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Choinière L, Guay-Hottin R, Picard R, Lajoie G, Bonizzato M, Dancause N. Gaussian-process-based Bayesian optimization for neurostimulation interventions in rats. STAR Protoc 2024; 5:102885. [PMID: 38358881 PMCID: PMC10876592 DOI: 10.1016/j.xpro.2024.102885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/11/2023] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
Effective neural stimulation requires adequate parametrization. Gaussian-process (GP)-based Bayesian optimization (BO) offers a framework to discover optimal stimulation parameters in real time. Here, we first provide a general protocol to deploy this framework in neurostimulation interventions and follow by exemplifying its use in detail. Specifically, we describe the steps to implant rats with multi-channel electrode arrays in the hindlimb motor cortex. We then detail how to utilize the GP-BO algorithm to maximize evoked target movements, measured as electromyographic responses. For complete details on the use and execution of this protocol, please refer to Bonizzato and colleagues (2023).1.
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Affiliation(s)
- Léo Choinière
- Department of Neurosciences and Centre Interdisciplinaire de Recherche sur le Cerveau et l'Apprentissage (CIRCA), Université de Montréal, Montreal, QC H3T 1J4, Canada; Mila - Québec AI Institute, Montreal, QC H2S 3H1, Canada.
| | - Rose Guay-Hottin
- Department of Neurosciences and Centre Interdisciplinaire de Recherche sur le Cerveau et l'Apprentissage (CIRCA), Université de Montréal, Montreal, QC H3T 1J4, Canada; Department of Electrical Engineering and Institute of Biomedical Engineering, Polytechnique Montréal, Montreal, QC H3T 1J4, Canada; Mila - Québec AI Institute, Montreal, QC H2S 3H1, Canada
| | - Rémi Picard
- Department of Neurosciences and Centre Interdisciplinaire de Recherche sur le Cerveau et l'Apprentissage (CIRCA), Université de Montréal, Montreal, QC H3T 1J4, Canada; Department of Electrical Engineering and Institute of Biomedical Engineering, Polytechnique Montréal, Montreal, QC H3T 1J4, Canada
| | - Guillaume Lajoie
- Mila - Québec AI Institute, Montreal, QC H2S 3H1, Canada; Mathematics and Statistics Department, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Marco Bonizzato
- Department of Neurosciences and Centre Interdisciplinaire de Recherche sur le Cerveau et l'Apprentissage (CIRCA), Université de Montréal, Montreal, QC H3T 1J4, Canada; Department of Electrical Engineering and Institute of Biomedical Engineering, Polytechnique Montréal, Montreal, QC H3T 1J4, Canada; Mila - Québec AI Institute, Montreal, QC H2S 3H1, Canada
| | - Numa Dancause
- Department of Neurosciences and Centre Interdisciplinaire de Recherche sur le Cerveau et l'Apprentissage (CIRCA), Université de Montréal, Montreal, QC H3T 1J4, Canada.
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Bonizzato M, Guay Hottin R, Côté SL, Massai E, Choinière L, Macar U, Laferrière S, Sirpal P, Quessy S, Lajoie G, Martinez M, Dancause N. Autonomous optimization of neuroprosthetic stimulation parameters that drive the motor cortex and spinal cord outputs in rats and monkeys. Cell Rep Med 2023; 4:101008. [PMID: 37044093 PMCID: PMC10140617 DOI: 10.1016/j.xcrm.2023.101008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 02/16/2023] [Accepted: 03/20/2023] [Indexed: 04/14/2023]
Abstract
Neural stimulation can alleviate paralysis and sensory deficits. Novel high-density neural interfaces can enable refined and multipronged neurostimulation interventions. To achieve this, it is essential to develop algorithmic frameworks capable of handling optimization in large parameter spaces. Here, we leveraged an algorithmic class, Gaussian-process (GP)-based Bayesian optimization (BO), to solve this problem. We show that GP-BO efficiently explores the neurostimulation space, outperforming other search strategies after testing only a fraction of the possible combinations. Through a series of real-time multi-dimensional neurostimulation experiments, we demonstrate optimization across diverse biological targets (brain, spinal cord), animal models (rats, non-human primates), in healthy subjects, and in neuroprosthetic intervention after injury, for both immediate and continual learning over multiple sessions. GP-BO can embed and improve "prior" expert/clinical knowledge to dramatically enhance its performance. These results advocate for broader establishment of learning agents as structural elements of neuroprosthetic design, enabling personalization and maximization of therapeutic effectiveness.
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Affiliation(s)
- Marco Bonizzato
- Department of Neurosciences and Centre interdisciplinaire de recherche sur le cerveau et l'apprentissage (CIRCA), Université de Montréal, Montreal, QC H3T 1J4, Canada; Department of Electrical Engineering and Institute of Biomedical Engineering, Polytechnique Montréal, Montreal, QC H3T 1J4, Canada; CIUSSS du Nord-de-l'Île-de-Montréal, Montreal, QC H4J 1C5, Canada; Mila - Québec AI Institute, Montreal, QC H2S 3H1, Canada.
| | - Rose Guay Hottin
- Department of Neurosciences and Centre interdisciplinaire de recherche sur le cerveau et l'apprentissage (CIRCA), Université de Montréal, Montreal, QC H3T 1J4, Canada; Department of Electrical Engineering and Institute of Biomedical Engineering, Polytechnique Montréal, Montreal, QC H3T 1J4, Canada; Mila - Québec AI Institute, Montreal, QC H2S 3H1, Canada
| | - Sandrine L Côté
- Department of Neurosciences and Centre interdisciplinaire de recherche sur le cerveau et l'apprentissage (CIRCA), Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Elena Massai
- Department of Neurosciences and Centre interdisciplinaire de recherche sur le cerveau et l'apprentissage (CIRCA), Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Léo Choinière
- Department of Neurosciences and Centre interdisciplinaire de recherche sur le cerveau et l'apprentissage (CIRCA), Université de Montréal, Montreal, QC H3T 1J4, Canada; Mila - Québec AI Institute, Montreal, QC H2S 3H1, Canada
| | - Uzay Macar
- Department of Neurosciences and Centre interdisciplinaire de recherche sur le cerveau et l'apprentissage (CIRCA), Université de Montréal, Montreal, QC H3T 1J4, Canada; Mila - Québec AI Institute, Montreal, QC H2S 3H1, Canada
| | - Samuel Laferrière
- Mila - Québec AI Institute, Montreal, QC H2S 3H1, Canada; Computer Science Department, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Parikshat Sirpal
- Department of Neurosciences and Centre interdisciplinaire de recherche sur le cerveau et l'apprentissage (CIRCA), Université de Montréal, Montreal, QC H3T 1J4, Canada; Mila - Québec AI Institute, Montreal, QC H2S 3H1, Canada
| | - Stephan Quessy
- Department of Neurosciences and Centre interdisciplinaire de recherche sur le cerveau et l'apprentissage (CIRCA), Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Guillaume Lajoie
- Mila - Québec AI Institute, Montreal, QC H2S 3H1, Canada; Mathematics and Statistics Department, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Marina Martinez
- Department of Neurosciences and Centre interdisciplinaire de recherche sur le cerveau et l'apprentissage (CIRCA), Université de Montréal, Montreal, QC H3T 1J4, Canada; CIUSSS du Nord-de-l'Île-de-Montréal, Montreal, QC H4J 1C5, Canada
| | - Numa Dancause
- Department of Neurosciences and Centre interdisciplinaire de recherche sur le cerveau et l'apprentissage (CIRCA), Université de Montréal, Montreal, QC H3T 1J4, Canada.
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Lambert DM, Mamer OA, Akerman BR, Choinière L, Gaudet D, Hamet P, Treacy EP. In vivo variability of TMA oxidation is partially mediated by polymorphisms of the FMO3 gene. Mol Genet Metab 2001; 73:224-9. [PMID: 11461189 DOI: 10.1006/mgme.2001.3189] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [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: 11/22/2022]
Abstract
Trimethylaminuria (TMAU) results from an accumulation of an excessive amount of unoxidized trimethylamine that is excreted in urine and body secretions. Mutations of the flavin-containing monooxygenase 3 (FMO3) gene (a hepatic phase I drug-metabolizing enzyme) account for the severe recessively encoded form of this condition. We have previously described a number of FMO3 polymorphisms which in vitro exhibit reduced substrate affinity for several FMO substrates. Here we show that three prevalent polymorphisms (E158K, V257M, and E308G) inherited in particular combinations confer a slight decrease in TMA oxidation under normal physiological conditions, which may be clinically "silent." With the use of substrate loading or with the interaction of other known modulators of FMO3 activity such as hormonal influences, these genotypes may predispose to mild TMAU.
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Affiliation(s)
- D M Lambert
- Biochemical Genetics, Montreal Children's Hospital, Montreal, Quebec, Canada
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Mamer OA, Choinière L, Treacy EP. Measurement of trimethylamine and trimethylamine N-oxide independently in urine by fast atom bombardment mass spectrometry. Anal Biochem 1999; 276:144-9. [PMID: 10603236 DOI: 10.1006/abio.1999.4351] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [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: 11/22/2022]
Abstract
We report a method based upon fast atom bombardment mass spectrometry (FAB-MS) and stable isotope dilution techniques for the measurement of urinary trimethylamine (TMA) and trimethylamine N-oxide (TMAOx). TMA is extracted from urine that was spiked with (15)N-labeled TMA. The extracted TMA isotopomers are quaternized with trideuteromethyl iodide and analyzed in FAB-MS with hexaethylene glycol as matrix. TMAOx is measured by evaporation of another sample of the urine spiked with (15)N-labeled TMAOx on the FAB probe and analyzed as for the TMA. The method allows the ready and simple distinguishing of controls and patients with TMAuria, and is useful in monitoring patients with the disorder. We give examples of its use in determining normal control ranges for these metabolites and in evaluating patients.
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Affiliation(s)
- O A Mamer
- The Mass Spectrometry Unit, McGill University, 1130 Pine Avenue West, Montreal, Canada H3A 1A3
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Tassé D, Choinière L, Morgan S, Bernard D. Recurrent duodenal ulcer. Can J Surg 1978; 21:306-8. [PMID: 679076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In the past 6 years 26 patients underwent operation for recurrent duodenal ulcer after what was considered to be an "adequate" initial operation. In such patients it is necessary first to demonstrate the recurrent ulcer and then to determine its cause. Endoscopy was the best means of confirming the diagnosis. The cause of recurrence was determined by tests for gastric acid secretion; 70% of patients had hyperacidity and 80% had positive results of the Hollander test. Treatment is always surgical but varies depending on the type of initial surgery, the primary cause of recurrence and the condition of the patient. Ten patients underwent vagotomy, 12 had vagotomy with antrectomy and 4 had antrectomy alone. There were no operative deaths but nine (35%) patients experienced 11 significant postoperative complications.
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