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Bharathan NK, Giang W, Hoffman CL, Aaron JS, Khuon S, Chew TL, Preibisch S, Trautman ET, Heinrich L, Bogovic J, Bennett D, Ackerman D, Park W, Petruncio A, Weigel AV, Saalfeld S, Wayne Vogl A, Stahley SN, Kowalczyk AP. Author Correction: Architecture and dynamics of a desmosome-endoplasmic reticulum complex. Nat Cell Biol 2024; 26:660. [PMID: 38347183 DOI: 10.1038/s41556-024-01376-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Affiliation(s)
- Navaneetha Krishnan Bharathan
- Departments of Dermatology and Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - William Giang
- Departments of Dermatology and Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Coryn L Hoffman
- Departments of Dermatology and Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jesse S Aaron
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Satya Khuon
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Teng-Leong Chew
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Stephan Preibisch
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Eric T Trautman
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Larissa Heinrich
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - John Bogovic
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Davis Bennett
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - David Ackerman
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Woohyun Park
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Alyson Petruncio
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Aubrey V Weigel
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Stephan Saalfeld
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - A Wayne Vogl
- Life Sciences Institute and the Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sara N Stahley
- Departments of Dermatology and Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Andrew P Kowalczyk
- Departments of Dermatology and Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
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Knox C, Wilson M, Klinger C, Franklin M, Oler E, Wilson A, Pon A, Cox J, Chin NE, Strawbridge S, Garcia-Patino M, Kruger R, Sivakumaran A, Sanford S, Doshi R, Khetarpal N, Fatokun O, Doucet D, Zubkowski A, Rayat D, Jackson H, Harford K, Anjum A, Zakir M, Wang F, Tian S, Lee B, Liigand J, Peters H, Wang RQ, Nguyen T, So D, Sharp M, da Silva R, Gabriel C, Scantlebury J, Jasinski M, Ackerman D, Jewison T, Sajed T, Gautam V, Wishart D. DrugBank 6.0: the DrugBank Knowledgebase for 2024. Nucleic Acids Res 2024; 52:D1265-D1275. [PMID: 37953279 PMCID: PMC10767804 DOI: 10.1093/nar/gkad976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 11/14/2023] Open
Abstract
First released in 2006, DrugBank (https://go.drugbank.com) has grown to become the 'gold standard' knowledge resource for drug, drug-target and related pharmaceutical information. DrugBank is widely used across many diverse biomedical research and clinical applications, and averages more than 30 million views/year. Since its last update in 2018, we have been actively enhancing the quantity and quality of the drug data in this knowledgebase. In this latest release (DrugBank 6.0), the number of FDA approved drugs has grown from 2646 to 4563 (a 72% increase), the number of investigational drugs has grown from 3394 to 6231 (a 38% increase), the number of drug-drug interactions increased from 365 984 to 1 413 413 (a 300% increase), and the number of drug-food interactions expanded from 1195 to 2475 (a 200% increase). In addition to this notable expansion in database size, we have added thousands of new, colorful, richly annotated pathways depicting drug mechanisms and drug metabolism. Likewise, existing datasets have been significantly improved and expanded, by adding more information on drug indications, drug-drug interactions, drug-food interactions and many other relevant data types for 11 891 drugs. We have also added experimental and predicted MS/MS spectra, 1D/2D-NMR spectra, CCS (collision cross section), RT (retention time) and RI (retention index) data for 9464 of DrugBank's 11 710 small molecule drugs. These and other improvements should make DrugBank 6.0 even more useful to a much wider research audience ranging from medicinal chemists to metabolomics specialists to pharmacologists.
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Affiliation(s)
- Craig Knox
- OMx Personal Health Analytics, Inc., 700–10130 103 St NW, Edmonton, AB T5J 1B9, Canada
| | - Mike Wilson
- OMx Personal Health Analytics, Inc., 700–10130 103 St NW, Edmonton, AB T5J 1B9, Canada
| | - Christen M Klinger
- OMx Personal Health Analytics, Inc., 700–10130 103 St NW, Edmonton, AB T5J 1B9, Canada
| | - Mark Franklin
- OMx Personal Health Analytics, Inc., 700–10130 103 St NW, Edmonton, AB T5J 1B9, Canada
| | - Eponine Oler
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Alex Wilson
- OMx Personal Health Analytics, Inc., 700–10130 103 St NW, Edmonton, AB T5J 1B9, Canada
| | - Allison Pon
- OMx Personal Health Analytics, Inc., 700–10130 103 St NW, Edmonton, AB T5J 1B9, Canada
| | - Jordan Cox
- OMx Personal Health Analytics, Inc., 700–10130 103 St NW, Edmonton, AB T5J 1B9, Canada
| | - Na Eun (Lucy) Chin
- OMx Personal Health Analytics, Inc., 700–10130 103 St NW, Edmonton, AB T5J 1B9, Canada
| | - Seth A Strawbridge
- OMx Personal Health Analytics, Inc., 700–10130 103 St NW, Edmonton, AB T5J 1B9, Canada
| | - Marysol Garcia-Patino
- OMx Personal Health Analytics, Inc., 700–10130 103 St NW, Edmonton, AB T5J 1B9, Canada
| | - Ray Kruger
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Aadhavya Sivakumaran
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Selena Sanford
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Rahil Doshi
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Nitya Khetarpal
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Omolola Fatokun
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Daphnee Doucet
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Ashley Zubkowski
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Dorsa Yahya Rayat
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Hayley Jackson
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Karxena Harford
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Afia Anjum
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Mahi Zakir
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Fei Wang
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Siyang Tian
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Brian Lee
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Jaanus Liigand
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Harrison Peters
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Ruo Qi (Rachel) Wang
- OMx Personal Health Analytics, Inc., 700–10130 103 St NW, Edmonton, AB T5J 1B9, Canada
| | - Tue Nguyen
- OMx Personal Health Analytics, Inc., 700–10130 103 St NW, Edmonton, AB T5J 1B9, Canada
| | - Denise So
- OMx Personal Health Analytics, Inc., 700–10130 103 St NW, Edmonton, AB T5J 1B9, Canada
| | - Matthew Sharp
- OMx Personal Health Analytics, Inc., 700–10130 103 St NW, Edmonton, AB T5J 1B9, Canada
| | - Rodolfo da Silva
- OMx Personal Health Analytics, Inc., 700–10130 103 St NW, Edmonton, AB T5J 1B9, Canada
| | - Cyrella Gabriel
- OMx Personal Health Analytics, Inc., 700–10130 103 St NW, Edmonton, AB T5J 1B9, Canada
| | - Joshua Scantlebury
- OMx Personal Health Analytics, Inc., 700–10130 103 St NW, Edmonton, AB T5J 1B9, Canada
| | - Marissa Jasinski
- OMx Personal Health Analytics, Inc., 700–10130 103 St NW, Edmonton, AB T5J 1B9, Canada
| | - David Ackerman
- OMx Personal Health Analytics, Inc., 700–10130 103 St NW, Edmonton, AB T5J 1B9, Canada
| | - Timothy Jewison
- OMx Personal Health Analytics, Inc., 700–10130 103 St NW, Edmonton, AB T5J 1B9, Canada
| | - Tanvir Sajed
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Vasuk Gautam
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2H1, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 1C9, Canada
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Heinrich L, Patton W, Bennett D, Ackerman D, Park G, Bogovic JA, Eckstein N, Petruncio A, Clements J, Pang S, Shan Xu C, Funke J, Korff W, Hess H, Lippincott-Schwartz J, Saalfeld S, Weigel A. Towards Generalizable Organelle Segmentation in Volume Electron Microscopy. Microsc Microanal 2023; 29:975. [PMID: 37613645 DOI: 10.1093/micmic/ozad067.487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Larissa Heinrich
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | - Will Patton
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | - Davis Bennett
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | - David Ackerman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | - Grace Park
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | - John A Bogovic
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | | | - Alyson Petruncio
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | - Jody Clements
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | - Song Pang
- Yale School of Medicine, New Haven, Connecticut, United States
| | - C Shan Xu
- Yale School of Medicine, New Haven, Connecticut, United States
| | - Jan Funke
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | - Wyatt Korff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | - Harald Hess
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | | | - Stephan Saalfeld
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
| | - Aubrey Weigel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States
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4
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Bharathan NK, Giang W, Hoffman CL, Aaron JS, Khuon S, Chew TL, Preibisch S, Trautman ET, Heinrich L, Bogovic J, Bennett D, Ackerman D, Park W, Petruncio A, Weigel AV, Saalfeld S, Wayne Vogl A, Stahley SN, Kowalczyk AP. Architecture and dynamics of a desmosome-endoplasmic reticulum complex. Nat Cell Biol 2023; 25:823-835. [PMID: 37291267 PMCID: PMC10960982 DOI: 10.1038/s41556-023-01154-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 04/24/2023] [Indexed: 06/10/2023]
Abstract
The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signalling and lipid transfer. Here, using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometre proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization, mobility and expression of ER stress transcripts. These findings indicate that desmosomes and the keratin cytoskeleton regulate the distribution, function and dynamics of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction.
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Affiliation(s)
- Navaneetha Krishnan Bharathan
- Departments of Dermatology and Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - William Giang
- Departments of Dermatology and Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Coryn L Hoffman
- Departments of Dermatology and Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jesse S Aaron
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Satya Khuon
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Teng-Leong Chew
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Stephan Preibisch
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Eric T Trautman
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Larissa Heinrich
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - John Bogovic
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Davis Bennett
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - David Ackerman
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Woohyun Park
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Alyson Petruncio
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Aubrey V Weigel
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Stephan Saalfeld
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - A Wayne Vogl
- Life Sciences Institute and the Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sara N Stahley
- Departments of Dermatology and Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Andrew P Kowalczyk
- Departments of Dermatology and Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
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McClung G, Vijayakumar V, Nagar K, Islam A, Nadolski G, Hunt S, Ackerman D, Gade T. Abstract No. 141 Development and Characterization of Patient-Derived Rat Models of Hepatocellular Carcinoma for Interventional Oncology. J Vasc Interv Radiol 2023. [DOI: 10.1016/j.jvir.2022.12.193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
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6
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Bulumulla C, Krasley AT, Cristofori-Armstrong B, Valinsky WC, Walpita D, Ackerman D, Clapham DE, Beyene AG. Visualizing synaptic dopamine efflux with a 2D composite nanofilm. eLife 2022; 11:78773. [PMID: 35786443 PMCID: PMC9363124 DOI: 10.7554/elife.78773] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/01/2022] [Indexed: 11/23/2022] Open
Abstract
Chemical neurotransmission constitutes one of the fundamental modalities of communication between neurons. Monitoring release of these chemicals has traditionally been difficult to carry out at spatial and temporal scales relevant to neuron function. To understand chemical neurotransmission more fully, we need to improve the spatial and temporal resolutions of measurements for neurotransmitter release. To address this, we engineered a chemi-sensitive, two-dimensional composite nanofilm that facilitates visualization of the release and diffusion of the neurochemical dopamine with synaptic resolution, quantal sensitivity, and simultaneously from hundreds of release sites. Using this technology, we were able to monitor the spatiotemporal dynamics of dopamine release in dendritic processes, a poorly understood phenomenon. We found that dopamine release is broadcast from a subset of dendritic processes as hotspots that have a mean spatial spread of ≈ 3.2 µm (full width at half maximum [FWHM]) and are observed with a mean spatial frequency of one hotspot per ≈ 7.5 µm of dendritic length. Major dendrites of dopamine neurons and fine dendritic processes, as well as dendritic arbors and dendrites with no apparent varicose morphology participated in dopamine release. Remarkably, these release hotspots co-localized with Bassoon, suggesting that Bassoon may contribute to organizing active zones in dendrites, similar to its role in axon terminals. To form the vast and complex network necessary for an organism to sense and react to the world, neurons must connect at highly specialized junctions. Individual cells communicate at these ‘synapses’ by releasing chemical signals (or neurotransmitters) such as dopamine, a molecule involved in learning and motivation. Despite the central role that synapses play in the brain, it remains challenging to measure exactly where neurotransmitters are released and how far they travel from their release site. Currently, most tools available to scientists only allow bulk measurements of neurotransmitter release. To tackle this limitation, Bulumulla et al. developed a new way to measure neurotransmitter release from neurons, harnessing a technique which uses fluorescent nanosensors that glow brighter when exposed to dopamine. These sensors form a very thin film upon which neurons can grow; when the cells release dopamine, the sensors ‘light up’ as they encounter the molecule. Dubbed DopaFilm, the technology reveals exactly where the neurotransmitter comes from and how it spreads between cells in real time. In particular, the approach showed that dopamine emerges from 'hot spots' at specific sites in cells; it also helped Bulumulla et al. study how dopamine is released from subcellular compartments that have previously not been well characterized. Improving the sensors so that the film could detect other neurotransmitters besides dopamine would broaden the use of this approach. In the future, combining this technology with other types of imaging should enable studies of individual synapses with intricate detail.
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Alam S, Eom TY, Steinberg J, Ackerman D, Schmitt JE, Akers WJ, Zakharenko SS, Khairy K. An End-To-End Pipeline for Fully Automatic Morphological Quantification of Mouse Brain Structures From MRI Imagery. Front Bioinform 2022; 2:865443. [PMID: 36304320 PMCID: PMC9580949 DOI: 10.3389/fbinf.2022.865443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/03/2022] [Indexed: 11/29/2022] Open
Abstract
Segmentation of mouse brain magnetic resonance images (MRI) based on anatomical and/or functional features is an important step towards morphogenetic brain structure characterization of murine models in neurobiological studies. State-of-the-art image segmentation methods register image volumes to standard presegmented templates or well-characterized highly detailed image atlases. Performance of these methods depends critically on the quality of skull-stripping, which is the digital removal of tissue signal exterior to the brain. This is, however, tedious to do manually and challenging to automate. Registration-based segmentation, in addition, performs poorly on small structures, low resolution images, weak signals, or faint boundaries, intrinsic to in vivo MRI scans. To address these issues, we developed an automated end-to-end pipeline called DeepBrainIPP (deep learning-based brain image processing pipeline) for 1) isolating brain volumes by stripping skull and tissue from T2w MRI images using an improved deep learning-based skull-stripping and data augmentation strategy, which enables segmentation of large brain regions by atlas or template registration, and 2) address segmentation of small brain structures, such as the paraflocculus, a small lobule of the cerebellum, for which DeepBrainIPP performs direct segmentation with a dedicated model, producing results superior to the skull-stripping/atlas-registration paradigm. We demonstrate our approach on data from both in vivo and ex vivo samples, using an in-house dataset of 172 images, expanded to 4,040 samples through data augmentation. Our skull stripping model produced an average Dice score of 0.96 and residual volume of 2.18%. This facilitated automatic registration of the skull-stripped brain to an atlas yielding an average cross-correlation of 0.98. For small brain structures, direct segmentation yielded an average Dice score of 0.89 and 5.32% residual volume error, well below the tolerance threshold for phenotype detection. Full pipeline execution is provided to non-expert users via a Web-based interface, which exposes analysis parameters, and is powered by a service that manages job submission, monitors job status and provides job history. Usability, reliability, and user experience of DeepBrainIPP was measured using the Customer Satisfaction Score (CSAT) and a modified PYTHEIA Scale, with a rating of excellent. DeepBrainIPP code, documentation and network weights are freely available to the research community.
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Affiliation(s)
- Shahinur Alam
- Center for Bioimage Informatics, St. Jude Children’s Research Hospital, Memphis, TN, United States
- *Correspondence: Shahinur Alam, ; Khaled Khairy,
| | - Tae-Yeon Eom
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Jeffrey Steinberg
- Center for in Vivo Imaging and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - David Ackerman
- Scientific Computing, Janelia Research Campus, Ashburn, VA, United States
| | - J. Eric Schmitt
- Brain Behavior Laboratory, Departments of Psychiatry and Radiology, University of Pennsylvania, Philadelphia, PA, United States
| | - Walter J. Akers
- Center for in Vivo Imaging and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Stanislav S. Zakharenko
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Khaled Khairy
- Center for Bioimage Informatics, St. Jude Children’s Research Hospital, Memphis, TN, United States
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
- *Correspondence: Shahinur Alam, ; Khaled Khairy,
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Ritter AT, Shtengel G, Xu CS, Weigel A, Hoffman DP, Freeman M, Iyer N, Alivodej N, Ackerman D, Voskoboinik I, Trapani J, Hess HF, Mellman I. ESCRT-mediated membrane repair protects tumor-derived cells against T cell attack. Science 2022; 376:377-382. [PMID: 35446649 DOI: 10.1126/science.abl3855] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Cytotoxic T lymphocytes (CTLs) and natural killer cells kill virus-infected and tumor cells through the polarized release of perforin and granzymes. Perforin is a pore-forming toxin that creates a lesion in the plasma membrane of the target cell through which granzymes enter the cytosol and initiate apoptosis. Endosomal sorting complexes required for transport (ESCRT) proteins are involved in the repair of small membrane wounds. We found that ESCRT proteins were precisely recruited in target cells to sites of CTL engagement immediately after perforin release. Inhibition of ESCRT machinery in cancer-derived cells enhanced their susceptibility to CTL-mediated killing. Thus, repair of perforin pores by ESCRT machinery limits granzyme entry into the cytosol, potentially enabling target cells to resist cytolytic attack.
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Affiliation(s)
| | - Gleb Shtengel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - C Shan Xu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Aubrey Weigel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - David P Hoffman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Melanie Freeman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Nirmala Iyer
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Nensi Alivodej
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - David Ackerman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Ilia Voskoboinik
- Rosie Lew Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne VIC, Australia
| | - Joseph Trapani
- Rosie Lew Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne VIC, Australia
| | - Harald F Hess
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Ira Mellman
- Genentech, Inc., South San Francisco, CA 94080, USA
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Vázquez Salgado A, Preziosi M, Yin D, Holczbauer A, Zahm A, Erez N, Kieckhaefer J, Ackerman D, Gade T, Kaestner K, Wangensteen K. In Vivo Screen Identifies Liver X Receptor Alpha Agonism Potentiates Sorafenib Killing of Hepatocellular Carcinoma. Gastro Hep Advances 2022; 1:905-908. [PMID: 36117551 PMCID: PMC9481113 DOI: 10.1016/j.gastha.2022.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Weinfurtner K, Cho J, Ackerman D, Woodard A, Li W, Soulen M, Dagli M, Shamimi-Noori S, Mondschein J, Sudheendra D, Stavropoulos S, Jhala D, Hunt S, Nadolski G, Kaplan D, Siegelman E, Furth E, Gade T. Abstract No. 560 Quality of large-volume percutaneous core biopsies of hepatocellular carcinoma for research applications. J Vasc Interv Radiol 2021. [DOI: 10.1016/j.jvir.2021.03.370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Barksdale A, Santarpia J, Herrera V, Ackerman D, Lowe J, Wadman M, Zeger W. 200 Implementation of a COVID-19 Cohort Area Resulted in No Surface or Air Contamination in Surrounding Areas in One Academic Emergency Department. Ann Emerg Med 2020. [PMCID: PMC7598749 DOI: 10.1016/j.annemergmed.2020.09.212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Scheffer LK, Xu CS, Januszewski M, Lu Z, Takemura SY, Hayworth KJ, Huang GB, Shinomiya K, Maitlin-Shepard J, Berg S, Clements J, Hubbard PM, Katz WT, Umayam L, Zhao T, Ackerman D, Blakely T, Bogovic J, Dolafi T, Kainmueller D, Kawase T, Khairy KA, Leavitt L, Li PH, Lindsey L, Neubarth N, Olbris DJ, Otsuna H, Trautman ET, Ito M, Bates AS, Goldammer J, Wolff T, Svirskas R, Schlegel P, Neace E, Knecht CJ, Alvarado CX, Bailey DA, Ballinger S, Borycz JA, Canino BS, Cheatham N, Cook M, Dreher M, Duclos O, Eubanks B, Fairbanks K, Finley S, Forknall N, Francis A, Hopkins GP, Joyce EM, Kim S, Kirk NA, Kovalyak J, Lauchie SA, Lohff A, Maldonado C, Manley EA, McLin S, Mooney C, Ndama M, Ogundeyi O, Okeoma N, Ordish C, Padilla N, Patrick CM, Paterson T, Phillips EE, Phillips EM, Rampally N, Ribeiro C, Robertson MK, Rymer JT, Ryan SM, Sammons M, Scott AK, Scott AL, Shinomiya A, Smith C, Smith K, Smith NL, Sobeski MA, Suleiman A, Swift J, Takemura S, Talebi I, Tarnogorska D, Tenshaw E, Tokhi T, Walsh JJ, Yang T, Horne JA, Li F, Parekh R, Rivlin PK, Jayaraman V, Costa M, Jefferis GSXE, Ito K, Saalfeld S, George R, Meinertzhagen IA, Rubin GM, Hess HF, Jain V, Plaza SM. A connectome and analysis of the adult Drosophila central brain. eLife 2020; 9:e57443. [PMID: 32880371 PMCID: PMC7546738 DOI: 10.7554/elife.57443] [Citation(s) in RCA: 406] [Impact Index Per Article: 101.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/01/2020] [Indexed: 12/26/2022] Open
Abstract
The neural circuits responsible for animal behavior remain largely unknown. We summarize new methods and present the circuitry of a large fraction of the brain of the fruit fly Drosophila melanogaster. Improved methods include new procedures to prepare, image, align, segment, find synapses in, and proofread such large data sets. We define cell types, refine computational compartments, and provide an exhaustive atlas of cell examples and types, many of them novel. We provide detailed circuits consisting of neurons and their chemical synapses for most of the central brain. We make the data public and simplify access, reducing the effort needed to answer circuit questions, and provide procedures linking the neurons defined by our analysis with genetic reagents. Biologically, we examine distributions of connection strengths, neural motifs on different scales, electrical consequences of compartmentalization, and evidence that maximizing packing density is an important criterion in the evolution of the fly's brain.
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Affiliation(s)
- Louis K Scheffer
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - C Shan Xu
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | | | - Zhiyuan Lu
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
- Life Sciences Centre, Dalhousie UniversityHalifaxCanada
| | - Shin-ya Takemura
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Kenneth J Hayworth
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Gary B Huang
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Kazunori Shinomiya
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | | | - Stuart Berg
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Jody Clements
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Philip M Hubbard
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - William T Katz
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Lowell Umayam
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Ting Zhao
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - David Ackerman
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | | | - John Bogovic
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Tom Dolafi
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Dagmar Kainmueller
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Takashi Kawase
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Khaled A Khairy
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | | | - Peter H Li
- Google ResearchMountain ViewUnited States
| | | | - Nicole Neubarth
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Donald J Olbris
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Hideo Otsuna
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Eric T Trautman
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Masayoshi Ito
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
- Institute for Quantitative Biosciences, University of TokyoTokyoJapan
| | | | - Jens Goldammer
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
- Institute of Zoology, Biocenter Cologne, University of CologneCologneGermany
| | - Tanya Wolff
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Robert Svirskas
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | | | - Erika Neace
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | | | - Chelsea X Alvarado
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Dennis A Bailey
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Samantha Ballinger
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | | | - Brandon S Canino
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Natasha Cheatham
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Michael Cook
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Marisa Dreher
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Octave Duclos
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Bryon Eubanks
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Kelli Fairbanks
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Samantha Finley
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Nora Forknall
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Audrey Francis
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | | | - Emily M Joyce
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - SungJin Kim
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Nicole A Kirk
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Julie Kovalyak
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Shirley A Lauchie
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Alanna Lohff
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Charli Maldonado
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Emily A Manley
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Sari McLin
- Life Sciences Centre, Dalhousie UniversityHalifaxCanada
| | - Caroline Mooney
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Miatta Ndama
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Omotara Ogundeyi
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Nneoma Okeoma
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Christopher Ordish
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Nicholas Padilla
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | | | - Tyler Paterson
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Elliott E Phillips
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Emily M Phillips
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Neha Rampally
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Caitlin Ribeiro
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | | | - Jon Thomson Rymer
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Sean M Ryan
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Megan Sammons
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Anne K Scott
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Ashley L Scott
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Aya Shinomiya
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Claire Smith
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Kelsey Smith
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Natalie L Smith
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Margaret A Sobeski
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Alia Suleiman
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Jackie Swift
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Satoko Takemura
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Iris Talebi
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | | | - Emily Tenshaw
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Temour Tokhi
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - John J Walsh
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Tansy Yang
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | | | - Feng Li
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Ruchi Parekh
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Patricia K Rivlin
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Vivek Jayaraman
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Marta Costa
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
| | - Gregory SXE Jefferis
- MRC Laboratory of Molecular BiologyCambridgeUnited States
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
| | - Kei Ito
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
- Institute for Quantitative Biosciences, University of TokyoTokyoJapan
- Institute of Zoology, Biocenter Cologne, University of CologneCologneGermany
| | - Stephan Saalfeld
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Reed George
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Ian A Meinertzhagen
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
- Life Sciences Centre, Dalhousie UniversityHalifaxCanada
| | - Gerald M Rubin
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Harald F Hess
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Viren Jain
- Google Research, Google LLCZurichSwitzerland
| | - Stephen M Plaza
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
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Perkons N, Mercadante M, Johnson O, Pilla G, Profka E, Ackerman D, Nadolski G, Hunt S, Gade T. 3:45 PM Abstract No. 195 Leveraging transarterial chemoembolization–induced metabolic reprogramming and CRISPR-based genome editing to identify latent tumor viability with DNP-13C-NMRS in hepatocellular carcinoma. J Vasc Interv Radiol 2020. [DOI: 10.1016/j.jvir.2019.12.234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Tischfield D, Ackerman D, Noji M, Chen J, Perkons N, Nadolski G, Hunt S, Soulen M, Furth E, Gade T, Tischfield D. 03:45 PM Abstract No. 378 Establishment of hepatocellular carcinoma patient-derived xenografts from minimally invasive image-guided percutaneous biopsies. J Vasc Interv Radiol 2019. [DOI: 10.1016/j.jvir.2018.12.452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Perkons N, Nwaezeapu C, Wildenberg J, Stein E, Itkin-Ofer R, Ackerman D, Soulen M, Hunt S, Nadolski G, Gade T. Abstract No. 496 Electrochemical treatment causes necrosis by inducing pH changes in the microenvironment. J Vasc Interv Radiol 2018. [DOI: 10.1016/j.jvir.2018.01.541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Benjamin J, Silk M, Ackerman D, Hunt S, Nadolski G, Gade T. 4:00 PM Abstract No. 348 Epigenetic alterations enable hepatocellular carcinoma cell survival under metabolic stress. J Vasc Interv Radiol 2018. [DOI: 10.1016/j.jvir.2018.01.386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Naik HS, Zhang J, Lofquist A, Assefa T, Sarkar S, Ackerman D, Singh A, Singh AK, Ganapathysubramanian B. A real-time phenotyping framework using machine learning for plant stress severity rating in soybean. Plant Methods 2017; 13:23. [PMID: 28405214 PMCID: PMC5385078 DOI: 10.1186/s13007-017-0173-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 03/29/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND Phenotyping is a critical component of plant research. Accurate and precise trait collection, when integrated with genetic tools, can greatly accelerate the rate of genetic gain in crop improvement. However, efficient and automatic phenotyping of traits across large populations is a challenge; which is further exacerbated by the necessity of sampling multiple environments and growing replicated trials. A promising approach is to leverage current advances in imaging technology, data analytics and machine learning to enable automated and fast phenotyping and subsequent decision support. In this context, the workflow for phenotyping (image capture → data storage and curation → trait extraction → machine learning/classification → models/apps for decision support) has to be carefully designed and efficiently executed to minimize resource usage and maximize utility. We illustrate such an end-to-end phenotyping workflow for the case of plant stress severity phenotyping in soybean, with a specific focus on the rapid and automatic assessment of iron deficiency chlorosis (IDC) severity on thousands of field plots. We showcase this analytics framework by extracting IDC features from a set of ~4500 unique canopies representing a diverse germplasm base that have different levels of IDC, and subsequently training a variety of classification models to predict plant stress severity. The best classifier is then deployed as a smartphone app for rapid and real time severity rating in the field. RESULTS We investigated 10 different classification approaches, with the best classifier being a hierarchical classifier with a mean per-class accuracy of ~96%. We construct a phenotypically meaningful 'population canopy graph', connecting the automatically extracted canopy trait features with plant stress severity rating. We incorporated this image capture → image processing → classification workflow into a smartphone app that enables automated real-time evaluation of IDC scores using digital images of the canopy. CONCLUSION We expect this high-throughput framework to help increase the rate of genetic gain by providing a robust extendable framework for other abiotic and biotic stresses. We further envision this workflow embedded onto a high throughput phenotyping ground vehicle and unmanned aerial system that will allow real-time, automated stress trait detection and quantification for plant research, breeding and stress scouting applications.
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Affiliation(s)
- Hsiang Sing Naik
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011 USA
| | - Jiaoping Zhang
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
| | - Alec Lofquist
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011 USA
| | - Teshale Assefa
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
| | - Soumik Sarkar
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011 USA
| | - David Ackerman
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011 USA
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
| | - Asheesh K. Singh
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
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Simpson R, Ackerman D, Feigenson G. Membrane Bending Modulus for Ternary Mixture Models of the Cell Plasma Membrane. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.1336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Rubin LH, Opsahl M, Ackerman D. P02.163. Acupuncture and donor egg in vitro fertilization cycles: a retrospective chart review comparing two acupuncture protocols. BMC Complement Altern Med 2012. [PMCID: PMC3373733 DOI: 10.1186/1472-6882-12-s1-p219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Ackerman D, Shinto L, Hardy M, Heyman A, Nguyen L, Senders A, Abrams D, Ali A, Enebo B, Homel P, Horowitz R, Reardon M, Torkelson C. P02.08. Patient reported outcomes from complementary, alternative, and integrative medicine (PROCAIM): a feasibility practice network study. BMC Complement Altern Med 2012. [PMCID: PMC3373882 DOI: 10.1186/1472-6882-12-s1-p64] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Rubin LH, Opsahl M, Ackerman D. P02.15. Acupuncture improves in vitro fertilization live birth outcomes: a retrospective chart review. Altern Ther Health Med 2012. [PMCID: PMC3373844 DOI: 10.1186/1472-6882-12-s1-p71] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Ackerman D, Amazon J, Heberle F, Feigenson G. Assessing Perturbations of a Fluorescent Lipid in a DPPC Bilayer with Molecular Dynamics. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.3631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Abstract
We report a case in which a regular prostate massage (chronic prostatitis) turned into a life-threatening event. After the prostate massage, an enormous periprostatic hemorrhage developed. During hospitalization the patient developed an embolic insult to the lungs. To our knowledge no ther cases have been published. This report shows the potentially serious consequences, and we conclude that any pain after prostate massage needs further diagnostic steps (ultrasound, CT scan).
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Affiliation(s)
- S Buse
- Klinik für Urologie, Kantonspital St. Gallen, Switzerland.
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Pokorny RM, Wrightson WR, Lewis RK, Paris KJ, Hofmeister A, LaRocca R, Myers SR, Ackerman D, Galandiuk S. Suppository administration of chemotherapeutic drugs with concomitant radiation for rectal cancer. Dis Colon Rectum 1997; 40:1414-20. [PMID: 9407977 DOI: 10.1007/bf02070704] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
PURPOSE Preoperative radiation with combined chemotherapy is effective in shrinking advanced rectal cancer locally and facilitating subsequent surgery. Suppository delivery of 5-fluorouracil is associated with less toxicity and higher rectal tissue concentrations than intravenous administration. This prompted us to evaluate suppository and intravenous administration of 5-fluorouracil and mitomycin C with concomitant radiation to determine associated toxicity. METHODS Rectal, liver, lymph node, and lung tissue and systemic and portal blood were collected serially from male Sprague Dawley rats to determine drug concentrations following suppository or intravenous delivery of 5-fluorouracil or mitomycin C. Thirty-six animals were randomly assigned to treatment groups and received 5-fluorouracil suppositories, mitomycin C suppositories, or an equivalent intravenous dose of 5-fluorouracil or mitomycin C 30 minutes before radiation therapy. Before and 3, 6, 10, and 15 days following this treatment, blood was collected, colonoscopy was performed, and rectal tissue was harvested for histologic examination. RESULTS Mitomycin C suppository was significantly less toxic compared with intravenous delivery, and higher rectal tissue concentrations were observed from 10 to 30 minutes (P < 0.05). Compared with intravenous 5-fluorouracil administration and radiation, 5-fluorouracil suppository and radiation resulted in additive myelosuppression at day 6 (P < 0.05) with rapid recovery. CONCLUSIONS 5-Fluorouracil and mitomycin C suppository delivery combined with radiation causes less systemic toxicity and is more effective than intravenous administration.
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Affiliation(s)
- R M Pokorny
- Price Institute of Surgical Research and Department of Surgery, University of Louisville School of Medicine, Kentucky 40292, USA
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Joseph A, Dunker D, Talley JD, Seeger J, Ackerman D. Directional coronary atherectomy for the diagnosis and treatment of radiation-induced coronary artery stenosis. J Interv Cardiol 1995; 8:355-8. [PMID: 10172446 DOI: 10.1111/j.1540-8183.1995.tb00557.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
While radiation therapy has been known to cause myocardial and pericardial damage, its role in accentuating coronary artery disease in the absence of traditional cardiovascular risk factors has been controversial. As younger patients with treatable cancers are being treated with mediastinal radiation, coronary artery disease as a cause for severe chest pain should be entertained as a possible diagnosis. We describe a 25-year-old male who presented with an inferior wall myocardial infarction 6 years after receiving mediastinal radiation and chemotherapy for Hodgkin's disease. He was subsequently treated by directional atherectomy to a 95% lesion in the right coronary artery. Histological examination of the atherectomy specimen revealed evidence of radiation-induced endothelial damage that had resulted in plaque formation and subsequent ischemia. Possible mechanisms for radiation-induced coronary artery disease and treatment options are discussed.
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Affiliation(s)
- A Joseph
- Department of Pathology, University of Louisville School of Medicine, USA
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Pierangeli SS, Barker JH, Stikovac D, Ackerman D, Anderson G, Barquinero J, Acland R, Harris EN. Effect of human IgG antiphospholipid antibodies on an in vivo thrombosis model in mice. Thromb Haemost 1994; 71:670-4. [PMID: 8091396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
High levels of IgG antiphospholipid antibodies (aPL) have been associated with clinical thrombosis. It is uncertain however whether these antibodies play a direct role in thrombosis or are merely epiphenomena. To investigate whether antiphospholipid antibodies might play a role in thrombosis, we utilized a novel mouse model in which the dynamics of in vivo thrombosis can be studied. CD1 mice (26-30 g) were passively immunized with 25 mg of human IgG from a patient with the Antiphospholipid Syndrome (IgG-APS) (n = 17), IgG from normal pooled sera (IgG-NHS) (n = 9), or saline solution (n = 12), followed by 40 mg of the same preparations at 48 h. At 72 h, levels of human aPL antibodies, detected using the anticardiolipin ELISA test (aCL ELISA test), in mice immunized with IgG-APS, were 50-100 GPL units. Each animal was anesthetized, femoral vein minimally mobilized and subjected to a standardized "pinch" injury to induce thrombosis. The vessel was transilluminated using acrylic optical fibers connected to a light source, and clot formation and dissolution were visualized by a standard surgical microscope equipped with a video camera, video recorder, and computer assisted analysis system. Results showed that average clot size was significantly larger in mice immunized with IgG-APS compared to those treated with saline (p < 0.037). In addition, the thrombus persisted longer in a significantly higher number of mice immunized with IgG-APS (10/17) compared to mice immunized with IgG-NHS (1/9) or saline (2/12) (p < 0.02).(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- S S Pierangeli
- Department of Medicine, University of Louisville, KY 40292
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Abstract
OBJECTIVES The aim of this study was to look at the prevalence of coronary atherosclerosis, its severity and site of involvement in patients < 35 years old who died from noncardiac trauma. BACKGROUND Autopsies performed on casualties of the Korean War revealed coronary artery involvement in 77.3% of the hearts studied, and data after the Vietnam War noted the presence of atherosclerosis in 45% of casualties with severe disease in 5%, suggesting a decline in the prevalence of coronary atherosclerosis in young men. METHODS One hundred eleven victims of noncardiac trauma (86.4% white with a mean age of 26 +/- 6 years) underwent pathologic examination of their coronary arteries to estimate the presence and severity of coronary atherosclerosis grossly, microscopically and through computerized planimetry. Identified segments of the coronary arteries were sectioned at 3-mm intervals, stained with special stains and after microscopic examination transferred to videotape and digitized to allow estimation of the percent compromise in the lumen area by atherosclerotic plaque. RESULTS Signs of coronary atherosclerosis were seen in 78.3% of the total study group, with > 50% narrowing in 20.7% and > 75% narrowing in 9%. No demographic or anatomic features separated the groups with less or more severe involvement of their coronary arteries. Proximal involvement was more common except in the right coronary artery, which was as frequently involved distally. CONCLUSIONS The overall prevalence of coronary atherosclerosis in a young, predominantly male study group was comparable with that noted after the Korean War. Left main or significant two- and three-vessel involvement was noted in 20% of the group studied and emphasizes the need for aggressive risk factor modification in this group.
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Affiliation(s)
- A Joseph
- Department of Medicine, University of Louisville, Kentucky
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30
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Standage BA, Schuman ES, Ackerman D, Gross GF, Ragsdale JW. Does the use of erythropoietin in hemodialysis patients increase dialysis graft thrombosis rates? Am J Surg 1993; 165:650-4. [PMID: 8488954 DOI: 10.1016/s0002-9610(05)80454-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Erythropoietin (EPO) is highly efficacious in the treatment of the anemia of chronic renal failure. Evidence for a reported serious side effect, increased dialysis graft thrombosis, is equivocal. Sixty-four hemodialysis patients utilizing polytetrafluoroethylene (PTFE) grafts were treated with EPO. The patients served as their own historical controls. There were 1.188 thrombectomies and 0.222 mechanical problems per 1,000 patient-days prior to the initiation of EPO treatment. With EPO, the values were 0.656 and 0.222, respectively. Patients were separated into low-, medium-, and high-dose EPO groups and analyzed within groups for the effect of EPO and between groups for a dose-dependent response. According to an analysis of variance procedure, there was no statistically significant differences between the groups, which suggests that EPO is not thrombogenic to dialysis grafts.
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Affiliation(s)
- B A Standage
- Department of Surgery, Good Samaritan Hospital and Medical Center, Portland, OR
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Jones SC, Curtsinger LJ, Whalen JD, Pietsch JD, Ackerman D, Brown GL, Schultz GS. Effect of topical recombinant TGF-beta on healing of partial thickness injuries. J Surg Res 1991; 51:344-52. [PMID: 1921375 DOI: 10.1016/0022-4804(91)90119-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Peptide growth factors produced by platelets, macrophages, epidermal, and dermal cells may play key roles in regulating healing of partial-thickness skin wounds. We examined the effects of recombinant transforming growth factor beta (TGF-beta) on cultures of epidermal and dermal cells in vitro and on healing of partial-thickness injuries in vivo. Increasing concentrations of TGF-beta (0.1, 1, and 10 ng/ml) progressively inhibited serum-stimulated DNA synthesis by up to 95% in cultures of adult human keratinocytes during 48 hr of exposure to TGF-beta. In contrast, TGF-beta (10 and 100 ng/ml) in serum-free media stimulated DNA synthesis by up to 80% compared to serum-free control cultures of adult human dermal fibroblasts. To evaluate the effects of TGF-beta on healing of partial-thickness injuries in vivo, wounds (20 x 20 x 0.6 mm) were created on the dorsal thoracolumbar region of adult pigs by an electrokeratome and were treated daily for 5 days after injury with vehicle or vehicle containing 0.1 or 1 microgram/ml TGF-beta and covered with occlusive dressing. Computerized planimetry of wound photographs demonstrated that TGF-beta treatment stimulated statistically significantly increases in the area of regenerated epidermis compared to wounds treated with saline vehicle on Days 3, 4, 5, and 7 after injury probably due to TGF-beta increasing the rate of epidermal cell migration. In addition, morphometry of biopsy specimens showed that TGF-beta treatment stimulated statistically significant increases in the cross-sectional depths of regenerated dermis compared to wounds treated with saline or Silvadene vehicles on Days 5, 6, and 8 after injury.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- S C Jones
- Department of Surgery, University of Louisville, Kentucky 40292
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32
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Sasser RL, Smith SM, Morris G, Ackerman D. Familial cardiac amyloidosis. Diagnosis by immunocytochemistry. J Ky Med Assoc 1991; 89:325-7. [PMID: 1919307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Familial cardiac amyloidosis is a rare disorder that is difficult to diagnose. There is no specific therapy for this disease, but it is important to distinguish the cardiac and gastrointestinal symptoms of this disease from those of other treatable causes. We have treated a patient with this disorder who presented with cardiac and gastrointestinal symptoms. The diagnosis of amyloidosis was suspected on rectal biopsy and was confirmed by immunocytochemistry and immunoalkaline phosphatase technique. Pre-albumin was demonstrated in the lesion. We concluded that when familial amyloidosis is suspected, a biopsy from the suspected organ system is helpful for the diagnosis. The detection of pre-albumin by immunocytochemistry can elucidate the diagnosis of familial amyloidosis.
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Affiliation(s)
- R L Sasser
- University of Louisville School of Medicine, KY 40292
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33
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Singer I, Maldonado C, Ackerman D, Shvartsman VA, Kupersmith J. Low energy partial ablation of the atrioventricular node junction in the dog using a suction-ablation catheter. J Am Coll Cardiol 1990; 15:222-30. [PMID: 2295735 DOI: 10.1016/0735-1097(90)90206-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A suction electrode catheter was used for low energy, partial ablation of the atrioventricular (AV) node junction in 12 dogs. In 10 dogs, partial injury of the AV node was induced. In six dogs, delivered energy was measured precisely with use of a specially designed electronic circuit. The total energy required for partial ablation was 225 +/- 91 J. The increase in PR (p less than 0.0001) and AH (p less than 0.001) intervals was proportional to the energy delivered. After ablation, the PR interval increased from 98 +/- 10 to 154 +/- 33 ms (p less than 0.004) and the AH interval from 59 +/- 8 to 102 +/- 16 ms (p less than 0.004). There was no significant change in QRS, QTc, HV or RR intervals. AH and PR intervals were significantly prolonged at 3, 7 and 14 days after ablation (p less than 0.05). Anterograde conduction was significantly altered in 10 dogs. Anterograde AV node effective refractory period increased from 157 +/- 14 to 214 +/- 45 ms (p less than 0.005). Anterograde AV node Wenckebach cycle length increased from 196 +/- 30 to 244 +/- 44 ms (p less than 0.002). Retrograde conduction was assessed in three dogs. Retrograde AV node effective refractory period increased from 156 +/- 21 to 260 ms in two dogs, with complete retrograde block in the third. These changes persisted for up to 2 weeks. Pathologic changes were limited to the region of the AV node. In four dogs adherent thrombus without pulmonary emboli was noted. Partial focal injury to the AV node is feasible in the canine model.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- I Singer
- Cardiovascular Division, University of Louisville, School of Medicine, Kentucky 40292
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Nachbur B, Marincek B, Jakob R, Ackerman D. The impact of computed tomography in the diagnosis and postoperative follow-up of ureteric obstruction in aorto-iliac aneurysmal disease. Eur J Vasc Surg 1989; 3:475-92. [PMID: 2625158 DOI: 10.1016/s0950-821x(89)80121-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Between 1979, the advent of computed tomography in our institution, and 1987 we have treated 520 aorto iliac aneurysms surgically, almost 2/3 on an elective basis, the others (183 = 35.2%) being ruptured. Among non-ruptured aneurysms 220 were symptomatic and 19 of 20 cases with ureteric entrapment occurred in these patients corresponding to 8.6% of this subgroup and verified at surgery. In all of these cases the association between ureteric obstruction and the underlying aneurysmal disease was clearly documented by computed tomography. In 8 patients ureteric entrapment was caused by an inflammatory aneurysm, in 12 cases by an arteriosclerotic aneurysm which in one case was a largely expanded internal iliac aneurysm left behind during previous surgery for a ruptured aorta aneurysm. Postoperative follow-up studies of the 8 patients with an inflammatory aneurysm revealed a time-dependent regression heading towards complete disappearance of perivascular fibrosis. Because of potential difficulties associated with the surgical treatment of inflammatory aneurysms it is important to identify perivascular fibrosis and its extent and localization pre-operatively, which can only be achieved by a CT scan. Simultaneously, CT offers information concerning the presence and degree of pyelectasis and calyceal dilatation, identifies the localisation of ureteric entrapment, defines the extent of aneurysmal disease of the iliac arteries, is best-suited for postoperative follow-up in all of the cases and has the most to offer if contrast medium investigations are contra-indicated in the presence of renal insufficiency. Probably the main reason, if not the only one for preoperative angiography, is to demonstrate associated anomalies of the visceral arteries the state of which however, can be just as well assessed by duplex sonography. Thus, computed tomography is the single most important diagnostic tool in the assessment of aorto-iliac aneurysmal disease especially when associated with ureteric entrapment.
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Affiliation(s)
- B Nachbur
- Department of Thoracic and Cardiovascular Surgery, Inselspital, University of Berne, Switzerland
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Curtsinger LJ, Pietsch JD, Brown GL, von Fraunhofer A, Ackerman D, Polk HC, Schultz GS. Reversal of Adriamycin-impaired wound healing by transforming growth factor-beta. Surg Gynecol Obstet 1989; 168:517-22. [PMID: 2786258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Impaired wound healing remains an important clinical problem. Treatment with systemic Adriamycin (doxorubicin) is known to impair wound healing in patients, and it has been used to produce animal models of impaired healing. The results of previous studies have shown that local treatment of incisions in normal rats with transforming growth factor beta (TGF-beta) or epidermal growth factor (EGF) stimulated early increases in tensile strength of surgical incisions in normal rats. We investigated the effects of locally applied, biosynthetic TGF-beta or EGF on the tensile strength of standardized incisions in rats treated with Adriamycin. Systemic Adriamycin treatment (8 milligrams per kilogram) produced significant decreases in wound tear strength (WTS) and wound tear energy (WTE) when compared with that of normal rats at seven and ten days (p less than 0.01). A single dose of TGF-beta (2 micrograms) in a collagen vehicle stimulated a reversal of this wound healing impairment at ten days (p less than 0.05), returning the WTS and WTE to near normal levels. A single dose of EGF (50 micrograms) in hyaluronic acid failed to increase tensile strength, probably because of formulation of EGF in a vehicle that does not prolong its release in incisions. These results suggest that exogenous growth factors may be clinically useful in stimulating healing in incisions in healing impaired conditions.
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Affiliation(s)
- L J Curtsinger
- Price Institute of Surgical Research, Department of Surgery, University of Louisville, Kentucky
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Abstract
Photodynamic therapy with dihematoporphyrin ether was used to treat superficial bladder tumors in 7 patients with a followup of at least 1 year. Each patient received treatment to the whole bladder and those with papillary lesions received additional focal treatment. At 3 months 4 of the 5 patients with papillary tumors (stages Ta and T1) and 1 of the 2 with diffuse carcinoma in situ (Tis) were free of disease. However, at 1 year only 3 patients remained free of disease. Of 5 patients with an increase in irritative bladder symptoms 4 had a contracted bladder, hydroureteronephrosis and vesicoureteral reflux. Deep bladder biopsies showed replacement of smooth muscle by fibrous tissue. Six patients had mild to moderate skin phototoxicity. We conclude that although photodynamic therapy is an attractive and exciting method to treat cancer, its use with dihematoporphyrin ether in cases of bladder carcinoma can be associated with significant complications. The correct treatment parameters for safe, effective therapy are not known to date.
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Affiliation(s)
- J I Harty
- Department of Surgery, University of Louisville School of Medicine, Kentucky
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Akins EW, Ackerman D, Garner J, Hawkins IF, Newman RC. Percutaneous Stone Removal Using a Combined Retrograde-Antegrade Access Technique. Urolithiasis 1989. [DOI: 10.1007/978-1-4899-0873-5_332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Brown GL, Richardson JD, Malangoni MA, Tobin GR, Ackerman D, Polk HC. Comparison of Prosthetic Materials for Abdominal Wall Reconstruction in the Presence of Contamination and Infection. Vet Surg 1985. [DOI: 10.1111/j.1532-950x.1985.tb00892.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Abstract
Thirteen healthy adult subjects, 34.2 +/- 7.4 years of age received oral lithium carbonate, 900 or 1200 mg daily for 10 days. Refraction, visual acuity, visual fields, corneal sensation, basal tear secretion, ocular motility, convergence amplitude, near point of convergence, Hertel exophthalmometry, pupillary reflexes, intraocular pressure, voluntary and pilocarpine-induced accommodation, and biomicroscopy and ophthalmoscopy of the anterior and posterior ocular segments were determined 4 days prior to starting lithium, 10 days after commencing lithium, and 14 days after discontinuing lithium. Some subjective visual or ocular complaints were reported, but no clinically or statistically significant change occurred in any parameter studied. There were slight, non-significant tendencies toward constriction of the measured visual field, reduction of voluntary and pilocarpine-induced accommodation, and reduction of near convergence amplitude while taking lithium; the former two were reversed when lithium was discontinued, the latter was not.
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Brown GL, Richardson JD, Malangoni MA, Tobin GR, Ackerman D, Polk HC. Comparison of prosthetic materials for abdominal wall reconstruction in the presence of contamination and infection. Ann Surg 1985; 201:705-11. [PMID: 3159353 PMCID: PMC1250799 DOI: 10.1097/00000658-198506000-00006] [Citation(s) in RCA: 169] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abdominal wall defects resulting from trauma, invasive infection, or hernia present a difficult problem for the surgeon. In order to study the problems associated with the prosthetic materials used for abdominal wall reconstruction, an animal model was used to simulate abdominal wall defects in the presence of peritonitis and invasive infection. One hundred guinea pigs were repaired with either polytetrafluorethylene (PTFE) or polypropylene mesh (PPM). Our experiments included intra-operative contamination with Staphylococcus aureus. We found significantly fewer organisms (p less than 0.05) adherent to the PTFE than to the PPM when antibiotics were administered after surgery, as well as when no antibiotics were given. In the presence of peritonitis, we found no real difference in numbers of intraperitoneal bacteria present whether PTFE or PPM was used. In all instances, the PTFE patches produced fewer adhesions and were more easily removed. From these experiments, it appears that PTFE may be associated with fewer problems than PPM in the presence of contamination and infection.
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41
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Jefferson JW, Kaufman P, Ackerman D. Tear lithium concentration: a measurement of dubious clinical value. J Clin Psychiatry 1984; 45:304-5. [PMID: 6429127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A mean tear/serum lithium ratio of 0.77 +/- 0.06 was found in 13 volunteers who were given lithium carbonate for 7 days. This finding differs considerably from those of another study, which reported tear and plasma lithium levels to be quite similar. It is suggested that measurement of tear lithium concentration has no clinical utility and that further research along these lines should be discouraged.
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Abstract
1. The thermoregulatory characteristics of the neurogenic hyperthermia produced in rats by unilateral mechanical destruction of the rostral hypothalamic/preoptic region were studied. 2. The investigational methods employed included (a) observing the thermoregulatory effector activities which were responsible for generation of hyperthermia, (b) observing the thermoregulatory reactions elicited by forcefully elevating or lowering core temperature during neurogenic hyperthermia and (c) observing the effect of ambient temperature on hyperthermia magnitude. 3. At 26 degrees C, hyperthermia was effected by a transient increase in shivering thermogenesis and a concomitant minimization of heat loss through the tail. 4. At 26 degrees C, perturbations of core temperature during the plateau phase of hyperthermia were induced by internal or external heating and cooling. The disturbances elicited compensatory changes in shivering activity and in tail vasomotor tonus, and core temperature was rapidly and precisely returned to its pre-perturbation level. 5. The magnitudes of hyperthermias experienced by rats lesioned at 10, 15, 26 and 32 degrees C, as measured by the change in colonic temperature and by the area under the fever curve, were not significantly different. At 36 degrees C, rats were hyperthermic prior to lesioning, and the magnitude of the lesion-induced hyperthermia was significantly attenuated. 6. The results indicate that the neurogenic hyperthermia produced by unilateral hypothalamic puncture in the rat is generated by a coordinated modulation of thermogenic and heat retentive effectors and that the plateau level of hyperthermia is well regulated. These characteristics are compatible with the hypothesis that neurogenic hyperthermia is mediated by prostaglandins released from injured tissue and acting on surviving rostral hypothalamic tissue.
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Ackerman D, Vicha D. A quality assurance program based on a financial model. QRB Qual Rev Bull 1980; 6:2-4. [PMID: 6777734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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