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- Creator:
- Liemohn, Michael W., Ganushkina, Natalia Y., Welling, Daniel T., and Azari, Abigail R.
- Description:
- When we assess a model's ability to predict observed events, there are many equations to choose from, commonly called metrics, that quantify particular aspects of that data-model relationship. One set of such relationships are called skill scores, in which the value from a metric is compared against the same metric but from a different model, a reference model. For assessing event detection, there are several well-known skill scores, all of which are based on a particular reference model. It is shown here that this reference model is not ideal for assessing a new model's skill because it is, unfortunately, based in part on the new model's performance against the data. It is shown that these well-known skill scores have an ambiguous connection to the underlying metric score. Holding the metric value of the new model constant, there is a range of possible skill scores, and conversely, a given skill score value could result from a range of original metric values. It is recommended to stop using these famous skill scores and instead adopt one of several presented alternatives, all of which are fully independent of the new model. All of the plots for this study were created in Excel spreadsheets. The resulting plot files were then combined into the multi-panel figures for the paper using Adobe Illustrator. Specifically, the "xlsx" files were created using Excel Version 16.94 for the Mac and the "txt" files are were generated with Save As -> Tab Delimited Text format.
- Keyword:
- Skill scores, Heidke skill score, Peirce skill score, Gilbert skill score, event detection analysis, and data-model comparison
- Citation to related publication:
- Liemohn, Michael W., Ganushkina, Natalia Yu., Welling, Daniel T., & Azari, Abigail R. (2025). Defining an independent reference model for event detection skill scores. Submitted to AGU Advances, 21 February 2025, manuscript # 2025AV001xxx.
- Discipline:
- Science
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- Creator:
- Castro, Santiago, Azab, Mahmoud, Stroud, Jonathan C., Noujaim, Cristina, Wang, Ruoyao, Deng, Jia, and Mihalcea, Rada
- Description:
- We introduce LifeQA, a benchmark dataset for video question answering focusing on daily real-life situations. Current video question-answering datasets consist of movies and TV shows. However, it is well-known that these visual domains do not represent our day-to-day lives. Movies and TV shows, for example, benefit from professional camera movements, clean editing, crisp audio recordings, and scripted dialog between professional actors. While these domains provide a large amount of data for training models, their properties make them unsuitable for testing real-life question-answering systems. Our dataset, by contrast, consists of video clips that represent only real-life scenarios. We collect 275 such video clips and over 2.3k multiple-choice questions. In this paper, we analyze the challenging but realistic aspects of LifeQA and apply several state-of-the-art video question-answering models to provide benchmarks for future research. For more information, refer to https://lit.eecs.umich.edu/lifeqa/.
- Citation to related publication:
- Castro, S., Azab, M., Stroud, J., Noujaim, C., Wang, R., Deng, J., & Mihalcea, R. (2020, May). LifeQA: A real-life dataset for video question answering. In Proceedings of the Twelfth Language Resources and Evaluation Conference (pp. 4352-4358). https://aclanthology.org/2020.lrec-1.536/
- Discipline:
- Science
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Supporting data: Domain-agnostic predictions of nanoscale interactions in proteins and nanoparticles
- Creator:
- Saldinger, Jacob, Raymond, Matt, Elvati, Paolo, and Violi, Angela
- Description:
- The accurate and rapid prediction of generic nanoscale interactions is a challenging problem with broad applications. Much of biology functions at the nanoscale, and our ability to manipulate materials and purposefully engage biological machinery requires knowledge of nano-bio interfaces. While several protein-protein interaction models are available, they leverage protein-specific information, limiting their abstraction to other structures. Here, we present NeCLAS, a general, and rapid machine learning pipeline that predicts the location of nanoscale interactions, providing human-intelligible predictions. Two key aspects distinguish NeCLAS: coarse-grained representations, and the use of environmental features to encode the chemical neighborhood. We showcase NeCLAS with challenges for protein-protein, protein-nanoparticle and nanoparticle-nanoparticle systems, demonstrating that NeCLAS replicates computationally- and experimentally-observed interactions. NeCLAS outperforms current nanoscale prediction models, and it shows cross-domain validity, qualifying as a tool for basic research, rapid prototyping, and design of nanostructures., Software: - To reproduce all-atom molecular dynamics (MD) NAMD is required (version 2.14 or later is suggested). NAMD software and documentation can be found at https://www.ks.uiuc.edu/Research/namd/, - To reproduce coarse-grained MD simulations, LAMMPS (version 29 Sep 2021 - Update 2 or later is suggested). LAMMPS software and documentation can be found at https://www.lammps.org, - To rebuild free energy profiles, the PLUMED plugin (version 2.6) was used. PLUMED software and documentation can be found at https://www.plumed.org/ , and - To generate force matching potentials, the was used the OpenMSCG software was used. OpenMSCG software and documentation can be found at https://software.rcc.uchicago.edu/mscg/
- Keyword:
- Neural Networks, Proteins, Dimensionality Reduction, Nanoparticles, and Coarse-Graining
- Citation to related publication:
- https://www.biorxiv.org/content/10.1101/2022.08.09.503361v2
- Discipline:
- Science
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- Creator:
- Velez Rosado, Kevin I.
- Description:
- This collection includes computed tomography (CT) scans of cranial and post-cranial remains of Dolichochampsa minima (Crocodylia) from the Cretaceous of Bolivia. The specimen was collected by the auspice of Princeton University. The specimen is currently housed at the University of Michigan Museum of Paleontology.
- Keyword:
- Paleontology, Bolivia, Crocodylia, Cretaceous
- Citation to related publication:
- Kevin I. Vélez-Rosado, Olga I. Zalles-Grebetskaya, Jeffrey A. Wilson Mantilla, Blaire Schoene, Adam Maloof, and Bolton, Howes. 2025. New material of Dolichochampsa minima (Archosauria: Crocodylia) from the Cretaceous–Paleogene El Molino Formation of Bolivia sheds light on the early evolution of Gavialinae. Unpublished manuscript.
- Discipline:
- Science
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- Creator:
- Lydick, Nathanial and Deng, Hui
- Description:
- The included python scripts and Jupyter notebook generate and analyze the data.
- Keyword:
- Molecular Polariton, Dimensional Dependence, Tavis-Cummings Model, Strong Coupling, and Disorder
- Citation to related publication:
- N. Lydick, J. Hu, and H. Deng, "Dimensional dependence of a molecular-polariton mode number," J. Opt. Soc. Am. B 41, C247-C253 (2024). https://doi.org/10.1364/JOSAB.524026
- Discipline:
- Science
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- Creator:
- Nicholas, Benjamin and López-Fernández, Hernán
- Description:
- Understanding how continental assemblages have diversified can be difficult as they are products of extinction, biogeographic rearrangements, and changing environments over millions of years. Much of our knowledge of adaptive radiations stems from relatively recent, insular-like systems. However, increasing evidence supports the idea that adaptive radiations have a major role in hyper diverse continental radiations like Neotropical cichlids. This primarily riverine group has undergone adaptive diversification in many into ecologically, morphologically, and behaviorally complex lineages. Surprisingly, the macroevolutionary patterns of the entire pharyngeal jaw is relatively understudied in Neotropical cichlids. In this study we use µCT scans to characterize the entire pharyngeal system across Neotropical cichlids to test for signatures of adaptive radiation. We describe the morphological diversity of the upper and lower pharyngeal jaw, fit models of evolutionary divergence, and measure morphological disparity through time and among clades. Until now, studies of various axes of diversification in Cichlinae found a congruent signals an early bursts of divergence in multiple trait dimensions, however we find no evidence of an early burst in the pharyngeal jaws. We find evidence of highly specialized pharyngeal jaws establishing early in the continental radiation and also evidence of recent morphological divergence in the three major tribes of Cichlinae. Our results further highlight the necessity to study adaptively radiating lineages in multiple trait dimensions as some axes of diversification may be overlooked. and This dataset contains landmarked files of 204 landmarks for 95 species (one specimen per species) of Neotropical cichlids. Files are named "Genus_species.mrk.json". Landmark files can be read with the programming language R with the scripts found in the supplemental files of the cited paper, Nicholas and López-Fernandez 2024.
- Keyword:
- Landmarks, Cichlid, Pharyngeal Jaw, and Neotropics
- Citation to related publication:
- Benjamin Nicholas, Hernán López-Fernández, Analysis of the whole pharyngeal jaw adds nuance to the continental radiation of Neotropical cichlids, Evolutionary Journal of the Linnean Society, Volume 3, Issue 1, 2024, kzae038, https://doi.org/10.1093/evolinnean/kzae038
- Discipline:
- Science
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- Creator:
- Soni, Shirsh Lata and Akhavan-Tafti, Mojtaba
- Description:
- The Sun Radio Interferometer Space Experiment (SunRISE) Ground Radio Lab (GRL) is a Science, Technology, Engineering, Arts, and Mathematics (STEAM) project aiming to engage and train the next generations of scholars. To achieve this, the project 1) recruited students to participate in the design, development, and testing of a simple antenna kit that were sent to high schools nationwide free of charge, 2) prepared online, self-paced training modules to educate students on topics including radio astronomy and space weather, and 3) recruited high schools to host antenna installations, participate in regular data collection and analysis campaigns, and engage in monthly webinars and Q&A sessions with space industry experts. and For more information about SunRISE GRL, visit https://sunrise.umich.edu/
- Keyword:
- Solar Radio Bursts, SunRISE Ground Radio Lab (GRL), and Dual Dipole Antenna
- Citation to related publication:
- Mojtaba Akhavan-Tafti, Shirsh Soni, Charles Higgins, et al. SunRISE Ground Radio Lab. Authorea. September 26, 2024. Preprint. 10.22541/au.172737940.04250524/v1
- Discipline:
- Science
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- Creator:
- Su, Xue, Zhang, Youxue, Liu, Yang, and Holder, Robert M.
- Description:
- Volcanic glass beads on the Moon have traditionally been thought to only record volatile loss during pyroclastic eruptions. However, recent discoveries have shown that lunar orange glass beads, representing primitive high-Ti basalts, experienced both outgassing and in-gassing of volatile elements such as Na, K, Cu, and S. In this work, we examine lunar green glass beads from sample 15421 and 15366, representing primitive very-low-Ti basalts, for the distribution of Na, K and Cu using EMP analyses and LA-ICP-MS mapping. It is found that all studied lunar green beads show increased Na, K and Cu concentrations near bead surfaces, indicative of in-gassing. A quantitative model is developed to simulate the concentration evolution of Na and Cu in individual green glass beads during eruption and cooling. The presence of similar in-gassing diffusion profiles of volatile elements in beads from different eruptions indicates a common behavior of lunar volcanic gas. In addition to volatile in-gassing, LA-ICP-MS mapping of Na and K in one green bead from sample 15366 shows features suggesting collision of melt droplets during the fire-fountain eruption, revealing more details in the dynamic aspects of lunar fire-fountain eruptions. Compared to orange glass beads, the varying boundary conditions of green glass beads during formation may suggest that their eruption plume evolved and dissipated more rapidly, potentially linked to changes in the global lunar atmosphere.
- Keyword:
- Moon, Lunar green glass beads, Diffusion, Outgassing and in-gassing, Moderately volatile elements, Cooling time scales, and Lunar pyroclastic beads
- Discipline:
- Science
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- Creator:
- Haynes, Laura M, Holding, Matthew L, DiGiovanni, Hannah L, Siemieniak, David, and Ginsburg, David
- Description:
- This data set contains FASTQ files of PAI-1 sequence variants that differentially inhibit different target proteases. The software needed to analyze these files can be found at https://github.com/hayneslm/PAI-1_and_divergent_proteases.
- Keyword:
- serpins, serine proteases, coevolution, deep mutational scanning, fibrinolysis, phage display, protein-protein interactions, sequence space, DNA sequencing
- Citation to related publication:
- Haynes LM, Holding ML, DiGiovanni H, Siemieniak D, Ginsburg D. High-throughput amino acid-level characterization of the interactions of plasminogen activator inhibitor-1 with variably divergent proteases. bioRxiv [Preprint]. 2024 Sep 20:2024.09.16.612699. doi: 10.1101/2024.09.16.612699. PMID: 39345533; PMCID: PMC11429915.
- Discipline:
- Science
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- Creator:
- Kinsky, Nathaniel R
- Description:
- This research investigated how blocking protein synthesis with anisomycin disrupted hippocampal neural dynamics underlying memory consolidation. We tracked neural activity using calcium before (2 days), during, and after (1, 2, and 7 days after) memory formation and consolidation using calcium imaging. We blocked memory consolidation in a subset of mice via systemic injections of the protein synthesis inhibitor anisomycin following fear conditioning. We examined place field remapping and stability, the formation of freeze-predictive hippocampal ensemble activity, and analyzed how blocking memory consolidation influenced these two phenomena.
- Keyword:
- Hippocampus, Memory Consolidation, Calcium imaging, and Electrophysiology
- Citation to related publication:
- Erasable Hippocampal Neural Signatures Predict Memory Discrimination. Kinsky, N.R.; Orlin, D.O.; Ruesch, E. A.; Kim, B.; Coello, S.; Diba, K; Ramirez, S., Cell Reports, in press.
- Discipline:
- Science