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- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen UMMZ:mammals:99103 (Desmodus rotundus) - Skull. Reconstructed Dataset includes 1464 TIF images (each 1443 x 1496 x 1 voxel at 0.023324 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen UMMZ:mammals:99103 (Desmodus rotundus) - Skull. Raw Dataset includes 3141 TIF images (each 1443 x 1496 x 1 voxel at 0.02332415 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Chiroptera, Phyllostomidae, Desmodus rotundus, 1987245972, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987245972
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen UMMZ:mammals:99103 (Desmodus rotundus) - WholeBody. Reconstructed Dataset includes 2000 TIF images (each 881 x 1326 x 1 voxel at 0.041457 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen UMMZ:mammals:99103 (Desmodus rotundus) - WholeBody. Raw Dataset includes 3141 TIF images (each 881 x 1326 x 1 voxel at 0.04145749 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Chiroptera, Phyllostomidae, Desmodus rotundus, 1987245972, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987245972
- Discipline:
- Science
-
Computed tomography voxel dataset for ummz:mammals:154691-Blarina brevicauda brevicauda-Skull-DiceCT
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:mammals:154691 (Blarina brevicauda brevicauda) - Skull. Reconstructed Dataset includes 1035 TIF images (each 1322 x 910 x 1 voxel at 0.027133 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:mammals:154691 (Blarina brevicauda brevicauda) - Skull. Raw Dataset includes 3141 TIF images (each 1322 x 910 x 1 voxel at 0.02713322 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Soricomorpha, Soricidae, Blarina brevicauda brevicauda, 1987241426, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987241426
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen UMMZ:mammals:112964 (Desmodus rotundus) - WholeBody. Raw Dataset includes 3141 TIF images (each 1047 x 1326 x 1 voxel at 0.04145749 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen UMMZ:mammals:112964 (Desmodus rotundus) - WholeBody. Reconstructed Dataset includes 2000 TIF images (each 1047 x 1326 x 1 voxel at 0.041457 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Chiroptera, Phyllostomidae, Desmodus rotundus, 1987291741, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987291741
- Discipline:
- Science
-
Computed tomography voxel dataset for ummz:mammals:154693-Blarina brevicauda brevicauda-Skull-DiceCT
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:mammals:154693 (Blarina brevicauda brevicauda) - Skull. Reconstructed Dataset includes 1219 TIF images (each 1013 x 1693 x 1 voxel at 0.033795 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:mammals:154693 (Blarina brevicauda brevicauda) - Skull. Raw Dataset includes 3141 TIF images (each 1013 x 1693 x 1 voxel at 0.03379497 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Soricomorpha, Soricidae, Blarina brevicauda brevicauda, 1987337719, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987337719
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:mammals:166889 (Blarina brevicauda kirtlandi) - WholeBody. Raw Dataset includes 3141 TIF images (each 877 x 1047 x 1 voxel at 0.03681702 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:mammals:166889 (Blarina brevicauda kirtlandi) - WholeBody. Reconstructed Dataset includes 1882 TIF images (each 877 x 1047 x 1 voxel at 0.036817 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Soricomorpha, Soricidae, Blarina brevicauda kirtlandi, 1987233799, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987233799
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:mammals:166889 (Blarina brevicauda kirtlandi) - Skull. Raw Dataset includes 3141 TIF images (each 1570 x 1531 x 1 voxel at 0.01919876 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:mammals:166889 (Blarina brevicauda kirtlandi) - Skull. Reconstructed Dataset includes 1978 TIF images (each 1570 x 1531 x 1 voxel at 0.019199 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Soricomorpha, Soricidae, Blarina brevicauda kirtlandi, 1987233799, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987233799
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:mammals:154691 (Blarina brevicauda brevicauda) - WholeBody. Raw Dataset includes 3141 TIF images (each 1187 x 834 x 1 voxel at 0.03976336 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:mammals:154691 (Blarina brevicauda brevicauda) - WholeBody. Reconstructed Dataset includes 2000 TIF images (each 1187 x 834 x 1 voxel at 0.039763 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Soricomorpha, Soricidae, Blarina brevicauda brevicauda, 1987241426, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987241426
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen UMMZ:mammals:112964 (Desmodus rotundus) - Skull. Raw Dataset includes 3141 TIF images (each 1554 x 1520 x 1 voxel at 0.02332415 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen UMMZ:mammals:112964 (Desmodus rotundus) - Skull. Reconstructed Dataset includes 1656 TIF images (each 1554 x 1520 x 1 voxel at 0.023324 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Chiroptera, Phyllostomidae, Desmodus rotundus, 1987291741, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987291741
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:mammals:154693 (Blarina brevicauda brevicauda) - WholeBody. Raw Dataset includes 3141 TIF images (each 1611 x 1121 x 1 voxel at 0.03882457 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:mammals:154693 (Blarina brevicauda brevicauda) - WholeBody. Reconstructed Dataset includes 1959 TIF images (each 1611 x 1121 x 1 voxel at 0.038825 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Soricomorpha, Soricidae, Blarina brevicauda brevicauda, 1987337719, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987337719
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:mammals:123037 (Tscherskia TRITON) - WholeBody. Raw Dataset includes 1601 TIF images (each 715 x 1288 x 1 voxel at 0.0493711582967448 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:mammals:123037 (Tscherskia TRITON) - WholeBody. Reconstructed Dataset includes 2000 TIF images (each 715 x 1288 x 1 voxel at 0.049371 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Rodentia, Cricetidae, Tscherskia TRITON, 1987305166, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987305166
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:mammals:111984 (Handleyomys ALFAROI ALFAROI) - WholeBody. Raw Dataset includes 1601 TIF images (each 815 x 1310 x 1 voxel at 0.0421497172804555 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:mammals:111984 (Handleyomys ALFAROI ALFAROI) - WholeBody. Reconstructed Dataset includes 2000 TIF images (each 815 x 1310 x 1 voxel at 0.042150 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Rodentia, Cricetidae, Handleyomys ALFAROI ALFAROI, 1987286466, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987286466
- Discipline:
- Science
-
- Creator:
- Stockbridge, Randy B. and Christian B. Macdonald
- Description:
- This data set includes text files (.csv files) for the bioinformatic annotation of SMR genes found in a dataset of phylogenetically diverse bacterial genomes. Bioinformatic analysis includes genome mining to identify SMR genes, prediction of the functional transporter subtype, and prediction of the direction of insertion in the bacterial membrane. Research overview: This bioinformatic dataset was prepared for a review on the structures, functions, and occurrence of Small Multidrug Resistance (SMR) Transporters. This dataset includes bioinformatic annotation of SMR genes identified in bacterial genomes from the Joint Genome Institute’s curated set of ~1000 Genomic Encyclopedia of Bacteria and Archaea (GEBA) genomes. The file GEBA_SMR_annotation.csv provides NCBI identification information (genome, species and chromosome information, locus tag, translation) and bioinformatic predictions of the SMR subtype and membrane insertion direction for each gene identified in the GEBA genome set. The file GEBA_SMR_species_table.csv has a separate entry for species in the GEBA genome set, along with the bioinformatic prediction of SMR subtype and membrane insertion direction for each SMR gene identified in the genome of that species. Dataset was generated by Christian B. Macdonald and Randy B. Stockbridge (Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48019) Generation of this dataset was supported by National Institutes of Health grants R35-GM128768 to Randy B. Stockbridge. Use and access: This dataset is provided as a .csv file (comma separated values) and can be read using any text editor or spreadsheet software such as Microsoft Excel.
- Citation to related publication:
- Burata OE, Yeh TJ, Macdonald CB, Stockbridge RB. (2022). Still rocking in the structural era: a molecular overview of the Small Multidrug Resistance transporters. Journal of Biological Chemistry. In press.
- Discipline:
- Science
-
- 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:
- Chung, Taewon , McClain, Taylor P. , Alonso-Mori, Roberto , Chollet, Matthieu , Deb, Aniruddha , Garcia-Esparza, Angel T. , Huang, Joel Ze En , Lamb, Ryan M. , Michocki, Lindsay B. , Reinhard, Marco , van Driel, Tim B. , Penner-Hahn, James E. , and Sension, Roseanne J.
- Description:
- UV-visible, X-ray absorption, and X-ray emission data used to characterize the dynamics of methyl cobalamin at low pH, so called "base off" configuration. Details of data collection and reduction are provided in the associated manuscript. Data files are all text files which contain tab-delimited columns of data corresponding to each figure in the manuscript
- Keyword:
- Ultrafast, X-ray, Transient absorption, cobalamin, vitamin B12, XAS, and XANES
- Citation to related publication:
- Chung, T., et al. (2024). "Ultrafast X-ray Absorption Spectroscopy Reveals Excited State Dynamics of B12 Coenzymes Controlled by the Axial Base". J. Phys. Chem. B. 2024, in press https://pubs.acs.org/doi/10.1021/acs.jpcb.3c07779
- Discipline:
- Science
-
- Creator:
- Xiantong Wang
- Description:
- Bursty bulk flows (BBFs) are identified as the fast earthward-propagating flows from magnetic reconnection in Earth's magnetotail. BBFs are related to particle energization process reported by satellite observations. For the first time, we use a novel numerical model that simulates kinetic physics directly in a global model. The energization of the electrons associated with BBF is demonstrated by the model. The electron velocity distribution functions (VDFs) extracted from multiple locations associated with BBF demonstrate good agreements with the observations. The energy-dependent electron pitch angle distribution at the leading part of the BBF can be explained by the enhancement of the local magnetic field.
- Discipline:
- Science
-
- Creator:
- Skinner, Katherine A., Vasudevan, Ram, Ramanagopal, Manikandasriram S., Ravi, Radhika, Carmichael, Spencer, and Buchan, Austin D.
- Description:
- This dataset is part of a collection created to facilitate research in the use of novel sensors for autonomous vehicle perception. , The dataset collection platform is a Ford Fusion vehicle with a roof-mounted novel sensing suite, which specifically consists of forward-facing stereo uncooled thermal cameras (FLIR 40640U050-6PAAX), event cameras (iniVation DVXplorer), monochrome cameras (FLIR BFS-PGE-16S2M), and RGB cameras (FLIR BFS-PGE-50S5C) time synchronized with ground truth poses from a high precision navigation system. , Further information and resources (such as software tools for converting, managing, and viewing data files) are available on the project website: https://umautobots.github.io/nsavp , and CHANGE NOTICE (January 2024): We identified an error in our timestamp post-processing procedure that caused all camera timestamps to be offset by the exposure time of one of the cameras. We corrected the error, applied the corrected post-processing, and reuploaded the corrected files. The change impacts all camera data files. Prior to the change, the timestamps between the cameras were synchronized with submillisecond accuracy, but the camera and ground truth pose timestamps were offset by up to 0.4 ms, 3 ms, and 15 ms in the afternoon, sunset, and night sequences, respectively. This amounted in up to ~0.25 meters of position error in the night sequences. For consistency, camera calibration was rerun with the corrected calibration sequence files. The camera calibration results have therefore been updated as well, although they have not changed significantly. Finally, we previously downsampled the frame data in the uploaded calibration seqeuence, but we decided to provide the full frame data in the reupload.
- Keyword:
- novel sensing, perception, autonomous vehicles, thermal sensing, neuromorphic imaging, and event cameras
- Citation to related publication:
- https://sites.google.com/umich.edu/novelsensors2023, https://github.com/umautobots/nsavp_tools, and https://umautobots.github.io/nsavp
- Discipline:
- Engineering
-
- Creator:
- Skinner, Katherine A., Vasudevan, Ram, Ramanagopal, Manikandasriram S., Ravi, Radhika, Carmichael, Spencer, and Buchan, Austin D.
- Description:
- This dataset is part of a collection created to facilitate research in the use of novel sensors for autonomous vehicle perception. , The dataset collection platform is a Ford Fusion vehicle with a roof-mounted novel sensing suite, which specifically consists of forward-facing stereo uncooled thermal cameras (FLIR 40640U050-6PAAX), event cameras (iniVation DVXplorer), monochrome cameras (FLIR BFS-PGE-16S2M), and RGB cameras (FLIR BFS-PGE-50S5C) time synchronized with ground truth poses from a high precision navigation system. , Further information and resources (such as software tools for converting, managing, and viewing data files) are available on the project website: https://umautobots.github.io/nsavp , and CHANGE NOTICE (January 2024): We identified an error in our timestamp post-processing procedure that caused all camera timestamps to be offset by the exposure time of one of the cameras. We corrected the error, applied the corrected post-processing, and reuploaded the corrected files. The change impacts all camera data files. Prior to the change, the timestamps between the cameras were synchronized with submillisecond accuracy, but the camera and ground truth pose timestamps were offset by up to 0.4 ms, 3 ms, and 15 ms in the afternoon, sunset, and night sequences, respectively. This amounted in up to ~0.25 meters of position error in the night sequences. For consistency, camera calibration was rerun with the corrected calibration sequence files. The camera calibration results have therefore been updated as well, although they have not changed significantly. Finally, we previously downsampled the frame data in the uploaded calibration seqeuence, but we decided to provide the full frame data in the reupload.
- Keyword:
- novel sensing, perception, autonomous vehicles, thermal sensing, neuromorphic imaging, and event cameras
- Citation to related publication:
- https://sites.google.com/umich.edu/novelsensors2023, https://github.com/umautobots/nsavp_tools, and https://umautobots.github.io/nsavp
- Discipline:
- Engineering
-
- Creator:
- Skinner, Katherine A., Vasudevan, Ram, Ramanagopal, Manikandasriram S., Ravi, Radhika, Carmichael, Spencer, and Buchan, Austin D.
- Description:
- This dataset is part of a collection created to facilitate research in the use of novel sensors for autonomous vehicle perception. , The dataset collection platform is a Ford Fusion vehicle with a roof-mounted novel sensing suite, which specifically consists of forward-facing stereo uncooled thermal cameras (FLIR 40640U050-6PAAX), event cameras (iniVation DVXplorer), monochrome cameras (FLIR BFS-PGE-16S2M), and RGB cameras (FLIR BFS-PGE-50S5C) time synchronized with ground truth poses from a high precision navigation system. , Further information and resources (such as software tools for converting, managing, and viewing data files) are available on the project website: https://umautobots.github.io/nsavp , and CHANGE NOTICE (January 2024): We identified an error in our timestamp post-processing procedure that caused all camera timestamps to be offset by the exposure time of one of the cameras. We corrected the error, applied the corrected post-processing, and reuploaded the corrected files. The change impacts all camera data files. Prior to the change, the timestamps between the cameras were synchronized with submillisecond accuracy, but the camera and ground truth pose timestamps were offset by up to 0.4 ms, 3 ms, and 15 ms in the afternoon, sunset, and night sequences, respectively. This amounted in up to ~0.25 meters of position error in the night sequences. For consistency, camera calibration was rerun with the corrected calibration sequence files. The camera calibration results have therefore been updated as well, although they have not changed significantly. Finally, we previously downsampled the frame data in the uploaded calibration seqeuence, but we decided to provide the full frame data in the reupload.
- Keyword:
- novel sensing, perception, autonomous vehicles, thermal sensing, neuromorphic imaging, and event cameras
- Citation to related publication:
- https://sites.google.com/umich.edu/novelsensors2023, https://github.com/umautobots/nsavp_tools, and https://umautobots.github.io/nsavp
- Discipline:
- Engineering
-
- Creator:
- Skinner, Katherine A., Vasudevan, Ram, Ramanagopal, Manikandasriram S., Ravi, Radhika, Carmichael, Spencer, and Buchan, Austin D.
- Description:
- This dataset is part of a collection created to facilitate research in the use of novel sensors for autonomous vehicle perception. , The dataset collection platform is a Ford Fusion vehicle with a roof-mounted novel sensing suite, which specifically consists of forward-facing stereo uncooled thermal cameras (FLIR 40640U050-6PAAX), event cameras (iniVation DVXplorer), monochrome cameras (FLIR BFS-PGE-16S2M), and RGB cameras (FLIR BFS-PGE-50S5C) time synchronized with ground truth poses from a high precision navigation system. , Further information and resources (such as software tools for converting, managing, and viewing data files) are available on the project website: https://umautobots.github.io/nsavp , and CHANGE NOTICE (January 2024): We identified an error in our timestamp post-processing procedure that caused all camera timestamps to be offset by the exposure time of one of the cameras. We corrected the error, applied the corrected post-processing, and reuploaded the corrected files. The change impacts all camera data files. Prior to the change, the timestamps between the cameras were synchronized with submillisecond accuracy, but the camera and ground truth pose timestamps were offset by up to 0.4 ms, 3 ms, and 15 ms in the afternoon, sunset, and night sequences, respectively. This amounted in up to ~0.25 meters of position error in the night sequences. For consistency, camera calibration was rerun with the corrected calibration sequence files. The camera calibration results have therefore been updated as well, although they have not changed significantly. Finally, we previously downsampled the frame data in the uploaded calibration seqeuence, but we decided to provide the full frame data in the reupload.
- Keyword:
- novel sensing, perception, autonomous vehicles, thermal sensing, neuromorphic imaging, and event cameras
- Citation to related publication:
- https://sites.google.com/umich.edu/novelsensors2023, https://github.com/umautobots/nsavp_tools, and https://umautobots.github.io/nsavp
- Discipline:
- Engineering
-
- Creator:
- Skinner, Katherine A., Vasudevan, Ram, Ramanagopal, Manikandasriram S., Ravi, Radhika, Carmichael, Spencer, and Buchan, Austin D.
- Description:
- This dataset is part of a collection created to facilitate research in the use of novel sensors for autonomous vehicle perception. , The dataset collection platform is a Ford Fusion vehicle with a roof-mounted novel sensing suite, which specifically consists of forward-facing stereo uncooled thermal cameras (FLIR 40640U050-6PAAX), event cameras (iniVation DVXplorer), monochrome cameras (FLIR BFS-PGE-16S2M), and RGB cameras (FLIR BFS-PGE-50S5C) time synchronized with ground truth poses from a high precision navigation system. , Further information and resources (such as software tools for converting, managing, and viewing data files) are available on the project website: https://umautobots.github.io/nsavp , and CHANGE NOTICE (January 2024): We identified an error in our timestamp post-processing procedure that caused all camera timestamps to be offset by the exposure time of one of the cameras. We corrected the error, applied the corrected post-processing, and reuploaded the corrected files. The change impacts all camera data files. Prior to the change, the timestamps between the cameras were synchronized with submillisecond accuracy, but the camera and ground truth pose timestamps were offset by up to 0.4 ms, 3 ms, and 15 ms in the afternoon, sunset, and night sequences, respectively. This amounted in up to ~0.25 meters of position error in the night sequences. For consistency, camera calibration was rerun with the corrected calibration sequence files. The camera calibration results have therefore been updated as well, although they have not changed significantly. Finally, we previously downsampled the frame data in the uploaded calibration seqeuence, but we decided to provide the full frame data in the reupload.
- Keyword:
- novel sensing, perception, autonomous vehicles, thermal imaging, neuromorphic imaging, and event cameras
- Citation to related publication:
- https://sites.google.com/umich.edu/novelsensors2023, https://github.com/umautobots/nsavp_tools, and https://umautobots.github.io/nsavp
- Discipline:
- Engineering
-
- Creator:
- Skinner, Katherine A., Vasudevan, Ram, Ramanagopal, Manikandasriram S., Ravi, Radhika, Carmichael, Spencer, and Buchan, Austin D.
- Description:
- This dataset is part of a collection created to facilitate research in the use of novel sensors for autonomous vehicle perception. , The dataset collection platform is a Ford Fusion vehicle with a roof-mounted novel sensing suite, which specifically consists of forward-facing stereo uncooled thermal cameras (FLIR 40640U050-6PAAX), event cameras (iniVation DVXplorer), monochrome cameras (FLIR BFS-PGE-16S2M), and RGB cameras (FLIR BFS-PGE-50S5C) time synchronized with ground truth poses from a high precision navigation system. , Further information and resources (such as software tools for converting, managing, and viewing data files) are available on the project website: https://umautobots.github.io/nsavp , and CHANGE NOTICE (January 2024): We identified an error in our timestamp post-processing procedure that caused all camera timestamps to be offset by the exposure time of one of the cameras. We corrected the error, applied the corrected post-processing, and reuploaded the corrected files. The change impacts all camera data files. Prior to the change, the timestamps between the cameras were synchronized with submillisecond accuracy, but the camera and ground truth pose timestamps were offset by up to 0.4 ms, 3 ms, and 15 ms in the afternoon, sunset, and night sequences, respectively. This amounted in up to ~0.25 meters of position error in the night sequences. For consistency, camera calibration was rerun with the corrected calibration sequence files. The camera calibration results have therefore been updated as well, although they have not changed significantly. Finally, we previously downsampled the frame data in the uploaded calibration seqeuence, but we decided to provide the full frame data in the reupload.
- Keyword:
- novel sensing, perception, autonomous vehicles, thermal sensing, neuromorphic imaging, and event cameras
- Citation to related publication:
- https://sites.google.com/umich.edu/novelsensors2023, https://github.com/umautobots/nsavp_tools, and https://umautobots.github.io/nsavp
- Discipline:
- Engineering
-
- Creator:
- Sheppard, Anja, Sethuraman, Advaith V, Bagoren, Onur, Pinnow, Christopher, Anderson, Jamey, Havens, Timothy C, and Skinner, Katherine A
- Description:
- The AI4Shipwrecks dataset contains sidescan sonar images of shipwrecks and corresponding binary labels collected during 2022 and 2023 at the NOAA Thunder Bay National Marine Sanctuary in Alpena, MI. The data collection platform was an Iver3 Autonomous Underwater Vehicle (AUV) equipped with an EdgeTech 2205 dual-frequency ultra-high resolution sidescan sonar and 3D bathymetric system. The labels were compiled from reference labels created by experts in marine archaeology. The intended use of this dataset is to encourage development of semantic segmentation, object detection, or anomaly detection algorithms in the computer vision field. Comparisons of state-of-the-art segmentation networks on our dataset are shown in the paper. , The file structure is organized as described in the README.txt file, where images in 'images' directories are the waterfall product of sidescan sonar surveys, and images in 'labels' directories are binary representations of expert labels. Images across the 'images' and 'labels' directories are correlated by having identical filenames. In the label images, a pixel value of '0' represents the non-shipwreck/other class and '1' represents the shipwreck class for the correspondingly named image (<wreck_name>_<##>.png) in the images directory. , and The project webpage can be found at: https://umfieldrobotics.github.io/ai4shipwrecks/
- Keyword:
- machine learning, computer vision, field robotics, marine robotics, underwater robotics, sidescan sonar, semantic segmentation, and object detection
- Discipline:
- Engineering
-
- Creator:
- Hawes, Jason K, Goldstein, Benjamin P. , Newell, Joshua P. , Dorr, Erica , Caputo, Silvio , Fox-Kämper, Runrid , Grard, Baptiste , Ilieva, Rositsa T. , Fargue-Lelièvre, Agnès , Poniży, Lidia , Schoen, Victoria , Specht, Kathrin , and Cohen, Nevin
- Description:
- Urban agriculture (UA) is a widely proposed strategy to make cities and urban food systems more sustainable. However, its carbon footprint remains understudied. In fact, the few existing studies suggest that UA may be worse for the climate than conventional agriculture. This is the first large-scale study to resolve this uncertainty across cities and types of UA, employing citizen science at 73 UA sites in Europe and the United States to compare UA products to food from conventional farms. The results reveal that food from UA is six times as carbon intensive as conventional agriculture (420g vs 70g CO2 equivalent per serving). Some UA crops (e.g., tomatoes) and sites (e.g., 25% of individually-managed gardens), however, outperform conventional agriculture. These exceptions suggest that UA practitioners can reduce their climate impacts by cultivating crops that are typically greenhouse grown or air-freighted, maintaining UA sites for many years, and leveraging waste as inputs.This database contains the necessary reference material to trace the path of our analysis from raw garden data to carbon footprint and nutrient results. It also contains the final results of the analyses in various extended forms not available in the publication. For more information, see manuscript at link below. (Introduction partially quoted from Hawes et al., 2023)
- Citation to related publication:
- Hawes, J. K., Goldstein, B. P., Newell, J. P., Dorr, E., Caputo, S., Fox-Kämper, R., Grard, B., Ilieva, R. T., Fargue-Lelièvre, A., Poniży, L., Schoen, V., Specht, K., & Cohen, N. (2024). Comparing the carbon footprints of urban and conventional agriculture. Nature Cities, 1–10. https://doi.org/10.1038/s44284-023-00023-3
- Discipline:
- Engineering
-
- Creator:
- Srodawa, Kristy, Cerda, Peter A, Davis Rabosky, Alison R, and Crowe-Riddell, Jenna M
- Description:
- Snake venom research has historically focused on front-fanged species (Viperidae and Elapidae), limiting our knowledge of venom evolution in rear-fanged snakes across their ecologically-diverse phylogeny. Three finger toxins (3FTxs) are a known neurotoxic component in the venoms of some rear-fanged snakes (Colubrinae, Colubridae), but it is unclear how prevalent 3FTxs are both in expression within venom glands and more broadly among colubrine species. Here, we used a transcriptomic approach to characterize the venom expression profiles of four species of colubrine snakes from Neotropics that were dominated by 3FTx expression (in the genera Chironius, Oxybelis, Rhinobothryum, and Spilotes) and reconstructed the gene trees of 3FTxs. Overall, our results highlight the importance of exploring the venoms of understudied species in reconstructing the full evolutionary history of toxins across the tree of life.
- Keyword:
- snake venom, neurotoxin, molecular evolution, gene families, and opisthoglyphous
- Citation to related publication:
- Srodawa, K., Cerda, P.A., Davis Rabosky, A.R., Crowe-Riddell, J.M. Evolution of Three Finger Toxin Genes in Neotropical Colubrine Snakes (Colubridae). Toxins 2023, 15(9), 523; https://doi.org/10.3390/toxins15090523
- Discipline:
- Science
-
- Creator:
- Skinner, Katherine A., Vasudevan, Ram, Ramanagopal, Manikandasriram S., Ravi, Radhika, Carmichael, Spencer, and Buchan, Austin D.
- Description:
- This dataset is part of a collection created to facilitate research in the use of novel sensors for autonomous vehicle perception., The dataset collection platform is a Ford Fusion vehicle with a roof-mounted novel sensing suite, which specifically consists of forward-facing stereo uncooled thermal cameras (FLIR 40640U050-6PAAX), event cameras (iniVation DVXplorer), monochrome cameras (FLIR BFS-PGE-16S2M), and RGB cameras (FLIR BFS-PGE-50S5C) time synchronized with ground truth poses from a high precision navigation system. , and Further information and resources (such as software tools for converting, managing, and viewing data files) are available on the project website: https://umautobots.github.io/nsavp
- Keyword:
- novel sensing, perception, autonomous vehicles, thermal sensing, neuromorphic imaging, and event cameras
- Citation to related publication:
- https://umautobots.github.io/nsavp, https://github.com/umautobots/nsavp_tools, and https://sites.google.com/umich.edu/novelsensors2023
- Discipline:
- Engineering
-
- Creator:
- Skinner, Katherine A., Vasudevan, Ram, Ramanagopal, Manikandasriram S., Ravi, Radhika, Carmichael, Spencer, and Buchan, Austin D.
- Description:
- This dataset is part of a collection created to facilitate research in the use of novel sensors for autonomous vehicle perception., The dataset collection platform is a Ford Fusion vehicle with a roof-mounted novel sensing suite, which specifically consists of forward-facing stereo uncooled thermal cameras (FLIR 40640U050-6PAAX), event cameras (iniVation DVXplorer), monochrome cameras (FLIR BFS-PGE-16S2M), and RGB cameras (FLIR BFS-PGE-50S5C) time synchronized with ground truth poses from a high precision navigation system. , and Further information and resources (such as software tools for converting, managing, and viewing data files) are available on the project website: https://umautobots.github.io/nsavp
- Keyword:
- novel sensing, perception, autonomous vehicles, thermal sensing, neuromorphic imaging, and event cameras
- Citation to related publication:
- https://umautobots.github.io/nsavp, https://github.com/umautobots/nsavp_tools, and https://sites.google.com/umich.edu/novelsensors2023
- Discipline:
- Engineering
-
- Creator:
- Skinner, Katherine A., Vasudevan, Ram, Ramanagopal, Manikandasriram S., Ravi, Radhika, Carmichael, Spencer, and Buchan, Austin D.
- Description:
- This dataset is part of a collection created to facilitate research in the use of novel sensors for autonomous vehicle perception. , The dataset collection platform is a Ford Fusion vehicle with a roof-mounted novel sensing suite, which specifically consists of forward-facing stereo uncooled thermal cameras (FLIR 40640U050-6PAAX), event cameras (iniVation DVXplorer), monochrome cameras (FLIR BFS-PGE-16S2M), and RGB cameras (FLIR BFS-PGE-50S5C) time synchronized with ground truth poses from a high precision navigation system. , and Further information and resources (such as software tools for converting, managing, and viewing data files) are available on the project website: https://umautobots.github.io/nsavp
- Keyword:
- novel sensing, perception, autonomous vehicles, thermal sensing, neuromorphic imaging, and event cameras
- Citation to related publication:
- https://umautobots.github.io/nsavp, https://github.com/umautobots/nsavp_tools, and https://sites.google.com/umich.edu/novelsensors2023
- Discipline:
- Engineering
-
- Creator:
- Skinner, Katherine A., Vasudevan, Ram, Ramanagopal, Manikandasriram S., Ravi, Radhika, Carmichael, Spencer, and Buchan, Austin D.
- Description:
- This dataset is part of a collection created to facilitate research in the use of novel sensors for autonomous vehicle perception. , The dataset collection platform is a Ford Fusion vehicle with a roof-mounted novel sensing suite, which specifically consists of forward-facing stereo uncooled thermal cameras (FLIR 40640U050-6PAAX), event cameras (iniVation DVXplorer), monochrome cameras (FLIR BFS-PGE-16S2M), and RGB cameras (FLIR BFS-PGE-50S5C) time synchronized with ground truth poses from a high precision navigation system. , Further information and resources (such as software tools for converting, managing, and viewing data files) are available on the project website: https://umautobots.github.io/nsavp , and CHANGE NOTICE (January 2024): We identified an error in our timestamp post-processing procedure that caused all camera timestamps to be offset by the exposure time of one of the cameras. We corrected the error, applied the corrected post-processing, and reuploaded the corrected files. The change impacts all camera data files. Prior to the change, the timestamps between the cameras were synchronized with submillisecond accuracy, but the camera and ground truth pose timestamps were offset by up to 0.4 ms, 3 ms, and 15 ms in the afternoon, sunset, and night sequences, respectively. This amounted in up to ~0.25 meters of position error in the night sequences. For consistency, camera calibration was rerun with the corrected calibration sequence files. The camera calibration results have therefore been updated as well, although they have not changed significantly. Finally, we previously downsampled the frame data in the uploaded calibration seqeuence, but we decided to provide the full frame data in the reupload.
- Keyword:
- novel sensing, perception, autonomous vehicles, thermal sensing, neuromorphic imaging, and event cameras
- Citation to related publication:
- https://sites.google.com/umich.edu/novelsensors2023, https://github.com/umautobots/nsavp_tools, and https://umautobots.github.io/nsavp
- Discipline:
- Engineering
-
- Creator:
- Zhang, Yingxiao MI
- Description:
- We developed a new model framework based on WRF-Chem, simulating primary biological aerosol particle emissions and their interaction with clouds. We have designed different sensitivity tests to evaluate the effects of pollen and sub-pollen particles (SPPs), respectively. Our results show that SPPs have a larger effect on cloud microphysics and precipitation than whole pollen grains.
- Keyword:
- Aerosol-cloud interactions, Primary biological aerosol particles, Ice nucleating particles, Microphyscis scheme, and Pollen
- Discipline:
- Science
-
Novel Sensors for Autonomous Vehicle Perception
User Collection- Creator:
- Skinner, Katherine A, Vasudevan, Ram, Ramanagopal, Manikandasriram S, Ravi, Radhika, Buchan, Austin D, and Carmichael, Spencer
- Description:
- The Novel Sensors for Autonomous Vehicle Perception Collection of datasets are sequences collected with an autonomous vehicle platform including data from novel sensors. The dataset collection platform is a Ford Fusion vehicle with a roof-mounted novel sensing suite, which specifically consists of forward-facing stereo uncooled thermal cameras (FLIR 40640U050-6PAAX), event cameras (iniVation DVXplorer), monochrome cameras (FLIR BFS-PGE-16S2M), and RGB cameras (FLIR BFS-PGE-50S5C) time synchronized with ground truth poses from a high precision navigation system. Sequences include ~8 km routes, driven repeatedly under varying lighting conditions and/or opposing viewpoints. Further information and resources are available on the project website: https://umautobots.github.io/nsavp
- Keyword:
- novel sensing, perception, autonomous vehicles, thermal sensing, neuromorphic imaging, and event cameras
- Citation to related publication:
- https://umautobots.github.io/nsavp, https://github.com/umautobots/nsavp_tools, and https://sites.google.com/umich.edu/novelsensors2023
- Discipline:
- Engineering
12Works -
- Creator:
- Cevidanes, Lucia
- Description:
- Image Pre-Processing To allow reliable detection and comparison of changes between several individuals or within the same individual at different time points, before extracting the quantitative bone texture/morphometry features, all hr-CBCT scans were pre-processed using validated protocols. Extraction of Trabecular Bone Texture-based and Morphometry Imaging Features Using the “crop-volume” tool in 3D Slicer, a rectangular shaped volume of interest (VOI) was cropped from the trabecular bone in the mandibular condyles and the articular fossa. Then, using the average minimum and maximum intensity values of all VOIs, we standardized the grey level intensities of the VOIs to eliminate inaccuracies of textural features calculation and possible dependency on the global characteristics of the images. Lastly, imaging markers were extracted from the standardized VOIs using “BoneTexture” module in 3D-slicer. Measurement of the 3D Articular Joint Space To assess the progression/improvement of osteoarthritic changes in the affected individuals, we measured the 3D superior joint space. We pre-labelled two landmarks in the sagittal view of the oriented CBCT scans: on the most superior point of the condyle and on the opposing surface of the articular fossa. To avoid biasing the landmarks’ placements, pre-labelling was performed simultaneously on T1 and T2 scans, using two independent windows in ITK-SNAP. After the volumetric reconstruction of the identified landmarks, linear measurements were obtained in millimeters using the Q3DC tool in 3D Slicer. Three-dimensional Shape Analyses and Quantification of Remodeling in the Condyles SPHARM-PDM software was used to compute the correspondence across 4002 surface points among all condyles. The output point-based models displayed color-coded maps that enabled visual evaluation of consistent parametrization of all condyles. An average condyle shape for the TMJ OA and control groups was calculated through propagation of original surface point correspondences across all stages of deformations and averaging the condyle surface meshes. For visualization of the 3D qualitative changes of the average models within the same group at different time points or among different groups, semi-transparent overlays were created using 3D Slicer software. The vector differences were presented on the condyle surfaces, scaled according to the magnitude of difference, and pointing towards the direction of bone change. For quantification of remodeling in the condyles, calculation of signed distances across condyles surface meshes reflected the quantitative bone changes in the TMJ OA and control samples. To quantify regional bone changes across the lateral and anterior surfaces of the condyles, we used the Pick ‘n Paint tool in 3D Slicer to propagate regional surface points to the corresponding regions of shapes across all subjects and time points.
- Keyword:
- Degenerative joint disease, Temporomandibular joint osteoarthritis, TMJ OA, Machine learning, Prognosis
- Discipline:
- Health Sciences
-
- Creator:
- Lori, Jody R., Moyer, Cheryl, Lockhart, Nancy, Zielinski, Ruth E., Kukula, Vida, Apetorgbor, Veronica, Awini, Elizabeth, Badu-Gyan, Georgina, and Williams, John
- Description:
- GRAND is a five-year, cluster randomized controlled trial. The study is registered on ClinicalTrials.gov, [ID#: NCT04033003] and is a collaboration between University of Michigan in the United States and the Dodowa Health Research Center in Ghana. , The study setting for GRAND is four districts (Akwapim North, Yilo Krobo, Nsawam-Adoagyiri, and Lower Manya Krobo) within the Eastern Region of Ghana. Health facilities were selected based the number ANC registrants per month and average gestational age of women at registration in each facility., and Facilities were then matched based on facility type, district, and number of monthly ANC registrants. A cluster randomized controlled trial was conducted in 14 facilities in four districts of the Eastern Region of Ghana. Health facilities were randomized using a matched pairs design; each pair was similar in the number of deliveries and average gestational age of the women at enrollment in antenatal care. The locations of the facilities were far enough apart to avoid cross-group contamination. In each pair of facilities, one was randomly assigned to the intervention (G-ANC) and the other to the control (I-ANC). Recruitment began July 2019 and ended when enrollment targets were met. Data collection ended July 2023 when data collection was complete.
- Keyword:
- Antenatal care, Ghana, and Maternal health
- Citation to related publication:
- Lori, J., Kukula, V., Liu, L. et al. Improving health literacy through group antenatal care: results from a cluster randomized controlled trial in Ghana. BMC Pregnancy Childbirth 24, 37 (2024). https://doi.org/10.1186/s12884-023-06224-x
- Discipline:
- International Studies and Health Sciences
-
- Creator:
- Sealey, Briana A., Larson, Joanna G., Westeen, Erin P., Sánchez-Paredes, Ciara M., Moore, Talia Y., and Davis Rabosky, Alison R.
- Description:
- In this study, we experimentally tested for the effects of four simulated predator cues on defensive displays in two species of South American calico snakes (genus Oxyrhopus). We found that juvenile snakes were both more likely to respond and to respond more strongly than adults and that displays were most common in response to tactile stimuli than to other treatments. However, we also found broad similarity across both simulated predator treatments and species in the components used in each snake’s defensive display, suggesting a high degree of stereotyping. This research suggests an important role for both ontogeny and intensity of predation risk in structuring variation in defensive behavior in Neotropical snakes and emphasizes the foundational importance of context dependence in conceptual frameworks for understanding predator-prey interactions. and *On January 4, 2024, “Supplementary_material.pdf” was replaced with an updated version that has slightly different versions of Figures S4 and S8 after an error in code was corrected. Within “HeatmapFigures.zip,” two code files, “IndividualHeatmaps_matrices.R” and “FigureS4_S8_averagedHeatmaps.R” were updated to correct the code error. Three additional files were added to both the “figures” and “matrices” folders within the subfolder “heatmaps.” These files represent the correlation matrices, by body part, and graphical representation of the matrices for one experimental trial that had previously been excluded due to the code error.
- Keyword:
- context-dependence, anti-predator behavior, Peruvian Amazon, ontogeny, coral snake mimicry, Colubridae
- Citation to related publication:
- Sealey, B.A.*, Larson, J.G.*, Westeen, E.P., Sanchez-Paredes, C.M., Moore, T.Y., Davis Rabosky, A.R. Body size and predator cues structure variation in defensive displays of Neotropical calico snakes (Oxyrhopus spp.). Ethology. In press. *Authors contributed equally
- Discipline:
- Science
-
- Creator:
- Gebarski, Benjamin B. and Becker, Udo
- Description:
- Files are uploaded as text or crystallographic information files (.cif), the standard text file format for representing crystallographic information. These files contain the results for cyclic voltammetry, x-ray absorption spectroscopy, and optimized molecular models for uranium-60 nanocluster (U60) fragments, UO2 complexes, and adsorbates.
- Keyword:
- uranium, U60, electrochemistry, computational, molecular model, and adsorption
- Citation to related publication:
- Electrochemical and computational analysis of the thermodynamics of oxidation/reduction reactions of uranyl peroxide clusters (U60), and the derivation of Pourbaix diagrams for structural and adsorbed species. In process.
- Discipline:
- Science
-
- Creator:
- Rana, Gurpreet K., Reynolds, Christopher W., Rha, Jennifer Y., Lenselink, Allison M., Asokumar, Dhanya, Zebib, Laura, Giacona, Francesca L. , Islam, Nowshin N., Kannikeswaran, Sanjana, Manuel, Kara, Cheung, Allison, Marzoughi, Maedeh , and Heisler, Michele
- Description:
- The search data supports a literature review project on "Innovative strategies and implementation science approaches for health delivery among migrants in humanitarian settings". The data included in the dataset are the complete search strategies (rtf file) and the exported results of all citations from all databases (ris file) after removal of duplicate citations.
- Keyword:
- humanitarian setting, migrant, forced displacement , health delivery, implementation science, and scoping review
- Discipline:
- Health Sciences
-
- Creator:
- Lockhart, Nancy
- Description:
- GRAND is a five-year, cluster randomized controlled trial. The study is registered on ClinicalTrials.gov, [ID#: NCT04033003] and is a collaboration between University of Michigan in the United States and the Dodowa Health Research Center in Ghana. and The study setting for GRAND is four districts (Akwapim North, Yilo Krobo, Nsawam-Adoagyiri, and Lower Manya Krobo) within the Eastern Region of Ghana. Health facilities were selected based the number ANC registrants per month and average gestational age of women at registration in each facility. Facilities were then matched based on facility type, district, and number of monthly ANC registrants.
- Keyword:
- Antenatal care, Ghana, and Maternal health
- Discipline:
- Health Sciences and International Studies
2Works -
- Creator:
- Luyet, Chloe, Elvati, Paolo, Vinh, Jordan, and Violi, Angela
- Description:
- A growing body of work has linked key biological activities to the mechanical properties of cellular membranes, and as a means of identification. Here, we present a computational approach to simulate and compare the vibrational spectra in the low-THz region for mammalian and bacterial membranes, investigating the effect of membrane asymmetry and composition, as well as the conserved frequencies of a specific cell. We find that asymmetry does not impact the vibrational spectra, and the impact of sterols depends on the mobility of the components of the membrane. We demonstrate that vibrational spectra can be used to distinguish between membranes and, therefore, could be used in identification of different organisms. The method presented, here, can be immediately extended to other biological structures (e.g., amyloid fibers, polysaccharides, and protein-ligand structures) in order to fingerprint and understand vibrations of numerous biologically-relevant nanoscale structures.
- Keyword:
- molecular dynamics, membranes, mechanical vibration, bacterial identification, and Staphylococcus aureus
- Citation to related publication:
- Luyet C, Elvati P, Vinh J, Violi A. Low-THz Vibrations of Biological Membranes. Membranes. 2023; 13(2):139. https://doi.org/10.3390/membranes13020139
- Discipline:
- Engineering
-
- Creator:
- Elvati, Paolo, Luyet, Chloe, Wang, Yichun, Liu, Changjiang, VanEpps, J. Scott, Kotov, Nicholas A., and Violi, Angela
- Description:
- Amyloid nanofibers are abundant in microorganisms and are integral components of many biofilms, serving various purposes, from virulent to structural. Nonetheless, the precise characterization of bacterial amyloid nanofibers has been elusive, with incomplete and contradicting results. The present work focuses on the molecular details and characteristics of PSMa1-derived functional amyloids present in Staphylococcus aureus biofilms, using a combination of computational and experimental techniques, to develop a model that can aid the design of compounds to control amyloid formation. Results from molecular dynamics simulations, guided and supported by spectroscopy and microscopy, show that PSMa1 amyloid nanofibers present a helical structure formed by two protofilaments, have an average diameter of about 12 nm, and adopt a left-handed helicity with a periodicity of approximately 72 nm. The chirality of the self-assembled nanofibers, an intrinsic geometric property of its constituent peptides, is central to determining the fibers' lateral growth.
- Keyword:
- molecular self-assembly, computational nanotechnology, nanobiotechnology, and structural properties
- Citation to related publication:
- Paolo Elvati, Chloe Luyet, Yichun Wang, Changjiang Liu, J. Scott VanEpps, Nicholas A. Kotov, and Angela Violi ACS Applied Nano Materials 2023 6 (8), 6594-6604 DOI: 10.1021/acsanm.3c00174
- Discipline:
- Engineering and Science
-
- Creator:
- Penner-Hahn, James, Sension, Roseanne, McClain, Taylor, Lamb, Ryan, Alonso-Mori, Roberto, Lima, Frederico, Ardana-Lamas, Fernando, Biednov, Mykola, Chollet, Matthieu, Chung, Taewon, Deb, Aniruddha, Dewan, Paul, Gee, Leland, Huang, Joel, Yifeng, Khakhulin, Dmitry, Li, Jianhao, Michocki, Lindsay, Miller, Nicholas, Otte, Florian, Uemura, Yohei, and van Driel, Tim
- Description:
- UV-visible, X-ray absorption, and X-ray emission data used to characterize the dynamics of aquo and hydroxo cobalamin. Details of data collection and reduction are provided in the associated manuscript. Data files are all text files which contain tab-delimited columns of data corresponding to each figure in the manuscript.
- Keyword:
- Ultrafast, X-ray, Transient absorption, cobalamin, vitamin B12, XAS, XES, and XANES
- Citation to related publication:
- Sension, R.J., et al. (2023). Watching Excited State Dynamics with Optical and X-ray Probes: The Excited State Dynamics of Aquocobalamin and Hydroxocobalamin. J. Am. Chem. Soc. in press. and https://doi.org/10.1021/jacs.3c04099
- Discipline:
- Science
-
- Creator:
- Lee, Sophie Y., Schönhöfer Philipp W.A., and Glotzer, Sharon C.
- Description:
- This dataset was generated for our work: "Complex motion of steerable vesicular robots filled with active colloidal rods". In this project, we used Brownian molecular dynamics simulations to study the rich dynamical behavior of rigid kinked vesicles that contain self-propelling rod-shaped particles. We identified that kinks in the vesicle membrane bias the emergent clustering and alignment of the active agents. Based on the system's geometrical and material properties, we were able to design multiple types of directed motion of the vesicle superstructure. This dataset includes simulation data for two-dimensional systems of self-propelling rod particles confined by teardrop-shaped coarse-grained vesicles. The trajectory of each simulation is saved in a GSD format file with parameter metadata in a JSON file. Due to the large number of replicas of each pair of parameters, simulation data were grouped into 5 different folders. Collective quantitative analysis for simulated trajectories was performed with Jupyter Notebook. and Workspaces_simulations.zip contains all the workspaces of simulations Each folder has subfolders called 'dimer' and 'trimer' depending on the length of the propelling rod particles used in the simulation. (Except for the folder 'number-density_16' which has only 'dimer') In the subfolders, we include the Python scripts used in this work for simulating and trajectory analysis for individual trajectory data. The parameter space of each folder is noted in init.py. Analysis_jupyter_notebooks.zip includes Jupyter notebooks that can reproduce the collective analysis done for this work.
- Discipline:
- Engineering
-
- Creator:
- Zielinski, Ruth E, Kukula, Vida, Apetorgbor, Veronica, Awini, Elizabeth, Moyer, Cheryl, Badu-Gyan, Georgina, Williams, John, Lockhart, Nancy, and Lori, Jody R
- Description:
- This is a process evaluation of the RCT, Group Antenatal Care and Delivery project (GRAND) to identify and document patient, provider, and system barriers and facilitators to program implementation. Using both quantitative and qualitative methods, potential and actual influences on the quality and conduct of the program's operations, implementation, and service delivery were identified. Only the seven (7) sites randomized to the Group ANC (G-ANC) intervention were included for collection of process evaluation data since the evaluation was of G-ANC implementation. Data were collected from August 2019 to November 2020 and included both quantitative and qualitative data sources.
- Keyword:
- Group Antenatal Care, Ghana, and Process Evaluation
- Citation to related publication:
- Zielinski R, Kukula V, Apetorgbor V, Awini E, Moyer C, Badu-Gyan G, et al. (2023) “With group antenatal care, pregnant women know they are not alone”: The process evaluation of a group antenatal care intervention in Ghana. PLoS ONE 18(11): e0291855. https://doi.org/10.1371/journal.pone.0291855
- Discipline:
- International Studies and Health Sciences
-
- Creator:
- Chen, Kevin S, Noureldein, Mohamed H, McGinley, Lisa M, Hayes, John M, Rigan, Diana M, Kwentus, Jaquelin F, Mason, Shayna N, Mendelson, Faye E, Savelieff, Masha G, and Feldman, Eva L
- Description:
- Therapeutic mechanisms of human neural stem cells (hNSCs) were studied in an Alzheimer's disease mouse model (5XFAD). hNSCs restored spatial memory abilities in 5XFAD animals; however, amyloid beta levels were unchanged. Spatial transcriptomics was used to probe mechanisms of hNSCs. Focusing on a subset of plaque-induced genes, gene normalization was seen particularly in microglia, confirmed by PROGENy and Cell Chat analyses. and The spatial transcriptomics data from this publication have been deposited in NCBI Gene Expression Omnibus (16) and are accessible through GEO Series accession number GSE209583 ( https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE209583 and enter token gzglogqkvjqrhmt). Additional supporting data are available from the corresponding author upon reasonable request.
- Citation to related publication:
- Chen KS, Noureldein MH, McGinley LM, Hayes JM, Rigan DM, Kwentus JF, Mason SN, Mendelson FE, Savelieffd MG, Feldman EL. Human neural stem cells restore spatial memory in a transgenic Alzheimer's disease mouse model by an immunomodulating mechanism. bioRxiv [Preprint]. 2023 Nov 4:2023.11.01.565161. doi: 10.1101/2023.11.01.565161. PMID: 37961246; PMCID: PMC10635057.
- Discipline:
- Health Sciences
-
- Creator:
- Singer, Kanakadurga
- Description:
- Supplementary Figure 1. Example gating scheme for bone marrow mature leukocytes and hematopoietic progenitors. To stain for mature leukocytes antibodies used were against CD45, Ly6G, CD11b, CD115, CD19, and CD3e. All CD45+ cells were gated first. Neutrophils were defined as Ly6G+CD11b+, monocytes were defined as Ly6G-CD11b+CD115+ (17,18), B cells were defined as Ly6G-CD11b-CD19+, and T cells were defined as Ly6G-CD11b-CD3e+. To stain for hematopoietic stem and progenitor cells antibodies used were against lineage panel (B220, Gr1, TER119, CD11b, CD4, CD8), cKit, Sca1, CD48, CD150, CD16/32, and CD105. HSCs were defined as Lin-Sca1+cKit+CD48-CD150+, MPPs were defined as Lin-Sca1+cKit+CD48-CD150-, HPC1 were defined as Lin-Sca1+cKit+CD48+CD150-, HPC2 were defined as Lin-Sca1+cKit+CD48+CD150+, GMP were defined as Lin-Sca1-cKit+CD150-CD16/32+, PreGM were defined as Lin-Sca1+cKit+CD150-CD105-, preMegE were defined as Lin-Sca1+cKit+CD150+CD105-, and PreCFUe were defined as Lin-Sca1+cKit+CD150+CD105+. , Supplementary Figure 2. Hematopoietic stem and progenitor cell frequency by flow cytometry as a percentage of CD45 bone marrow cells in male and female Ctrl and HFD PN offspring. Hematopoietic stem cells (HSC), multipotent progenitor cells (MPP), Pre-Granulocyte Macrophage (Pre-GM), granulocyte monocyte precursors (GMP), Pre-Megakaryocyte-Erythroid Precursors (Pre-MegE) and erythroid precursors (Pre-CFUE). Analyses were Student’s t-test ang gating per Supplementary Figure 1., Supplementary Table 1. Differential gene expression between Ctrl and HFD PN male gonadal white adipose tissue (GWAT) from postnatal day 16. The significant gene expression differences were determined by the DESeq2 package for R Studio. Sequencing The RNA was extracted from adipose tissue using Trizol LS (Life Technologies) by Qiagen RNeasy Mini Kit (74106) according to the manual. The RNA was sent to the University of Michigan Advanced Genomics Core for RNA-sequencing. For RNAseq studies, gonadal white adipose tissue 3’ QuantSeq single-end poly-A mRNA libraries were generated (Lexogen). These were sequenced to a depth of 10-20M reads on Illumina NovaSeq platform. Data are available from GEO at accession number GSE227337., and Supplementary Table 2. Differentially expressed genes between Ctrl and HFD PN male gonadal white adipose tissue (GWAT) from postnatal day 16 that are significant after correction for false discovery rate were determined by the DESeq2 package for R Studio.
- Citation to related publication:
- Kim K, Varghese M, Sun H, Abrishami S, Bowers E, Bridges D, Meijer JL, Singer K* and Gregg B*. The influence of maternal high fat diet during lactation on offspring hematopoietic priming. Endocrinology. https://doi.org/10.1210/endocr/bqad182 PMID 38048597.
- Discipline:
- Health Sciences
-
- Creator:
- Wallace, Dylan M, Benyamini, Miri, Nason-Tomaszewski, Samuel R, Costello, Joseph T, Cubillos, Luis H, Mender, Matthew J, Temmar, Hisham, Willsey, Matthew S, Patil, Parag P, Chestek, Cynthia A, and Zacksenhouse, Miriam
- Description:
- This is data from Wallace, Benyamini et al., 2023, Journal of Neural Engineering. There are two sets of data included: 1. Neural features and error labels used to train error classifiers for each day used in the study 2. Trial data from an example experiment day (Monkey N, Day 6), with runs for offline calibration, online brain control, error monitoring, and error correction. The purpose of this study was to investigate the use of error signals in motor cortex to improve brain-machine interface (BMI) performance for control of two finger groups. All data is contained in .mat files, which can be opened using MATLAB or the Python SciPy library.
- Keyword:
- Brain-machine interface (BMI), Error detection, and Neural recording
- Citation to related publication:
- Wallace, D. M., Benyamini, M., Nason-Tomaszewski, S. R., Costello, J. T., Cubillos, L. H., Mender, M. J., Temmar, H., Willsey, M. S., Patil, P. G., Chestek, C. A., & Zacksenhouse, M. (2023). Error detection and correction in intracortical brain–machine interfaces controlling two finger groups. Journal of Neural Engineering, 20(4), 046037. https://doi.org/10.1088/1741-2552/acef95
- Discipline:
- Engineering, Science, and Health Sciences
-
- Creator:
- Sun, Hu, Ren, Jiaen, Chen, Yang, Zou, Shasha, Chang, Yurui, Wang, Zihan, and Coster, Anthea
- Description:
- Our research focuses on providing a fully-imputed map of the worldwide total electron content with high resolution and spatial-temporal smoothness. We fill in the missing values of the original Madrigal TEC maps via estimating the latent feature of each latitude and local time along the 2-D grid and give initial guess of the missing regions based on pre-computed spherical harmonics map. The resulting TEC map has high imputation accuracy and the ease of reproducing. All data are in HDF5 format and are easy to read using the h5py package in Python. The TEC map is grouped in folders based on years and each file contains a single-day data of 5-min cadence. Each individual TEC map is of size 181*361. and WARNING: 2023-12-01 the data file for 2019-Jan-03 has badly fitted values. Please avoid using it. All other days' files are ready to use.
- Keyword:
- Total Electron Content, Matrix Completion, VISTA, Spherical Harmonics, and Spatial-Temporal Smoothing
- Citation to related publication:
- Sun, H., Hua, Z., Ren, J., Zou, S., Sun, Y., & Chen, Y. (2022). Matrix completion methods for the total electron content video reconstruction. The Annals of Applied Statistics, 16(3), 1333-1358., Sun, H., Chen, Y., Zou, S., Ren, J., Chang, Y., Wang, Z., & Coster, A. (2023). Complete Global Total Electron Content Map Dataset based on a Video Imputation Algorithm VISTA. Scientific Data, in press., and Zou, S., Ren, J., Wang, Z., Sun, H., & Chen, Y. (2021). Impact of storm-enhanced density (SED) on ion upflow fluxes during geomagnetic storm. Frontiers in Astronomy and Space Sciences, 8, 746429.
- Discipline:
- Science and Engineering
-
- Creator:
- Klinich, Kathleen D, Lin, Brian, and Moore, Jamie L.
- Description:
- This dataset allows comparison of the different strategies implemented by vehicle manufacturers being used to communicate with drivers. Spreadsheets were created in MS Excel to summarize data for each vehicle, and include page numbers in each vehicle owner's manual for reference. The photos taken of each vehicle control panel allow detailed inspection of the displays and controls.
- Keyword:
- vehicle, controls, displays, and FMVSS 101
- Discipline:
- Engineering
-
- Creator:
- Brian, Chen
- Description:
- The procedure followed while creating this data is summarized in Section II of Chen, Brian, et al. "Behavioral cloning in atari games using a combined variational autoencoder and predictor model." 2021 IEEE Congress on Evolutionary Computation (CEC). IEEE, 2021. This data is not a result of a research but an intermediate product that is used in research. This dataset is generated to train a behavioral cloning framework from gameplay screen captures and keystrokes of an "expert" player. The RL agent that is trained using "RL Baselines Zoo package" acts as the "expert" player, whose decision making process we desire to learn. In addition to behavioral cloning experiments, this dataset is further used to demonstrate the efficacy of a novel incremental tensor decomposition algorithm on image-based data streams.
- Keyword:
- Imitation Learning, Behavioral Cloning, Reinforcement Learning, Machine Learning, and Gameplay Data
- Citation to related publication:
- Chen, Brian, et al. "Behavioral cloning in atari games using a combined variational autoencoder and predictor model." 2021 IEEE Congress on Evolutionary Computation (CEC). IEEE, 2021., Aksoy, Doruk, et al. "An Incremental Tensor Train Decomposition Algorithm." arXiv preprint arXiv:2211.12487 (2022)., and Chen, Brian, et al. "Low-Rank Tensor-Network Encodings for Video-to-Action Behavioral Cloning", forthcoming
- Discipline:
- Engineering and Science
-
- Creator:
- Heath, Jeffrey
- Description:
- The spreadsheets (in csv and xlsx formats) have columns for botanical family, genus-species binomials, synonymy (outdated binomials) on the left, folllowed by columns with native terms in several Dogon languages and in Bangime. Dogon languages included are Toro Tegu, Ben Tey, Bankan Tey, Nanga, Jamsay (main dialect), Perge Tegu (Jamsay of Pergé village), Gourou (aberrant variety of Jamsay), Togo Kan, Yorno So and Ibi So (in Toro So dialect complex), Donno So, Tomo Kan (of Segué and of Diangassagou), Tomo Kan, Dogul Dom, Tebul Ure, Yanda Dom, Najamba, Tiranige, Mombo, Ampari, Bunoge, and Penange. JH in column headings indicates that the material is from Dr. Heath's fieldwork. and For images of many of these plants, see the collection "Mali flora images" in Deep Blue Data ( https://doi.org/10.7302/aef4-fk26). For a practical guide to these plants, click on the link below in "related items in Deep Blue Documents".
- Keyword:
- Dogon, Bangime, and flora
- Discipline:
- Humanities
-
- Creator:
- Heath, Jeffrey
- Description:
- Documentary-style videos about villages and social relations in Dogon country. Documentaries are given in two or three video formats each.
- Keyword:
- Mali, Dogon, and villages
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities