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- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:124437A (CTENOTUS LABILLARDIERI) - Pectoral. Raw Dataset includes 1601 TIF images (each 610 x 1217 x 1 voxel at 0.0242240738844365 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:herps:124437A (CTENOTUS LABILLARDIERI) - Pectoral. Reconstructed Dataset includes 0.024224 TIF images (each 610 x 1217 x 1 voxel at 0.024224 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Reptilia, SAURIA, SCINCIDAE, CTENOTUS LABILLARDIERI, 1987192347, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987192347
- Discipline:
- Science
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- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:83484 (GLAPHYROMORPHUS GRACILIPES) - Pelvic. Raw Dataset includes 1601 TIF images (each 581 x 1088 x 1 voxel at 0.013893352621524 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:herps:83484 (GLAPHYROMORPHUS GRACILIPES) - Pelvic. Reconstructed Dataset includes 0.013893 TIF images (each 581 x 1088 x 1 voxel at 0.013893 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Reptilia, SAURIA, SCINCIDAE, GLAPHYROMORPHUS GRACILIPES, 1987103742, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987103742
- Discipline:
- Science
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- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:83484 (GLAPHYROMORPHUS GRACILIPES) - Pectoral. Raw Dataset includes 1601 TIF images (each 633 x 1601 x 1 voxel at 0.013893352621524 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:herps:83484 (GLAPHYROMORPHUS GRACILIPES) - Pectoral. Reconstructed Dataset includes 0.013893 TIF images (each 633 x 1601 x 1 voxel at 0.013893 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Reptilia, SAURIA, SCINCIDAE, GLAPHYROMORPHUS GRACILIPES, 1987103742, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987103742
- Discipline:
- Science
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- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:83439A (EULAMPRUS TYMPANUM) - Pelvic. Raw Dataset includes 1601 TIF images (each 753 x 1817 x 1 voxel at 0.0307810777841005 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:herps:83439A (EULAMPRUS TYMPANUM) - Pelvic. Reconstructed Dataset includes 0.030781 TIF images (each 753 x 1817 x 1 voxel at 0.030781 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Reptilia, SAURIA, SCINCIDAE, EULAMPRUS TYMPANUM, 1987159174, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987159174
- Discipline:
- Science
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- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:83439A (EULAMPRUS TYMPANUM) - Pectoral. Raw Dataset includes 1601 TIF images (each 744 x 1025 x 1 voxel at 0.0299168465519809 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:herps:83439A (EULAMPRUS TYMPANUM) - Pectoral. Reconstructed Dataset includes 0.029917 TIF images (each 744 x 1025 x 1 voxel at 0.029917 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Reptilia, SAURIA, SCINCIDAE, EULAMPRUS TYMPANUM, 1987159174, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987159174
- Discipline:
- Science
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- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:132451 (CTENOTUS DURICOLA) - Pelvic. Raw Dataset includes 1601 TIF images (each 468 x 1077 x 1 voxel at 0.0187617449426727 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:herps:132451 (CTENOTUS DURICOLA) - Pelvic. Reconstructed Dataset includes 0.018762 TIF images (each 468 x 1077 x 1 voxel at 0.018762 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Reptilia, SAURIA, SCINCIDAE, CTENOTUS DURICOLA, 1987073331, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987073331
- Discipline:
- Science
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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:
- Colón-Rodríguez, Stephanie, Liemohn, Michael, Raines, Jim, and Lepri, Susan T.
- Description:
- During its trajectory, Wind spent a significant amount of time in the magnetotail, where its SupraThermal Ion Composition Spectrometer (STICS) measured the mass and mass per charge of protons, alpha particles, and heavy ions with an energy/charge ratio up to 226 keV/e. Although STICS originally aimed to measure the abundance of these ion species in the solar wind, its measurements within the magnetosphere from 1995 to 2002 help us identify preferential entry between the different solar wind ion species. This study statistically analyzes how the ratio between solar wind heavy ions and alpha particles (Heavies Solar Wind / He2+) varies for different upstream conditions and locations within the magnetosphere: northward vs. southward Interplanetary Magnetic Field (IMF), low vs. high solar wind density (Nsw), low vs. high solar wind dynamic pressure (PDyn), slow vs. fast solar wind (Vsw), and dawn vs. dusk. Our results indicate that the HeaviesSolar Wind enter the magnetosphere more efficiently than He2+ during northward IMF and that the Heavies Solar Wind / He2+ ratios decrease during high PDyn. In addition, the Heavies Solar Wind / He2+ ratios exhibit a dawn-dusk asymmetry, highly skewed towards the dawn side for all upstream cases likely due to charge-exchange processes.
- Keyword:
- Magnetosphere, Wind STICS, Solar wind heavy ions, Alpha particles, and dawn-dusk asymmetry
- Citation to related publication:
- Colón-Rodríguez, S., Liemohn, M. W., Raines, J. M, & Lepri, S.T. (2024). Solar wind heavy ions and alpha particles within Earth’s magnetosphere and their variability with upstream conditions. Journal of Geophysical Research Space Physics. In preparation.
- 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