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Saghafi S, Rumbell T, Gurev V, Kozloski J, Tamagnini F, Wedgwood KCA, Diekman CO. Inferring Parameters of Pyramidal Neuron Excitability in Mouse Models of Alzheimer's Disease Using Biophysical Modeling and Deep Learning. Bull Math Biol 2024; 86:46. [PMID: 38528167 PMCID: PMC10963524 DOI: 10.1007/s11538-024-01273-5] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 02/19/2024] [Indexed: 03/27/2024]
Abstract
Alzheimer's disease (AD) is believed to occur when abnormal amounts of the proteins amyloid beta and tau aggregate in the brain, resulting in a progressive loss of neuronal function. Hippocampal neurons in transgenic mice with amyloidopathy or tauopathy exhibit altered intrinsic excitability properties. We used deep hybrid modeling (DeepHM), a recently developed parameter inference technique that combines deep learning with biophysical modeling, to map experimental data recorded from hippocampal CA1 neurons in transgenic AD mice and age-matched wildtype littermate controls to the parameter space of a conductance-based CA1 model. Although mechanistic modeling and machine learning methods are by themselves powerful tools for approximating biological systems and making accurate predictions from data, when used in isolation these approaches suffer from distinct shortcomings: model and parameter uncertainty limit mechanistic modeling, whereas machine learning methods disregard the underlying biophysical mechanisms. DeepHM addresses these shortcomings by using conditional generative adversarial networks to provide an inverse mapping of data to mechanistic models that identifies the distributions of mechanistic modeling parameters coherent to the data. Here, we demonstrated that DeepHM accurately infers parameter distributions of the conductance-based model on several test cases using synthetic data generated with complex underlying parameter structures. We then used DeepHM to estimate parameter distributions corresponding to the experimental data and infer which ion channels are altered in the Alzheimer's mouse models compared to their wildtype controls at 12 and 24 months. We found that the conductances most disrupted by tauopathy, amyloidopathy, and aging are delayed rectifier potassium, transient sodium, and hyperpolarization-activated potassium, respectively.
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Affiliation(s)
- Soheil Saghafi
- Department of Mathematical Sciences, New Jersey Institute of Technology, University Heights, Newark, NJ, 07102, USA
- Department of Biomedical Informatics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Timothy Rumbell
- IBM T.J. Watson Research Center, Yorktown Heights, NY, 10598, USA
| | | | - James Kozloski
- IBM T.J. Watson Research Center, Yorktown Heights, NY, 10598, USA
| | | | | | - Casey O Diekman
- Department of Mathematical Sciences, New Jersey Institute of Technology, University Heights, Newark, NJ, 07102, USA.
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Kiarashi Y, Saghafi S, Das B, Hegde C, Madala VSK, Nakum A, Singh R, Tweedy R, Doiron M, Rodriguez AD, Levey AI, Clifford GD, Kwon H. Graph Trilateration for Indoor Localization in Sparsely Distributed Edge Computing Devices in Complex Environments Using Bluetooth Technology. Sensors (Basel) 2023; 23:9517. [PMID: 38067890 PMCID: PMC10708633 DOI: 10.3390/s23239517] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023]
Abstract
Spatial navigation patterns in indoor space usage can reveal important cues about the cognitive health of participants. In this work, we present a low-cost, scalable, open-source edge computing system using Bluetooth low energy (BLE) beacons for tracking indoor movements in a large, 1700 m2 facility used to carry out therapeutic activities for participants with mild cognitive impairment (MCI). The facility is instrumented with 39 edge computing systems, along with an on-premise fog server. The participants carry a BLE beacon, in which BLE signals are received and analyzed by the edge computing systems. Edge computing systems are sparsely distributed in the wide, complex indoor space, challenging the standard trilateration technique for localizing subjects, which assumes a dense installation of BLE beacons. We propose a graph trilateration approach that considers the temporal density of hits from the BLE beacon to surrounding edge devices to handle the inconsistent coverage of edge devices. This proposed method helps us tackle the varying signal strength, which leads to intermittent detection of beacons. The proposed method can pinpoint the positions of multiple participants with an average error of 4.4 m and over 85% accuracy in region-level localization across the entire study area. Our experimental results, evaluated in a clinical environment, suggest that an ordinary medical facility can be transformed into a smart space that enables automatic assessment of individuals' movements, which may reflect health status or response to treatment.
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Affiliation(s)
- Yashar Kiarashi
- Department of Biomedical Informatics, School of Medicine, Emory University, Atlanta, GA 30322, USA; (Y.K.); (S.S.); (H.K.)
| | - Soheil Saghafi
- Department of Biomedical Informatics, School of Medicine, Emory University, Atlanta, GA 30322, USA; (Y.K.); (S.S.); (H.K.)
| | - Barun Das
- Department of Biomedical Informatics, School of Medicine, Emory University, Atlanta, GA 30322, USA; (Y.K.); (S.S.); (H.K.)
| | - Chaitra Hegde
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | | | - ArjunSinh Nakum
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ratan Singh
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Robert Tweedy
- Department of Biomedical Informatics, School of Medicine, Emory University, Atlanta, GA 30322, USA; (Y.K.); (S.S.); (H.K.)
| | - Matthew Doiron
- Department of Neurology, School of Medicine, Emory University, Atlanta, GA 30322, USA (A.D.R.); (A.I.L.)
| | - Amy D. Rodriguez
- Department of Neurology, School of Medicine, Emory University, Atlanta, GA 30322, USA (A.D.R.); (A.I.L.)
| | - Allan I. Levey
- Department of Neurology, School of Medicine, Emory University, Atlanta, GA 30322, USA (A.D.R.); (A.I.L.)
| | - Gari D. Clifford
- Department of Biomedical Informatics, School of Medicine, Emory University, Atlanta, GA 30322, USA; (Y.K.); (S.S.); (H.K.)
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
| | - Hyeokhyen Kwon
- Department of Biomedical Informatics, School of Medicine, Emory University, Atlanta, GA 30322, USA; (Y.K.); (S.S.); (H.K.)
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Khan E, Saghafi S, Diekman CO, Rotstein HG. The emergence of polyglot entrainment responses to periodic inputs in vicinities of Hopf bifurcations in slow-fast systems. Chaos 2022; 32:063137. [PMID: 35778129 DOI: 10.1063/5.0079198] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
Several distinct entrainment patterns can occur in the FitzHugh-Nagumo (FHN) model under external periodic forcing. Investigating the FHN model under different types of periodic forcing reveals the existence of multiple disconnected 1:1 entrainment segments for constant, low enough values of the input amplitude when the unforced system is in the vicinity of a Hopf bifurcation. This entrainment structure is termed polyglot to distinguish it from the single 1:1 entrainment region (monoglot) structure typically observed in Arnold tongue diagrams. The emergence of polyglot entrainment is then explained using phase-plane analysis and other dynamical system tools. Entrainment results are investigated for other slow-fast systems of neuronal, circadian, and glycolytic oscillations. Exploring these models, we found that polyglot entrainment structure (multiple 1:1 regions) is observed when the unforced system is in the vicinity of a Hopf bifurcation and the Hopf point is located near a knee of a cubic-like nullcline.
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Affiliation(s)
- Emel Khan
- Department of Mathematical Sciences, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - Soheil Saghafi
- Department of Mathematical Sciences, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - Casey O Diekman
- Department of Mathematical Sciences, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - Horacio G Rotstein
- Federated Department of Biological Sciences, New Jersey Institute of Technology & Rutgers University, Newark, New Jersey 07102, USA
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Jährling N, Couillard-Deprés S, Becker K, Saghafi S, Wegenast-Braun B, Kramer E, Weiler R, Dodt H. P36 Lightsheet microscopy: Ultramicroscopy in fundamental neuroscience research. Clin Neurophysiol 2019. [DOI: 10.1016/j.clinph.2019.04.689] [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: 10/26/2022]
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Taziki S, Saghafi S, Mousavi S, Modanlu M, Behnampour N. EPA-0337 – Is opioid dependency related to coping strategies? Eur Psychiatry 2014. [DOI: 10.1016/s0924-9338(14)77772-7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Dashti-Khavidaki S, Aghamohammadi A, Farshadi F, Movahedi M, Parvaneh N, Pouladi N, Moazzami K, Cheraghi T, Mahdaviani SA, Saghafi S, Heydari G, Abdollahzade S, Rezaei N. Adverse reactions of prophylactic intravenous immunoglobulin; a 13-year experience with 3004 infusions in Iranian patients with primary immunodeficiency diseases. J Investig Allergol Clin Immunol 2009; 19:139-145. [PMID: 19476018] [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: 05/27/2023] Open
Abstract
Intravenous immunoglobulin (IVIG) replacement therapy improves health-related quality of life in patients with a primary immunodeficiency disease, although there have been reports of adverse reactions associated with its regular administration. The study population was composed of 99 patients with primary antibody deficiencies. All the patients were diagnosed with a primary immunodeficiency disease and received at least 4 infusions of IVIG at the Children's Medical Center Hospital, Tehran, Iran over a 13-year period (1995-2007). A total of 3004 infusions were recorded, and 216 (7.2%) of these were associated with adverse reactions in 66 patients. Adverse reactions were classified as mild (172 reactions), moderate (41 reactions), and severe (3 reactions). The rate of adverse reaction varied by diagnosis from 3.35% in patients with X-linked agammaglobulinemia to 17.4% in IgG subclass deficiency. There were no age-related differences in the rates of adverse reactions. Adverse reactions to IVIG infusions are occasionally encountered; therefore, physicians and nurses should be aware of these reactions in order to manage and prevent them.
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Affiliation(s)
- S Dashti-Khavidaki
- Department of Clinical Pharmacy, School of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
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Ohadinia S, Noroozian M, Shahsavand S, Saghafi S. Evaluation of insomnia and daytime napping in Iranian Alzheimer disease patients: relationship with severity of dementia and comparison with normal adults. Am J Geriatr Psychiatry 2004; 12:517-22. [PMID: 15353390 DOI: 10.1176/appi.ajgp.12.5.517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Alzheimer disease (AD) is among the most common and disabling diseases in adulthood, and it has been largely neglected in traditional societies like Iran. Exacerbation of AD symptoms creates many severe problems, especially in traditional Iranian extended families. One of these problems is insomnia, which can very significantly affect patients' family members because of disturbing insomnia-related behaviors. METHODS The authors studied 53 patients with probable AD who had been interviewed for dementia and depression in the Neurology Clinic of Roozbeh Psychiatric Hospital (Tehran University of Medical Sciences). Excluding patients with overlapping multi-infarct dementia, 35 AD patients (22 men, 13 women) and 21 adults without dementia were studied as a comparison group (11 men, 10 women). RESULTS There was a significant relationship between duration of informant-reported symptoms and severity of dementia with daytime napping and more daytime napping among AD patients than in the comparison group. There was also a significant relationship between cognitive decline and daytime napping in the comparison group. Our study showed a relationship between insomnia and aggression, between daytime napping and paranoid delusions; and between onset of insomnia and anxiety. The comparison group showed a significant relationship between depression and daytime napping. CONCLUSIONS Daytime napping and insomnia are very common among Iranian AD patients, much more so than in normal adults. There is also a significant relationship among psychiatric symptoms, daytime napping, and insomnia, but it seems that daytime napping and insomnia in depressed AD patients are caused more by the progress of AD than by depression.
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Saghafi S, Withford MJ, Piper JA. Characterizing output beams for lasers that use high-magnification unstable resonators. J Opt Soc Am A Opt Image Sci Vis 2001; 18:1634-1643. [PMID: 11444555 DOI: 10.1364/josaa.18.001634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Laser beams generated from high-magnification on-axis unstable resonators by use of hard-edged optics typically have a doughnut-shaped distribution in the near field (i.e., a flat-top profile with a hole in the middle for an axially coupled beam). We derive analytical expressions describing this distribution by using the flattened Gaussian beams concept. The superposition of two flattened Gaussian beams whose flatness and steepness of edges are controlled by defined parameters (i.e., the beam width and the order) is used to analyze the output beam intensity along the propagation axis. Finally, experimental measurements of beam propagation from a copper-vapor laser fitted with a high-magnification unstable resonator show excellent agreement with theoretical predictions.
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Affiliation(s)
- S Saghafi
- Department of Physics, Macquarie University, Sydney, NSW, Australia
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Abstract
Transverse-electric and transverse-magnetic beam modes are considered based on a theory in which complex dipole sources and sinks are oriented along the beam axis; the theory is similar to one that was previously presented for transverse dipoles. The field in the region of the waist is explored. Modes with such polarization have been reported from a wide range of laser types.
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Affiliation(s)
- C J Sheppard
- Department of Physical Optics, School of Physics and The Australian Key Centre for Microscopy and Microanalysis, University of Sydney, Sydney, New South Wales 2006, Australia
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Abstract
Neuropeptides have been implicated in the short-term regulation of food intake and the long-term control of body weight. Previous studies have shown that central administration of neuropeptide Y (NPY), the most abundant of these peptides in the brain, produces robust increases of food intake. We now report that NPY, at doses that stimulate food intake when administered intraventricularly, also causes the formation of robust conditioned flavor aversions when given via the same cannula and at the same dose. This apparently paradoxical effect may be indicative of different populations of central NPY receptors having dissimilar effects on ingestive behaviors. The results also suggest that the use of conditioned aversions to investigate drug-induced malaise may not be appropriate when applied to ingestive behaviors.
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Affiliation(s)
- A J Sipols
- Department of Psychology, University of Washington, Seattle 98195
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