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.
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.
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.
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.
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.
The trajectory data and codes were generated for our work "Classification of complex local environments in systems of particle shapes through shape-symmetry encoded data augmentation" (amidst peer review process). The data sets contain trajectory data in GSD file format for 7 test systems, including cubic structures, two-dimensional and three-dimensional patchy particle shape systems, hexagonal bipyramids with two aspect ratios, and truncated shapes with two degrees of truncation. Besides, the corresponding Python code and Jupyter notebook used to perform data augmentation, MLP classifier training, and MLP classifier testing are included.
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.
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
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
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.
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.
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