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- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:mammals:158895 (Pteropus pumilus) - WholeBody. Raw Dataset includes 1601 TIF images (each 924 x 1093 x 1 voxel at 0.0783933 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:mammals:158895 (Pteropus pumilus) - WholeBody. Reconstructed Dataset includes 2000 TIF images (each 924 x 1093 x 1 voxel at 0.078393 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Chiroptera, Pteropodidae, Pteropus pumilus, 1987271498, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987271498
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:mammals:174732 (Microgale talazaci) - WholeBody. Raw Dataset includes 3141 TIF images (each 634 x 469 x 1 voxel at 0.06971601 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:mammals:174732 (Microgale talazaci) - WholeBody. Reconstructed Dataset includes 1957 TIF images (each 634 x 469 x 1 voxel at 0.069716 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Afrosoricida, Tenrecidae, Microgale talazaci, 1987232883, 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/1987232883
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:mammals:161555 (Rousettus amplexicaudatus AMPLEXICAUDATUS) - Skull. Raw Dataset includes 2401 TIF images (each 1512 x 1939 x 1 voxel at 0.03505111 mm resolution, derived from 2401 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Chiroptera, Pteropodidae, Rousettus amplexicaudatus AMPLEXICAUDATUS, 1987291962, 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/1987291962
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:mammals:163615 (Megaderma spasma SPASMA) - WholeBody. Raw Dataset includes 3141 TIF images (each 799 x 1057 x 1 voxel at 0.0414075 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:mammals:163615 (Megaderma spasma SPASMA) - WholeBody. Reconstructed Dataset includes 2000 TIF images (each 799 x 1057 x 1 voxel at 0.041408 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Chiroptera, Megadermatidae, Megaderma spasma SPASMA, 1987289689, 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/1987289689
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:mammals:161555 (Rousettus amplexicaudatus AMPLEXICAUDATUS) - WholeBody. Raw Dataset includes 3141 TIF images (each 801 x 1238 x 1 voxel at 0.06713326 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:mammals:161555 (Rousettus amplexicaudatus AMPLEXICAUDATUS) - WholeBody. Reconstructed Dataset includes 1951 TIF images (each 801 x 1238 x 1 voxel at 0.067133 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Chiroptera, Pteropodidae, Rousettus amplexicaudatus AMPLEXICAUDATUS, 1987291962, 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/1987291962
- Discipline:
- Science
-
- Creator:
- Penner-Hahn, James E, Alonso Mori, Roberto, Ardana-Lamas, Fernando , Biednov, Mykola , Chung, Taewon , Deb, Aniruddha, Jiang, Yifeng , Kaneshiro, April K. , Khakhulin, Dmitry , Kubarych, Kevin J. , Lamb, Ryan, Lima, Frederico Alves , McClain, Taylor P. , Meadows, Joseph H. , Michocki, Lindsay, Miller, Nicholas A. , Otte, Florian , Sension, Roseanne J, Sofferman, Danielle L. , Song, Sanghoon , Uemura, Yohei , and van Driel, Tim Brandt
- Description:
- The dataset contains the numerical data used to produce figures 2-14 and S1-S8 (Figure 1 is purely schematic and is uploaded as a tif file for completeness - it does not contain any new data). These files contain the transient UV-visible, X-ray absorption, and X-ray emission data that were used to characterize the dynamics of methyl cobalamin at neutral pH and to compare this to adenosyl 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 , XANES, and XES
- Citation to related publication:
- Journal of Physical Chemistry B, https://pubs.acs.org/doi/10.1021/acs.jpcb.4c03729
- Discipline:
- Science
-
- Creator:
- Wilson Mantilla, Jeffrey A.
- Description:
- The 3D model of the humerus was created from an isolated element that is referred to the pterosaur Arambourgiania philadelphiae. The element is accessioned to Yarmouk University (YUPC-RUSEIFA-1) in the Hashemite Kingdom of Jordan. The specimen was collected from Late Cretaceous-aged sediments at the Ruseifa Quarry in central Jordan. For inquiries about access to the specimen, please contact Jeff Wilson Mantilla ( wilsonja@umich.edu) or Iyad Zalmout ( izalmout@ksu.edu.sa). Casts of this element of Arambourgiania are available at the University of Michigan Museum of Paleontology.
- Keyword:
- Jordan pterosaur cretaceous vertebrate gondwana afro-arabia paleontology
- Citation to related publication:
- Rosenbach, K. L., D. M. Goodvin, M. G. Albshysh, H. A. Azzam, A. A. Smadi, H. A. Mustafa, I. S. A. Zalmout, and J. A. Wilson Mantilla. [in press] New pterosaur remains from the Late Cretaceous of Afro-Arabia provide insight into flight capacity of large pterosaurs. Journal of Vertebrate Paleontology.
- Discipline:
- Science
-
- Creator:
- Wilson Mantilla, Jeffrey A.
- Description:
- The left humerus is part of an associated skeleton of the pterosaur Inabtanin alarabia, accessioned to Yarmouk University (YUPC-INAB-6-001–010) in the Hashemite Kingdom of Jordan. The specimen was collected from Late Cretaceous-aged sediments near Tal Inab in south-central Jordan, which is 34 km north of the current border with Saudi Arabia. For inquiries about access, please contact Jeff Wilson Mantilla ( wilsonja@umich.edu) or Iyad Zalmout ( izalmout@ksu.edu.sa). Casts of this and other elements of Inabtanin alarabia are available at the University of Michigan Museum of Paleontology.
- Keyword:
- Jordan pterosaur cretaceous vertebrate gondwana afro-arabia paleontology
- Citation to related publication:
- Rosenbach, K. L., D. M. Goodvin, M. G. Albshysh, H. A. Azzam, A. A. Smadi, H. A. Mustafa, I. S. A. Zalmout, and J. A. Wilson Mantilla. [in press] New pterosaur remains from the Late Cretaceous of Afro-Arabia provide insight into flight capacity of large pterosaurs. Journal of Vertebrate Paleontology.
- Discipline:
- Science
-
- Creator:
- Wilson Mantilla, Jeffrey A.
- Description:
- The scanned distal right humerus is part of an associated skeleton of the pterosaur Inabtanin alarabia, accessioned to Yarmouk University (YUPC-INAB-6-001–010) in the Hashemite Kingdom of Jordan. The specimen was collected from Late Cretaceous-aged sediments near Tal Inab in south-central Jordan, which is 34 km north of the current border with Saudi Arabia. For inquiries about access, please contact Jeff Wilson Mantilla ( wilsonja@umich.edu) or Iyad Zalmout ( izalmout@ksu.edu.sa). Casts of this and other elements of Inabtanin alarabia are available at the University of Michigan Museum of Paleontology.
- Keyword:
- Jordan pterosaur cretaceous vertebrate gondwana afro-arabia paleontology
- Citation to related publication:
- Rosenbach, K. L., D. M. Goodvin, M. G. Albshysh, H. A. Azzam, A. A. Smadi, H. A. Mustafa, I. S. A. Zalmout, and J. A. Wilson Mantilla. [in press] New pterosaur remains from the Late Cretaceous of Afro-Arabia provide insight into flight capacity of large pterosaurs. Journal of Vertebrate Paleontology.
- Discipline:
- Science
-
- Creator:
- Hutson, Abby , Fujisaki-Manome, Ayumi, and Glassman, Ryan
- Description:
- The data herein resulted from a study documenting the characteristics of extratropical cyclones that pass through the Great Lakes Region (GLR) and how the cyclones are trending with time. All scripts used to create these data can be found in the Github repository https://github.com/abkenyon/GLStormTrends_2024. storm_track_slp_xxxx.npz - Structured numpy files containing all storm tracks identified over one cold season, regardless of whether the storm encountered the GLR, with the file name indicating the year on which the season ended. storm_composite_xxxx-xxxx.nc - NetCDF files containing one seasonal cyclone composite with different atmospheric variables. A composite is storm-centered, and covers a 20 degree square area.
- Keyword:
- Extratropical Cyclones, Climate Trends, Great Lakes Climate
- Citation to related publication:
- Hutson A, Fujisaki-Manome A, Glassman R.: Historical Trends in Cold-Season Mid-Latitude Cyclones. Geophysical Research Letters. In press..
- Discipline:
- Science
-
- Creator:
- Wilson Mantilla, Jeffrey A.
- Description:
- The scanned humerus is an isolated element that is referred to the pterosaur Arambourgiania philadelphiae. The element is accessioned to Yarmouk University (YUPC-RUSEIFA-1) in the Hashemite Kingdom of Jordan. The specimen was collected from Late Cretaceous-aged sediments at the Ruseifa Quarry in central Jordan. For inquiries about access to the specimen, please contact Jeff Wilson Mantilla ( wilsonja@umich.edu) or Iyad Zalmout ( izalmout@ksu.edu.sa). Casts of this element of Arambourgiania are available at the University of Michigan Museum of Paleontology.
- Keyword:
- Jordan pterosaur cretaceous vertebrate gondwana afro-arabia paleontology
- Citation to related publication:
- Rosenbach, K. L., D. M. Goodvin, M. G. Albshysh, H. A. Azzam, A. A. Smadi, H. A. Mustafa, I. S. A. Zalmout, and J. A. Wilson Mantilla. [in press] New pterosaur remains from the Late Cretaceous of Afro-Arabia provide insight into flight capacity of large pterosaurs. Journal of Vertebrate Paleontology.
- Discipline:
- Science
-
- Creator:
- Wilson Mantilla, Jeffrey A.
- Description:
- The scanned proximal left humerus is part of an associated skeleton of the pterosaur Inabtanin alarabia, accessioned to Yarmouk University (YUPC-INAB-6-001–010) in the Hashemite Kingdom of Jordan. The specimen was collected from Late Cretaceous-aged sediments near Tal Inab in south-central Jordan, which is 34 km north of the current border with Saudi Arabia. For inquiries about access, please contact Jeff Wilson Mantilla ( wilsonja@umich.edu) or Iyad Zalmout ( izalmout@ksu.edu.sa). Casts of this and other elements of Inabtanin are available at the University of Michigan Museum of Paleontology.
- Keyword:
- Jordan pterosaur cretaceous vertebrate gondwana afro-arabia paleontology
- Citation to related publication:
- Rosenbach, K. L., D. M. Goodvin, M. G. Albshysh, H. A. Azzam, A. A. Smadi, H. A. Mustafa, I. S. A. Zalmout, and J. A. Wilson Mantilla. [in press] New pterosaur remains from the Late Cretaceous of Afro-Arabia provide insight into flight capacity of large pterosaurs. Journal of Vertebrate Paleontology.
- Discipline:
- Science
-
- Creator:
- Marks, Thomas A and Gorodetsky, Alex A
- Description:
- WarpX simulations of the 2D axial-azimuthal Hall thruster benchmark, as described in IEPC paper 409 (2024): https://www.thomasmarks.space/files/Marks_T_IEPC_2024_WarpX.pdf Contains one subdirectory: baseline_20us: 20 us of data, saved every 5000 iterations (32 GB) The data is in AMReX plotfile format.
- Keyword:
- hall thruster, plasma, pic, particle in cell, particle, cell, kinetic, electric propulsion, and thruster
- Citation to related publication:
- @inproceedings{marksWarpX2024, title = {Hall thruster simulations in {{Warp-X}}}, booktitle = {38th {{International Electric Propulsion Conference}}}, author = {Marks, Thomas A. and Gorodetsky, Alex A.}, year = {2024}, month = jun, address = {Toulouse, France} }
- Discipline:
- Engineering
-
- Creator:
- Sosa Alfaro, Victor, Palomino, Hannah, Liu, Sophia, Lemuh Njimoh, Cybele, and Lehnert, Nicolai
- Description:
- Pharmaceutical synthesis has been a driving force behind advancements in the field of biocatalysis. In this paper, we report the further optimization of the heme protein YfeX for regio- and stereoselective carbene transfer reactions using mutagenesis to explore the role of important amino acids in the active site for catalysis. In this way, we identified YfeX variants that are efficient and selective carbene transferases towards primary and secondary amines, olefins, and indoles. Molecular Dynamic simulations reveal that mutations within the secondary coordination sphere induce distinct alterations in the conformation and electrostatic properties within the active site. These changes, in turn, affect substrate positioning both within the active site and at its entrance, which explains the distinct and sometimes surprising variations in selectivity observed experimentally between select YfeX variants. Our results show that the I230A single variant identified here is one of the most active N-H insertion catalysts known, producing >90% yields in only 1 hour (typical reaction times in the literature are 8 – 24 hours). On the other hand, the R232A variant catalyzes the C-H insertion of unprotected indole in 21% yield. The capacity to selectively act on unprotected indole offers a cost-effective, environmentally-friendly approach for late-stage functionalization of indoles and similar precursors in pharmaceuticals. In addition, YfeX is an efficient and fast biocatalyst that shows no structural degradation or heme loss during turnover, underscoring YfeX’s robustness as a viable biocatalyst for both industrial and academic applications.
- Keyword:
- Biocatalysis, Heme proteins, Carbene transfer reactions, Peroxidases , N-H insertion, Cyclopropanation, and Molecular dynamics
- Citation to related publication:
- Sosa Alfaro, Victor; Palomino, Hannah; Liu, Sophia; Lemuh Njimoh, Cybele; Lehnert, Nicolai, "Combined Experimental and Molecular Dynamics Approach Towards a Rational Design of the YfeX Biocatalyst for Enhanced Carbene Transferase Reactivity", Catalysis Science & Technology 2024, 14, DOI: 10.1039/D3CY01489D
- Discipline:
- Science
-
- Creator:
- El Shair, Zaid A. and Rawashdeh, Samir A.
- Description:
- The MEVDT dataset was created to fill a critical gap in event-based computer vision research by supplying a high-quality, real-world labeled dataset. Intended to facilitate the development of advanced algorithms for object detection and tracking applications, MEVDT includes multi-modal traffic scene data with synchronized grayscale images and high-temporal-resolution event streams. Additionally, it provides annotations for object detection and tracking with class labels, pixel-precise bounding box coordinates, and unique object identifiers. The dataset is organized into directories containing sequences of images and event streams, comprehensive ground truth labels, fixed-duration event samples, and data indexing sets for training and testing. and To access and utilize the dataset, researchers need specific software or scripts compatible with the data formats included, such as PNG for grayscale images, CSV for event stream data, AEDAT for the encoded fixed-duration event samples, and TXT for annotations. Recommended tools include standard image processing libraries for PNG files and CSV or text parsers for event data. A specialized Python script for reading AEDAT files is available at: https://github.com/Zelshair/cstr-event-vision/blob/main/scripts/data_processing/read_aedat.py, which streamlines access to the encoded event sample data.
- Keyword:
- Computer Vision, Event-Based Vision, Object Detection, Object Tracking, and Multi-Modal Vision Dataset
- Citation to related publication:
- El Shair, Z. and Rawashdeh, S., 2024. MEVDT: Multi-Modal Event-Based Vehicle Detection and Tracking Dataset. Data In Brief (under review)., El Shair, Z. and Rawashdeh, S.A., 2022. High-temporal-resolution object detection and tracking using images and events. Journal of Imaging, 8(8), p.210., El Shair, Z. and Rawashdeh, S., 2023. High-temporal-resolution event-based vehicle detection and tracking. Optical Engineering, 62(3), pp.031209-031209., and El Shair, Z.A., 2024. Advancing Neuromorphic Event-Based Vision Methods for Robotic Perception Tasks (Doctoral dissertation, University of Michigan-Dearborn).
- Discipline:
- Engineering
-
- Creator:
- Fahim, Abigail T
- Description:
- The purpose of this research is to compare levels of unprenylated Rab proteins in CHM-/- iPSC-RPE cells with and without compactin. Compactin is a statin that inhibits prenyl synthesis and thereby reduces prenylation overall and has an unbiased inhibitory effect on all protein prenylation. So we expect that for Rabs that are already poorly prenylated at baseline in choroideremia RPE cells, compactin will have minimal effect. However, for Rabs that are efficiently prenylated at baseline, compactin should have a much greater effect. And then we used tandem mass tag spectrometry to compare the ratio of each unprenylated Rab in compactin-treated choroideremia cells vs untreated choroideremia cells. In the spreadsheet, "F8" refers to the CHM-/- iPSC-RPE cells and "WT" refers to the isogenic control iPSC-RPE cells. In the "Proteins only" tab, column M shows the ratio of each protein in "DMSO" (untreated) choroideremia cells compared to Compactin-treated choroideremia cells. Compactin-treated control cells are also included in other columns. Untreated control cells could not be used because prenylation is so efficient in these cells, there is almost no material available after doing the in vitro prenylation assay (i.e. almost no unprenylated proteins to biotinylate). The column descriptions can be found in the sheet titled "Explanations." In addition, AAs= number of amino acids in the protein, MW= molecular weight of the protein, and pI= isoelectric point. The software is set to report abundance values only when certain criteria are met (S/N of 6, unique peptide etc). A value is NOT reported when the data for a protein fall below these criteria and the cell is instead left blank.
- Keyword:
- choroideremia, retinal pigment epithelium, prenylation, and Rab protein
- Citation to related publication:
- Raeker, M.O., Perera, N.D., Karoukis, A.J., Chen, L., Feathers, K.L., Ali, R.R., Thompson, D.A., Fahim, A.T. Reduced retinal pigment epithelial autophagy due to loss of Rab12 prenylation in a human iPSC-RPE model of choroideremia. Cells, manuscript accepted, in press.
- Discipline:
- Health Sciences and Science
-
- Creator:
- Shin, Satbyeol and Gronewold, Andrew D.
- Description:
- - Temporal coverage: 1/1/1941 to 12/31/2020 - Spatial coverage: Entire Great Lakes basin - Output format: The original modeling outputs are provided at a 1 km/daily resolution in NetCDF format. There are two kinds of modeling outputs, which are land surface modeling outputs (LDASOUT) and hydrological modeling outputs (CHRTOUT). The author recommend using the netCDF Operators (NCO) program for data processing. For visualization and plotting, the author recommend using software like MATLAB, Python or R.
- Keyword:
- Hydrologic modeling, Overland precipitation, Air temperature, Evapotranspiration, Snow Water Equivalent, Runoff, Surface Soil moisture, St. Lawrence river, Great Lakes basin, Reanalysis data, WRF-Hydro, and ERA-5
- Discipline:
- Science
-
- Creator:
- Yu, Chi-Lin
- Description:
- The study aims to describe how children worldwide progress through a sequence of theory of mind understandings in their development of insights into persons and minds. The focus is on the studies using Wellman and Liu's (2004) Theory of Mind Scale. A comprehensive search was run in PsycINFO, PsycArticles, Child Development & Adolescent Studies, Education Abstracts, Family & Society Studies Worldwide, and Social Sciences Abstracts. The dataset includes 91 studies using Wellman and Liu's (2004) Theory of Mind Scale.
- Keyword:
- meta-analysis, theory of mind, social cognitive development, culture, and conceptual sequences
- Discipline:
- Science
-
- Creator:
- Fu, Xun, Zhang, Bohao, Weber, Ceri J., Cooper, Kimberly L., Vasudevan, Ram, and Moore, Talia Y.
- Description:
- Tails used as inertial appendages induce body rotations of animals and robots---a phenomenon that is governed largely by the ratio of the body and tail moments of inertia. However, vertebrate tails have more degrees of freedom (e.g., number of joints, rotational axes) than most current theoretical models and robotic tails. To understand how morphology affects inertial appendage function, we developed an optimization-based approach that finds the maximally effective tail trajectory and measures error from a target trajectory. For tails of equal total length and mass, increasing the number of equal-length joints increased the complexity of maximally effective tail motions. When we optimized the relative lengths of tail bones while keeping the total tail length, mass, and number of joints the same, this optimization-based approach found that the lengths match the pattern found in the tail bones of mammals specialized for inertial maneuvering. In both experiments, adding joints enhanced the performance of the inertial appendage, but with diminishing returns, largely due to the total control effort constraint. This optimization-based simulation can compare the maximum performance of diverse inertial appendages that dynamically vary in moment of inertia in 3D space, predict inertial capabilities from skeletal data, and inform the design of robotic inertial appendages.
- Keyword:
- simulation, inertial maneuvering, caudal vertebrae, trajectory optimization, and reconfigurable appendages
- Citation to related publication:
- Xun Fu, Bohao Zhang, Ceri J. Weber, Kimberly L. Cooper, Ram Vasudevan, Talia Y. Moore. (in review) Jointed tails enhance control of three-dimensional body rotation.
- Discipline:
- Engineering and Science
-
- Creator:
- Kharbush, Jenan, Rahman, Raisha, and Pearson, Ann
- Description:
- Amino acids are the primary nitrogen-containing compounds in cells, participating in various metabolic processes such as protein synthesis and degradation into other nitrogenous compounds. Compound-specific nitrogen isotope analysis of amino acids in environmental samples can provide insight into nitrogen sources, cycling, and tropic modifications in ecosystems. However, we lack comprehensive understanding of N utilization patterns in microorganisms, which are the site of nitrogen assimilation in biological systems, due to the varied and complex mechanisms by which microbes can acquire and metabolize nitrogen-containing compounds. δ15N measurements for free intracellular amino acids and protein-bound amino acids for environmentally-relevant microbial groups may aid in untangling the biochemical processes involved in amino acid metabolism performed by these microbial communities. Here, we report intracellular amino acid δ15N values for R. palustris, a metabolically versatile anoxygenic phototrophic bacterium.
- Keyword:
- amino acids, nitrogen stable isotope analysis, compound-specific isotope analysis, and batch culture
- Discipline:
- Science