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Groves L, Whyte SK, Purcell SL, Michaud D, Cai WC, Garber AF, Fast MD. Temperature impacts Atlantic salmon's ( Salmo salar) immunological response to infectious salmon anemia virus (ISAv). FISH AND SHELLFISH IMMUNOLOGY REPORTS 2023; 4:100099. [PMID: 37293549 PMCID: PMC10245120 DOI: 10.1016/j.fsirep.2023.100099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/20/2023] [Accepted: 05/21/2023] [Indexed: 06/10/2023] Open
Abstract
Ocean temperatures continue to rise annually due to the ever-growing consequences of global climate change. These temperature changes can have an impact on the immunological robustness of cultured fish, especially cold-water species such as Atlantic salmon. The salmon farming industry already loses hundreds of millions of dollars each year to infectious and non-infectious diseases. One particularly important and WOAH reportable disease is infectious salmon anemia caused by the orthomyxovirus ISAv. Considering the changing environment, it is necessary to find ways to mitigate the effect of diseases on the industry. For this study, 20 Atlantic salmon families were housed in each of 38 different tanks at the AVC, with half of the fish being kept at 10 °C and half being kept at 20 °C. Donor Atlantic salmon IP- injected with a highly virulent ISAv isolate (HPR4; TCID50 of 1 × 105/mL) were added to each tank as the source of co-habitation infection. Both temperatures were sampled at onset of mortality in co-habited fish and at resolution of mortality. Family background and temperature significantly impacted ISAv load, as assessed by qPCR, time to mortality and overall mortality. Mortality was more acute at 20 °C, but overall mortality was higher at 10 °C. Based on percent mortality calculated over the course of the study, different families demonstrated different levels of survival. The three families that demonstrated the highest percent mortality, and the three families with the lowest percent mortality were then assessed for their antiviral responses using relative gene expression. Genes significantly upregulated between the unexposed fish and ISAv exposed fish included mx1, il4/13a, il12rb2, and trim25, and these were further impacted by temperature. Understanding how ISAv resistance is impacted by temperature can help identify seasonal risks of ISAv outbreaks as well as ideal responses to be targeted through immunopotentiation.
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Affiliation(s)
- L Groves
- Hoplite Lab, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI, Canada
| | - SK Whyte
- Hoplite Lab, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI, Canada
| | - SL Purcell
- Hoplite Lab, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI, Canada
| | - D Michaud
- Hoplite Lab, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI, Canada
| | - WC Cai
- Hoplite Lab, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI, Canada
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - AF Garber
- Huntsman Marine Science Centre, St. Andrews, NB, Canada
| | - MD Fast
- Hoplite Lab, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI, Canada
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Zhao Q, Adeli E, Pohl KM. Training confounder-free deep learning models for medical applications. Nat Commun 2020; 11:6010. [PMID: 33243992 PMCID: PMC7691500 DOI: 10.1038/s41467-020-19784-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/28/2020] [Indexed: 02/08/2023] Open
Abstract
The presence of confounding effects (or biases) is one of the most critical challenges in using deep learning to advance discovery in medical imaging studies. Confounders affect the relationship between input data (e.g., brain MRIs) and output variables (e.g., diagnosis). Improper modeling of those relationships often results in spurious and biased associations. Traditional machine learning and statistical models minimize the impact of confounders by, for example, matching data sets, stratifying data, or residualizing imaging measurements. Alternative strategies are needed for state-of-the-art deep learning models that use end-to-end training to automatically extract informative features from large set of images. In this article, we introduce an end-to-end approach for deriving features invariant to confounding factors while accounting for intrinsic correlations between the confounder(s) and prediction outcome. The method does so by exploiting concepts from traditional statistical methods and recent fair machine learning schemes. We evaluate the method on predicting the diagnosis of HIV solely from Magnetic Resonance Images (MRIs), identifying morphological sex differences in adolescence from those of the National Consortium on Alcohol and Neurodevelopment in Adolescence (NCANDA), and determining the bone age from X-ray images of children. The results show that our method can accurately predict while reducing biases associated with confounders. The code is available at https://github.com/qingyuzhao/br-net .
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Affiliation(s)
- Qingyu Zhao
- Department of Psychiatry & Behavioral Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Ehsan Adeli
- Department of Psychiatry & Behavioral Sciences, Stanford University, Stanford, CA, 94305, USA
- Department of Computer Science, Stanford University, Stanford, CA, 94305, USA
| | - Kilian M Pohl
- Department of Psychiatry & Behavioral Sciences, Stanford University, Stanford, CA, 94305, USA.
- Center for Biomedical Sciences, SRI International, Menlo Park, CA, 94205, USA.
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Tran AP, Ali Al-Radhawi M, Kareva I, Wu J, Waxman DJ, Sontag ED. Delicate Balances in Cancer Chemotherapy: Modeling Immune Recruitment and Emergence of Systemic Drug Resistance. Front Immunol 2020; 11:1376. [PMID: 32695118 PMCID: PMC7338613 DOI: 10.3389/fimmu.2020.01376] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/29/2020] [Indexed: 01/21/2023] Open
Abstract
Metronomic chemotherapy can drastically enhance immunogenic tumor cell death. However, the mechanisms responsible are still incompletely understood. Here, we develop a mathematical model to elucidate the underlying complex interactions between tumor growth, immune system activation, and therapy-mediated immunogenic cell death. Our model is conceptually simple, yet it provides a surprisingly excellent fit to empirical data obtained from a GL261 SCID mouse glioma model treated with cyclophosphamide on a metronomic schedule. The model includes terms representing immune recruitment as well as the emergence of drug resistance during prolonged metronomic treatments. Strikingly, a single fixed set of parameters, adjusted neither for individuals nor for drug schedule, recapitulates experimental data across various drug regimens remarkably well, including treatments administered at intervals ranging from 6 to 12 days. Additionally, the model predicts peak immune activation times, rediscovering experimental data that had not been used in parameter fitting or in model construction. Notably, the validated model suggests that immunostimulatory and immunosuppressive intermediates are responsible for the observed phenomena of resistance and immune cell recruitment, and thus for variation of responses with respect to different schedules of drug administration.
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Affiliation(s)
- Anh Phong Tran
- Department of Chemical Engineering, Northeastern University, Boston, MA, United States
| | - M Ali Al-Radhawi
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA, United States
| | - Irina Kareva
- Mathematical and Computational Sciences Center, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, United States
| | - Junjie Wu
- Clinical Research Institute, Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA, United States
| | - Eduardo D Sontag
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA, United States
- Department of Bioengineering, Northeastern University, Boston, MA, United States
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA, United States
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Grossman Z. Immunological Paradigms, Mechanisms, and Models: Conceptual Understanding Is a Prerequisite to Effective Modeling. Front Immunol 2019; 10:2522. [PMID: 31749803 PMCID: PMC6848063 DOI: 10.3389/fimmu.2019.02522] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 10/10/2019] [Indexed: 12/18/2022] Open
Abstract
Most mathematical models that describe the individual or collective actions of cells aim at creating faithful representations of limited sets of data in a self-consistent manner. Consistency with relevant physiological rules pertaining to the greater picture is rarely imposed. By themselves, such models have limited predictive or even explanatory value, contrary to standard claims. Here I try to show that a more critical examination of currently held paradigms is necessary and could potentially lead to models that pass the test of time. In considering the evolution of paradigms over the past decades I focus on the “smart surveillance” theory of how T cells can respond differentially, individually and collectively, to both self- and foreign antigens depending on various “contextual” parameters. The overall perspective is that physiological messages to cells are encoded not only in the biochemical connections of signaling molecules to the cellular machinery but also in the magnitude, kinetics, and in the time- and space-contingencies, of sets of stimuli. By rationalizing the feasibility of subthreshold interactions, the “dynamic tuning hypothesis,” a central component of the theory, set the ground for further theoretical and experimental explorations of dynamically regulated immune tolerance, homeostasis and diversity, and of the notion that lymphocytes participate in nonclassical physiological functions. Some of these efforts are reviewed. Another focus of this review is the concomitant regulation of immune activation and homeostasis through the operation of a feedback mechanism controlling the balance between renewal and differentiation of activated cells. Different perspectives on the nature and regulation of chronic immune activation in HIV infection have led to conflicting models of HIV pathogenesis—a major area of research for theoretical immunologists over almost three decades—and can have profound impact on ongoing HIV cure strategies. Altogether, this critical review is intended to constructively influence the outlook of prospective model builders and of interested immunologists on the state of the art and to encourage conceptual work.
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Affiliation(s)
- Zvi Grossman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, United States.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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Grebennikov DS, Donets DO, Orlova OG, Argilaguet J, Meyerhans A, Bocharov GA. Mathematical Modeling of the Intracellular Regulation of Immune Processes. Mol Biol 2019. [DOI: 10.1134/s002689331905008x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Moses ME, Cannon JL, Gordon DM, Forrest S. Distributed Adaptive Search in T Cells: Lessons From Ants. Front Immunol 2019; 10:1357. [PMID: 31263465 PMCID: PMC6585175 DOI: 10.3389/fimmu.2019.01357] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/29/2019] [Indexed: 11/13/2022] Open
Abstract
There are striking similarities between the strategies ant colonies use to forage for food and immune systems use to search for pathogens. Searchers (ants and cells) use the appropriate combination of random and directed motion, direct and indirect agent-agent interactions, and traversal of physical structures to solve search problems in a variety of environments. An effective immune response requires immune cells to search efficiently and effectively for diverse types of pathogens in different tissues and organs, just as different species of ants have evolved diverse search strategies to forage effectively for a variety of resources in a variety of habitats. Successful T cell search is required to initiate the adaptive immune response in lymph nodes and to eradicate pathogens at sites of infection in peripheral tissue. Ant search strategies suggest novel predictions about T cell search. In both systems, the distribution of targets in time and space determines the most effective search strategy. We hypothesize that the ability of searchers to sense and adapt to dynamic targets and environmental conditions enhances search effectiveness through adjustments to movement and communication patterns. We also suggest that random motion is a more important component of search strategies than is generally recognized. The behavior we observe in ants reveals general design principles and constraints that govern distributed adaptive search in a wide variety of complex systems, particularly the immune system.
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Affiliation(s)
- Melanie E Moses
- Moses Biological Computation Laboratory, Department of Computer Science, University of New Mexico, Albuquerque, NM, United States.,Biology Department, University of New Mexico, Albuquerque, NM, United States.,Santa Fe Institute, Santa Fe, NM, United States
| | - Judy L Cannon
- The Cannon Laboratory, Department of Molecular Genetics & Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, United States.,Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM, United States.,Autophagy, Inflammation, and Metabolism Center of Biomedical Research Excellence, University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Deborah M Gordon
- Santa Fe Institute, Santa Fe, NM, United States.,Department of Biology, Stanford University, Stanford, CA, United States
| | - Stephanie Forrest
- Santa Fe Institute, Santa Fe, NM, United States.,Biodesign Institute and School for Computing, Informatics, and Decision Sciences Engineering, Arizona State University, Tempe, AZ, United States
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