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- Creator:
- Martin, Tara L, Young, LR, Goldsteen, D, Nunamaker, EA, Reynolds, P, Thompson-Iritani, S, Thurston, SE, and LaFollette, MR
- Description:
- This dataset contains the results of a survey of mouse handling methods by personnel working with laboratory mice. The survey included questions about preferred handling methods, barriers to use of refined handling methods, and a knowledge quiz about refined mouse handling. Data was collected via Qualtrics survey as described in the methodology section. This dataset is associated with the following publication, accepted by PLOS One: PONE-D-23-01633R1 Title: Using refined methods to pick up mice: A survey benchmarking prevalence & beliefs about tunnel and cup handling Authors: Lauren Young, Donna Goldsteen, Elizabeth A. Nunamaker, Mark J. Prescott, Penny Reynolds, Sally Thompson-Iritani, Sarah E. Thurston, Tara L. Martin, Megan R. LaFollette
- Keyword:
- Mouse, Refined Handling, Tunnel Handling, Cup Handling, Laboratory Animal, and Animal Care
- Citation to related publication:
- Young LR, Goldsteen D, Nunamaker EA, Prescott MJ, Reynolds P, Thompson-Iritani S, Thurston SE, Martin TL, LaFollette MR. Using refined methods to pick up mice: A survey benchmarking prevalence & beliefs about tunnel and cup handling. PLOS ONE. 2023. In Press.
- Discipline:
- Science
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- Creator:
- Johnson, Jena E., Webb, Samuel M., Condit, Cailey B., Beukes, Nicolas J., and Fischer, Woodward W.
- Description:
- Manganese in the sedimentary record has been interpreted by many as a powerful redox proxy for paleoenvironments, and yet very little work has been done to ensure that the manganese-rich minerals in the rock record are actually recording primary signals. In the accompanying manuscript, we present an in-depth characterization of the manganese mineralogy from two correlated regions recording the Transvaal Supergroup in South Africa with markedly different alteration histories to investigate if there can be post-depositional emplacement of manganese-rich minerals. The data uploaded here are X-ray absorption spectra of (1) manganese standard minerals that were useful in our analyses and (2) minerals from an important well-characterized sample that may be useful as comparative standards in future studies.
- Keyword:
- manganese and X-ray absorption spectroscopy
- Citation to related publication:
- J.E. Johnson, S.M. Webb, C.B. Condit, N.J. Beukes, W.W. Fischer; Effects of metamorphism and metasomatism on manganese mineralogy: Examples from the Transvaal Supergroup. South African Journal of Geology doi: https://doi.org/10.25131/sajg.122.0034
- Discipline:
- Science
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Dataset: Models generated for the bioinformatic analysis of MPER/protein fusions binding to antibody
- Creator:
- Bylund, Tatsiana, Chuang, Gwo-Yu, Kwong, Peter, Lai, Yen-Ting, McIlwain, Benjamin, and Stockbridge, Randy B.
- Description:
- This project evaluated the binding of antibody fragments to membrane proteins fused to a short epitope sequence (“MPER”). This dataset includes atomic coordinates (.pdb files) for bioinformatic models of antibody fragment binding to an MPER epitope – membrane protein fusion.
- Keyword:
- MPER, cryo-EM fiducial, crystallography chaperone, and small membrane protein
- Citation to related publication:
- McIlwain, B. C., Erwin, A. L., Davis, A. R., Ben Koff, B., Chang, L., Bylund, T., Chuang, G.-Y., Kwong, P. D., Ohi, M. D., Lai, Y.-T., & Stockbridge, R. B. (2021). N-terminal Transmembrane-Helix Epitope Tag for X-ray Crystallography and Electron Microscopy of Small Membrane Proteins. Journal of Molecular Biology, 166909. https://doi.org/10.1016/j.jmb.2021.166909
- Discipline:
- Science
-
- Creator:
- Zhu, Jialei, Penner, Joyce E., Yu, Fangqun, Sillman, Sanford, Andreae, Meinrat O., and Coe, Hugh
- Description:
- The dataset contains the Fortran programs applied in the latest CESM/IMPACT model as well as the data created from this model, which are used in the referenced paper.
- Keyword:
- Organic nucleation and Radiative forcing
- Citation to related publication:
- Zhu, J. et al. Decrease in radiative forcing by organic aerosol nucleation, climate, and land use change. Nature Communications 10, 423 (24 January 2019). https://doi.org/10.1038/s41467-019-08407-7
- Discipline:
- Science
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- Creator:
- Dariya, Malyarenko, Tariq, Humera, Kushwaha, Aman, Mourad, Rami, Heist, Kevin, Chenevert, Thomas L, Ross, Brian D, Chen, Heang-Ping, and Hadjiiski, Lubomir
- Description:
- The 3D GRE MRI data for murine model of myelofbifrosis with expert segmentations of mouse tibia was used to train Attention UNET model to automate bone marrow segmentation for measurements of imaging biomarkers. This dataset consists of three archives: (1) containing the source MRI images in Meta-image-header (MHD) format with resulting segmentation labels by two experts and four UNET models with different training scenarios; (2) corresponding training models; and (3) deep-learning (DL)-based segmentation tools for application to future murine tibia MRI data. and The MHD images are an ITK compatible format that can be viewed in standard image viewer, like 3D Slicer. The image archive is structured with a directory tree that contains \"mouseID"\"scan-date"\"segmentaion-scenario"\. The "training model" archive containes DL-model labeled by the data subset, and "deployment" archive containes the DL-segmentation software.
- Keyword:
- deep-learning segmentation, preclinical MRI, murine tibia, and mouse model of myelofibrosis
- Citation to related publication:
- Kushwaha A, Mourad RF, Heist K, Tariq H, Chan HP, Ross BD, Chenevert TL, Malyarenko D, Hadjiiski LM. Improved Repeatability of Mouse Tibia Volume Segmentation in Murine Myelofibrosis Model Using Deep Learning. Tomography. 2023 Mar 7;9(2):589-602. doi: 10.3390/tomography9020048. PMID: 36961007; PMCID: PMC10037585. and https://github.com/dumichgh/MFJK1_Segmentation_MHDs
- Discipline:
- Health Sciences
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Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation
User Collection
- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- The outer epithelial layer of zebrafish retinae contains a crystalline array of cone photoreceptors, called the cone mosaic. As this mosaic grows by mitotic addition of new photoreceptors at the rim of the hemispheric retina, topological defects, called “Y-Junctions”, form to maintain approximately constant cell spacing. The generation of topological defects due to growth on a curved surface is a distinct feature of the cone mosaic not seen in other well-studied biological patterns like the R8 photoreceptor array in the _ Drosophila compound eye. Since defects can provide insight into cell-cell interactions responsible for pattern formation, here we characterize the arrangement of cones in individual Y-Junction cores (see Set of images for Figures 1 and 2 and 6 and Supplementary Figure 7) as well as the spatial distribution of Y-junctions across entire retinae (see Dataset for analyzing spatial distribution of Y-junctions in flat-mounted retinae). We find that for individual Y-junctions, the distribution of cones near the core corresponds closely to structures observed in physical crystals (see Set of images for Figures 1 and 2 and 6 and Supplementary Figure 7). In addition, Y-Junctions are organized into lines, called grain boundaries, from the retinal center to the periphery (see Dataset for analyzing spatial distribution of Y-junctions in flat-mounted retinae and Dataset for measuring tendency of Y-junctions to line up into grain boundaries during incorporation into retinae). In physical crystals, regardless of the initial distribution of defects, defects can coalesce into grain boundaries via the mobility of individual particles. By imaging in live fish, we demonstrate that grain boundaries in the cone mosaic instead appear during initial mosaic formation, without requiring defect motion (see Dataset for measuring tendency of Y-junctions to line up into grain boundaries during incorporation into retinae and Dataset for analyzing Y-junction motion in live fish retinae). Motivated by this observation, we show that a computational model of repulsive cell-cell interactions generates a mosaic with grain boundaries (see Code and example simulations of phase-field crystal model (for cone mosaic formation)). In contrast to paradigmatic models of fate specification in mostly motionless cell packings (see Code and accompanying input data for simulating lateral inhibition on motionless cell packing), this finding emphasizes the role of cell motion, guided by cell-cell interactions during differentiation, in forming biological crystals. Such a route to the formation of regular patterns may be especially valuable in situations, like growth on a curved surface, where the resulting long-ranged, elastic, effective interactions between defects can help to group them into grain boundaries.
- Keyword:
- zebrafish cone mosaic, lattice vectors, topological defects, tissue patterning, grain boundaries, lateral inhibition, photoconversion, phase-field crystal model, and defect motion
- Discipline:
- Science
7Works -
- Creator:
- Yao, Mengqi, Mathieu, Johanna L., Hiskens, Ian A., Molzahn, Daniel K., Koorehdavoudi, Kasra , and Roy, Sandip
- Description:
- The files include all the published paper and presentation source codes. Please install Matpower before running the code. The Matpower version is 5.1, which can be found in https://matpower.org/download/ Talks, papers, and poster in Deep Blue: http://hdl.handle.net/2027.42/150104
- Keyword:
- Demand response, Optimal power flow, Power system voltage stability, and Power system small signal stability L
- Citation to related publication:
- Yao, M., Molzahn, D. K., & Mathieu, J. L. (2019). An Optimal Power-Flow Approach to Improve Power System Voltage Stability Using Demand Response. IEEE Transactions on Control of Network Systems, 6(3), 1015–1025. https://doi.org/10.1109/TCNS.2019.2910455, Yao, M., Mathieu, J. L., & Molzahn, D. K. (2017). Using demand response to improve power system voltage stability margins. 2017 IEEE Manchester PowerTech, 1–6. https://doi.org/10.1109/PTC.2017.7980798 , Koorehdavoudi, K., Yao, M., & Mathieu, J. (2017). Using Demand Response to Shape the Fast Dynamics of the Bulk Power Network. https://www.semanticscholar.org/paper/Using-Demand-Response-to-Shape-the-Fast-Dynamics-of-Koorehdavoudi-Yao/6799c161744c29e7603e3601daa284ecc84788a8, Yao, M., Hiskens, I. A., & Mathieu, J. L. (2018). Improving Power System Voltage Stability by Using Demand Response to Maximize the Distance to the Closest Saddle-Node Bifurcation. 2018 IEEE Conference on Decision and Control (CDC), 2390–2395. https://doi.org/10.1109/CDC.2018.8619091 , and Yao, M., Molzahn, D. K., & Mathieu, J. L. (2017). The impact of load models in an algorithm for improving voltage stability via demand response. 2017 55th Annual Allerton Conference on Communication, Control, and Computing (Allerton), 149–156. https://doi.org/10.1109/ALLERTON.2017.8262731
- Discipline:
- Engineering
-
- Creator:
- de Oliveira, Stephanie and Nisbett, Richard E.
- Description:
- These studies assess the effect of social identity on judgement and are described in "Demographically diverse crowds are typically not much wiser than homogeneous crowds" (de Oliveira, S., & Nisbett, R. E. Proceedings of the National Academy of Sciences, 2018) and the article’s Supporting Information appendix. Some studies use a variety of questions to assess multiple social identity factors; the other studies are narrowed to particular social identity variables. Each study includes some type of estimation or prediction task, collects social identity variables, and asks participants to indicate their answer strategies. Study 1 is a trivia and prediction task based on football team fan identity. Study 2 reports on demographics plus political and religious identity and asks participants to predict vote percentages in presidential primaries. Study 3 participants estimate the percentage of Americans that support statements on various polarizing political views and give likelihood ratings for presidential candidates to win the Iowa caucus; a variety of identity questions are asked including political and religious identity. Study 4 includes demographics plus political and religious identity questions and asks participants to predict how the candidates would perform in the 2016 United States presidential election. Study 5 asks participants to guess the popularity rating of books that had either gender-specific or gender-neutral appeal, and also to rate their own interest in the books. Demographic-based social identity variables such as sex are included. Study 6 includes a wide variety of social identity variables and asks participants to estimate the likelihood of events occurring in the near future. Study 7 participants are from diverse national backgrounds and completed judgement tasks that predicted stock prices, Olympic performance, and news events outcomes. The data are generally interpretable when examined in conjunction with the target article. A new data file for Study 6 was uploaded on April 4, 2018 to include variables that were inadvertently left out of the original Study 6 file. A new data file for Study 7 was uploaded on April 6, 2018 to include variables that were inadvertently left out of the original Study 7 file. A codebook for this data set was added on April 6, 2018.
- Keyword:
- Judgment/Decision Making and Estimate aggregation
- Citation to related publication:
- Demographically diverse crowds are typically not much wiser than homogeneous crowds. Stephanie de Oliveira Richard E Nisbett Proceedings of the National Academy of Sciences of the United States of America vol. 115 issue 9 (2018) pp: 2066-2071. https://doi.org/10.1073/pnas.1717632115
- Discipline:
- Social Sciences
-
- Creator:
- Lin, Brian T. W.
- Description:
- This footage is an output of a USDOT-funded project titled "Development of Machine-Learning Models for Autonomous Vehicle Decisions on Weaving Sections of Freeway Ramps." It showcases an automated weaving maneuver within an augmented reality environment. During the demonstration, Mcity's automated vehicle navigates through a highway weaving section, making a lane change while interacting with a virtual vehicle. In this instance, Mcity's vehicle was operated by automated driving systems, which executed the lane change based on the detection for external environmental factors and parameter inputs received from the virtual vehicle.
- Discipline:
- Engineering
-
- Creator:
- Gradwohl, Kelsey M.
- Description:
- The data set includes one file: Dermatology Clerkship Chalk Talks Raw Dataset which is the raw data collected from the surveys. This raw data was then coded and scored with the following analysis. Objective knowledge questions were asked for each chalk talk which was scored by authors. A knowledge assessment score was calculated by adding the total number of points accumulated by the student, dividing it by the total number of points possible, and summarizing the score as a percentage. Pre- and post-talk knowledge assessment scores were compared for each chalk talk and for the entire curriculum using 2-tailed paired sample t-tests with statistical significance if p<0.05., Before and after each talk, students were asked how confident they felt differentiating conditions within each disease group. For the erythroderma and immunobullous talks, students were also asked how confident they felt working up the conditions. Answer choices were on a Likert scale ranging from 1 (not at all confident) to 5 (extremely confident). Pre- and post-chalk talk scores were summarized as means with standard deviations and compared using 2-tailed paired sample t-tests with statistical significance if p<0.05. , After each talk, students were asked about its efficacy in terms of enhancing their understanding of the diseases, providing a framework or approach to work-up, and facilitating interaction between student and teacher. Answer choices were on a Likert scale ranging from 1 (not at all effective) to 5 (extremely effective), and summarized as means with standard deviations. Students were asked for written feedback regarding what they liked about the talk and suggestions for improvement. Qualitative data were sorted into categories and scored by two independent raters (cohen's kappa =0.8)., and In the response Likert scale, "Not at all"=1, "Not so (much)"=2, "Somewhat"=3, "Very"=4, and "Extremely"=5.
- Keyword:
- Chalk talk, Dermatology clerkship, Dermatology education, Virtual learning, and Online learning
- Discipline:
- Health Sciences