restraints. The SBSM can also provide guidance for the development of anthropomorphic test devices and computational models of child occupants. The sampled manikins were predicted for a range of torso length and body weight dimensions. The SBSM model was exercised for two torso lengths and nine body weights to obtain 18 body shapes. The 3D shape models can be downloaded in a standard mesh format (PLY). Each body shape is accompanied by predicted landmark locations and standard anthropometric variables.
  • A Video-Based Intervention to Improve Belt Fit

    Work
    Creator: Jones, Monica L.H.
    Description: This study evaluated the performance of a video-based intervention for improving the belt fit obtained by drivers. Previous laboratory studies have demonstrated that some drivers position their seat belts suboptimally. Specifically, the lap portion of the belt may be higher and farther forward relative to the pelvis than best practice, and the shoulder portion of the belt may be outboard or inboard of mid-shoulder. A video was developed to present the most important aspects of belt fit best practices, with emphasis on the lap belt. The video demonstrated how a seat belt should be routed with respect to an individual’s anatomy to ensure a proper fit. The three key belt fit concepts conveyed in the video were: 1) Lap belt low on hips, touching the thighs. 2) Shoulder belt crossing middle of collarbone. 3) Belt snug, as close to bones as possible. Additional context about the ability to achieve to good belt fit, such as opening a heavy coat or adjusting the height adjusters on the B-pillar behind the windows, were also presented.
  • Neighborhood effects : Information and Education Environment

    Work
    Creator: Veinot, Tiffany C, Data Driven Detroit, Gomez-Lopez, Iris N., Clarke, Phillipa J., Goodspeed, Robert, Okullo, Dolorence, and Reddy, Shruthi
    Description: The information and education environment refers to: 1) the presence of information infrastructures such as broadband Internet access and public libraries in a location; 2) a person’s proximity to information infrastructures and sources; 3) the distribution of information infrastructures, sources and in a specific location; and 4) exposure to specific messages (information content) within a specific location. Coverage for all data: 10-county Detroit-Warren-Ann Arbor Combined Statistical Area.
  • Simulation Parameters used in the Study titled "Efficient Estimation of Binding Free Energies between Peptides and an MHC Class II Molecule Using Coarse-Grained Molecular Dynamics Simulations with a Weighted Histogram Analysis Method"

    Work
    Creator: Huang, Wenjun, Wen, Fei, Huang, Ming, and Larson, Ronald G.
    Description: We provide the parameters used in Umbrella Sampling simulations reported in our study "Efficient Estimation of Binding Free Energies between Peptides and an MHC Class II Molecule Using Coarse-Grained Molecular Dynamics Simulations with a Weighted Histogram Analysis Method", namely the set positions and spring constants for each window in simulations. Two tables are provided. Table 1 lists the names of the peptides and their corresponding sequences. Table 2 lists the parameters. The abstract of our work is the following: We estimate the binding free energy between peptides and an MHC class II molecule using molecular dynamics (MD) simulations with Weighted Histogram Analysis Method (WHAM). We show that, owing to its more thorough sampling in the available computational time, the binding free energy obtained by pulling the whole peptide using a coarse-grained (CG) force field (MARTINI) is less prone to significant error induced by biased-sampling than using an atomistic force field (AMBER). We further demonstrate that using CG MD to pull 3-4 residue peptide segments while leaving the remain-ing peptide segments in the binding groove and adding up the binding free energies of all peptide segments gives robust binding free energy estimations, which are in good agreement with the experimentally measured binding affinities for the peptide sequences studied. Our approach thus provides a promising and computationally efficient way to rapidly and relia-bly estimate the binding free energy between an arbitrary peptide and an MHC class II molecule.
  • Growth factor signaling to mTORC1 by amino acid–laden macropinosomes

    Work
    Creator: Swanson, Joel A and Yoshida, Sei
    Description: The rapid activation of the mechanistic target of rapamycin complex-1 (mTORC1) by growth factors is increased by extracellular amino acids through yet-undefined mechanisms of amino acid transfer into endolysosomes. Because the endocytic process of macropinocytosis concentrates extracellular solutes into endolysosomes and is increased in cells stimulated by growth factors or tumor-promoting phorbol esters, we analyzed its role in amino acid–dependent activation of mTORC1. Here, we show that growth factor-dependent activation of mTORC1 by amino acids, but not glucose, requires macropinocytosis. In murine bone marrow–derived macrophages and murine embryonic fibroblasts stimulated with their cognate growth factors or with phorbol myristate acetate, activation of mTORC1 required an Akt-independent vesicular pathway of amino acid delivery into endolysosomes, mediated by the actin cytoskeleton. Macropinocytosis delivered small, fluorescent fluid-phase solutes into endolysosomes sufficiently fast to explain growth factor–mediated signaling by amino acids. Therefore, the amino acid–laden macropinosome is an essential and discrete unit of growth factor receptor signaling to mTORC1
  • Neighborhood Effects: Food Environment

    Work
    Creator: Veinot, Tiffany C., Data Driven Detroit, Goodspeed, Robert, Okullo, Dolorence, Gomez-Lopez, Iris N., and Yan, Xiang (Jacob)
    Description: The food environment is: 1) The physical presence of food that affects a person’s diet; 2) A person’s proximity to food store locations; 3) The distribution of food stores, food service, and any physical entity by which food may be obtained; or 4) A connected system that allows access to food. (Source: https://www.cdc.gov/healthyplaces/healthtopics/healthyfood/general.htm) Data included here concern: 1) Food access; and 2) Liquor access. Spatial Coverage for most data: 10-county Detroit-Warren-Ann Arbor Combined Statistical Area, Michigan, USA. See exception for grocery store data below.
  • Dataset for Understanding the benefit, risk and cost relationship for patients in the emergency department

    Work
    Creator: Meurer, William
    Description: Full analytical dataset with labels in SPSS