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Podéus H, Simonsson C, Nasr P, Ekstedt M, Kechagias S, Lundberg P, Lövfors W, Cedersund G. A physiologically-based digital twin for alcohol consumption-predicting real-life drinking responses and long-term plasma PEth. NPJ Digit Med 2024; 7:112. [PMID: 38702474 PMCID: PMC11068902 DOI: 10.1038/s41746-024-01089-6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/29/2024] [Indexed: 05/06/2024] Open
Abstract
Alcohol consumption is associated with a wide variety of preventable health complications and is a major risk factor for all-cause mortality in the age group 15-47 years. To reduce dangerous drinking behavior, eHealth applications have shown promise. A particularly interesting potential lies in the combination of eHealth apps with mathematical models. However, existing mathematical models do not consider real-life situations, such as combined intake of meals and beverages, and do not connect drinking to clinical markers, such as phosphatidylethanol (PEth). Herein, we present such a model which can simulate real-life situations and connect drinking to long-term markers. The new model can accurately describe both estimation data according to a χ2 -test (187.0 < Tχ2 = 226.4) and independent validation data (70.8 < Tχ2 = 93.5). The model can also be personalized using anthropometric data from a specific individual and can thus be used as a physiologically-based digital twin. This twin is also able to connect short-term consumption of alcohol to the long-term dynamics of PEth levels in the blood, a clinical biomarker of alcohol consumption. Here we illustrate how connecting short-term consumption to long-term markers allows for a new way to determine patient alcohol consumption from measured PEth levels. An additional use case of the twin could include the combined evaluation of patient-reported AUDIT forms and measured PEth levels. Finally, we integrated the new model into an eHealth application, which could help guide individual users or clinicians to help reduce dangerous drinking.
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Affiliation(s)
- Henrik Podéus
- Department of Biomedical Engineering (IMT), Linköping University, Linköping, Sweden
| | - Christian Simonsson
- Department of Biomedical Engineering (IMT), Linköping University, Linköping, Sweden
- Center for Medicine Imaging and Visualization Science (CMIV), Linköping University, Linköping, Sweden
| | - Patrik Nasr
- Department of Health, Medicine, and Caring Sciences, Linköping University, Linköping, Sweden
- Wallenberg Center for Molecular Medicine, Linköping University, Linköping, Sweden
| | - Mattias Ekstedt
- Center for Medicine Imaging and Visualization Science (CMIV), Linköping University, Linköping, Sweden
- Department of Health, Medicine, and Caring Sciences, Linköping University, Linköping, Sweden
| | - Stergios Kechagias
- Department of Health, Medicine, and Caring Sciences, Linköping University, Linköping, Sweden
| | - Peter Lundberg
- Center for Medicine Imaging and Visualization Science (CMIV), Linköping University, Linköping, Sweden
- Department of Radiation Physics, and Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
| | - William Lövfors
- Department of Biomedical Engineering (IMT), Linköping University, Linköping, Sweden
- School of Medical Sciences and Inflammatory Response and Infection Susceptibility Centre (iRiSC), Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Gunnar Cedersund
- Department of Biomedical Engineering (IMT), Linköping University, Linköping, Sweden.
- Center for Medicine Imaging and Visualization Science (CMIV), Linköping University, Linköping, Sweden.
- School of Medical Sciences and Inflammatory Response and Infection Susceptibility Centre (iRiSC), Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
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Jakobsen P, Côté-Allard U, Riegler MA, Stabell LA, Stautland A, Nordgreen T, Torresen J, Fasmer OB, Oedegaard KJ. Early warning signals observed in motor activity preceding mood state change in bipolar disorder. Bipolar Disord 2024. [PMID: 38639725 DOI: 10.1111/bdi.13430] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
INTRODUCTION Alterations in motor activity are well-established symptoms of bipolar disorder, and time series of motor activity can be considered complex dynamical systems. In such systems, early warning signals (EWS) occur in a critical transition period preceding a sudden shift (tipping point) in the system. EWS are statistical observations occurring due to a system's declining ability to maintain homeostasis when approaching a tipping point. The aim was to identify critical transition periods preceding bipolar mood state changes. METHODS Participants with a validated bipolar diagnosis were included to a one-year follow-up study, with repeated assessments of the participants' mood. Motor activity was recorded continuously by a wrist-worn actigraph. Participants assessed to have relapsed during follow-up were analyzed. Recognized EWS features were extracted from the motor activity data and analyzed by an unsupervised change point detection algorithm, capable of processing multi-dimensional data and developed to identify when the statistical property of a time series changes. RESULTS Of 49 participants, four depressive and four hypomanic/manic relapses among six individuals occurred, recording actigraphy for 23.8 ± 0.2 h/day, for 39.8 ± 4.6 days. The algorithm detected change points in the time series and identified critical transition periods spanning 13.5 ± 7.2 days. For depressions 11.4 ± 1.8, and hypomania/mania 15.6 ± 10.2 days. CONCLUSION The change point detection algorithm seems capable of recognizing impending mood episodes in continuous flowing data streams. Hence, we present an innovative method for forecasting approaching relapses to improve the clinical management of bipolar disorder.
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Affiliation(s)
- Petter Jakobsen
- Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | | | | | - Lena Antonsen Stabell
- Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Andrea Stautland
- Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Tine Nordgreen
- Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Jim Torresen
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Ole Bernt Fasmer
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Ketil Joachim Oedegaard
- Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
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Nsubuga L, Duggen L, Balzer F, Høegh S, Marcondes TL, Greenbank W, Rubahn HG, de Oliveira Hansen R. Modeling Nonlinear Dynamics of Functionalization Layers: Enhancing Gas Sensor Sensitivity for Piezoelectrically Driven Microcantilever. ACS Sens 2024. [PMID: 38619068 DOI: 10.1021/acssensors.3c02393] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
This article presents a parametrized response model that enhances the limit of detection (LOD) of piezoelectrically driven microcantilever (PD-MC) based gas sensors by accounting for the adsorption-induced variations in elastic properties of the functionalization layer (binder) and the nonlinear motional dynamics of the PD-MC. The developed model is demonstrated for quantifying cadaverine, a volatile biogenic diamine whose concentration is used to assess the freshness of meat. At low concentrations of cadaverine, an increase in the resonance frequency is observed, contrary to the expected reduction due to mass added by adsorption. The study explores the variations in the elastic modulus vis-à-vis the adsorbed mass of cadaverine and derives the resonance frequency to the adsorbed mass response function. We advance a blended technique involving the analysis of atomic force microscopy (AFM) force-distance (f-d) curves and fitting of the quartz crystal microbalance (QCM) impedance response spectrum to deduce the adsorption-induced changes in the viscoelastic properties of the functionalization layer. The findings obtained are subsequently employed in modeling the response function for a structurally nonhomogenous PD-MC, highlighting the significance of the functionalization layer to the global elastic properties. The structural composition of the PD-MC beam adopted herein features a trapezoidal base hosting the actuating piezoelectric stratum and a rectangular free end with a functionalization layer. The Euler-Bernoulli beam theory coupled with Hamilton's principle is used to develop the equation of motion, which is subsequently discretized into a set of nonlinear ordinary differential equations via Galerkin expansion, and the solutions to the first fundamental mode of vibration are determined using the method of multiple scales. The obtained solutions provide a basis for deducing the nonlinear response function model to the adsorbed mass. The derived model is validated by recorded resonance frequency changes resulting from exposure to known concentrations of cadaverine. We demonstrate that the increase in resonance frequency for low concentrations of cadaverine is due to the dominance of the variation of the elastic modulus of the functionalization layer originating from the initial binder-analyte interactions over damping due to added mass. It is concluded that the developed nonlinear response function model can reliably be used to quantify the cadaverine concentration at low concentrations with an elevated Limit of Detection.
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Affiliation(s)
- Lawrence Nsubuga
- SDU NanoSYD, Mads Clausen Institute, University of Southern Denmark, Alsion 2, 6400 Sønderborg, Denmark
| | - Lars Duggen
- SDU Mechatronics, Department of Mechanical and Electrical Engineering, University of Southern Denmark, Alsion 2, 6400 Sønderborg, Denmark
| | - Frank Balzer
- SDU Centre for Photonics Engineering, Mads Clausen Institute, University of Southern Denmark, Alsion 2, 6400 Sønderborg, Denmark
| | - Simon Høegh
- AmiNIC ApS, Jernbanegade 75, 5500 Middelfart, Denmark
| | - Tatiana L Marcondes
- SDU NanoSYD, Mads Clausen Institute, University of Southern Denmark, Alsion 2, 6400 Sønderborg, Denmark
| | - William Greenbank
- SDU Centre for Industrial Electronics, University of Southern Denmark, Alsion 2, 6400 Sønderborg, Denmark
| | - Horst-Günter Rubahn
- SDU NanoSYD, Mads Clausen Institute, University of Southern Denmark, Alsion 2, 6400 Sønderborg, Denmark
| | - Roana de Oliveira Hansen
- SDU NanoSYD, Mads Clausen Institute, University of Southern Denmark, Alsion 2, 6400 Sønderborg, Denmark
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Staii C. Nonlinear Growth Dynamics of Neuronal Cells Cultured on Directional Surfaces. Biomimetics (Basel) 2024; 9:203. [PMID: 38667214 PMCID: PMC11048115 DOI: 10.3390/biomimetics9040203] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
During the development of the nervous system, neuronal cells extend axons and dendrites that form complex neuronal networks, which are essential for transmitting and processing information. Understanding the physical processes that underlie the formation of neuronal networks is essential for gaining a deeper insight into higher-order brain functions such as sensory processing, learning, and memory. In the process of creating networks, axons travel towards other recipient neurons, directed by a combination of internal and external cues that include genetic instructions, biochemical signals, as well as external mechanical and geometrical stimuli. Although there have been significant recent advances, the basic principles governing axonal growth, collective dynamics, and the development of neuronal networks remain poorly understood. In this paper, we present a detailed analysis of nonlinear dynamics for axonal growth on surfaces with periodic geometrical patterns. We show that axonal growth on these surfaces is described by nonlinear Langevin equations with speed-dependent deterministic terms and gaussian stochastic noise. This theoretical model yields a comprehensive description of axonal growth at both intermediate and long time scales (tens of hours after cell plating), and predicts key dynamical parameters, such as speed and angular correlation functions, axonal mean squared lengths, and diffusion (cell motility) coefficients. We use this model to perform simulations of axonal trajectories on the growth surfaces, in turn demonstrating very good agreement between simulated growth and the experimental results. These results provide important insights into the current understanding of the dynamical behavior of neurons, the self-wiring of the nervous system, as well as for designing innovative biomimetic neural network models.
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Affiliation(s)
- Cristian Staii
- Department of Physics and Astronomy, Tufts University, Medford, MA 02155, USA
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5
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Wytock TP, Motter AE. Cell reprogramming design by transfer learning of functional transcriptional networks. Proc Natl Acad Sci U S A 2024; 121:e2312942121. [PMID: 38437548 PMCID: PMC10945810 DOI: 10.1073/pnas.2312942121] [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: 07/28/2023] [Accepted: 01/26/2024] [Indexed: 03/06/2024] Open
Abstract
Recent developments in synthetic biology, next-generation sequencing, and machine learning provide an unprecedented opportunity to rationally design new disease treatments based on measured responses to gene perturbations and drugs to reprogram cells. The main challenges to seizing this opportunity are the incomplete knowledge of the cellular network and the combinatorial explosion of possible interventions, both of which are insurmountable by experiments. To address these challenges, we develop a transfer learning approach to control cell behavior that is pre-trained on transcriptomic data associated with human cell fates, thereby generating a model of the network dynamics that can be transferred to specific reprogramming goals. The approach combines transcriptional responses to gene perturbations to minimize the difference between a given pair of initial and target transcriptional states. We demonstrate our approach's versatility by applying it to a microarray dataset comprising >9,000 microarrays across 54 cell types and 227 unique perturbations, and an RNASeq dataset consisting of >10,000 sequencing runs across 36 cell types and 138 perturbations. Our approach reproduces known reprogramming protocols with an AUROC of 0.91 while innovating over existing methods by pre-training an adaptable model that can be tailored to specific reprogramming transitions. We show that the number of gene perturbations required to steer from one fate to another increases with decreasing developmental relatedness and that fewer genes are needed to progress along developmental paths than to regress. These findings establish a proof-of-concept for our approach to computationally design control strategies and provide insights into how gene regulatory networks govern phenotype.
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Affiliation(s)
- Thomas P. Wytock
- Department of Physics and Astronomy, Northwestern University, Evanston, IL60208
- Center for Network Dynamics, Northwestern University, Evanston, IL60208
| | - Adilson E. Motter
- Department of Physics and Astronomy, Northwestern University, Evanston, IL60208
- Center for Network Dynamics, Northwestern University, Evanston, IL60208
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL60208
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL60208
- National Institute for Theory and Mathematics in Biology, Evanston, IL60208
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Borrus DS, Stettler MK, Grover CJ, Kalajian EJ, Gu J, Conradi Smith GD, Del Negro CA. Inspiratory and sigh breathing rhythms depend on distinct cellular signalling mechanisms in the preBötzinger complex. J Physiol 2024; 602:809-834. [PMID: 38353596 PMCID: PMC10940220 DOI: 10.1113/jp285582] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 08/28/2023] [Accepted: 12/21/2023] [Indexed: 02/21/2024] Open
Abstract
Breathing behaviour involves the generation of normal breaths (eupnoea) on a timescale of seconds and sigh breaths on the order of minutes. Both rhythms emerge in tandem from a single brainstem site, but whether and how a single cell population can generate two disparate rhythms remains unclear. We posit that recurrent synaptic excitation in concert with synaptic depression and cellular refractoriness gives rise to the eupnoea rhythm, whereas an intracellular calcium oscillation that is slower by orders of magnitude gives rise to the sigh rhythm. A mathematical model capturing these dynamics simultaneously generates eupnoea and sigh rhythms with disparate frequencies, which can be separately regulated by physiological parameters. We experimentally validated key model predictions regarding intracellular calcium signalling. All vertebrate brains feature a network oscillator that drives the breathing pump for regular respiration. However, in air-breathing mammals with compliant lungs susceptible to collapse, the breathing rhythmogenic network may have refashioned ubiquitous intracellular signalling systems to produce a second slower rhythm (for sighs) that prevents atelectasis without impeding eupnoea. KEY POINTS: A simplified activity-based model of the preBötC generates inspiratory and sigh rhythms from a single neuron population. Inspiration is attributable to a canonical excitatory network oscillator mechanism. Sigh emerges from intracellular calcium signalling. The model predicts that perturbations of calcium uptake and release across the endoplasmic reticulum counterintuitively accelerate and decelerate sigh rhythmicity, respectively, which was experimentally validated. Vertebrate evolution may have adapted existing intracellular signalling mechanisms to produce slow oscillations needed to optimize pulmonary function in mammals.
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Affiliation(s)
- Daniel S. Borrus
- Applied Science and Neuroscience, William & Mary, Williamsburg, VA 23185
| | - Marco K. Stettler
- Applied Science and Neuroscience, William & Mary, Williamsburg, VA 23185
| | - Cameron J. Grover
- Applied Science and Neuroscience, William & Mary, Williamsburg, VA 23185
| | - Eva J. Kalajian
- Applied Science and Neuroscience, William & Mary, Williamsburg, VA 23185
| | - Jeffrey Gu
- Applied Science and Neuroscience, William & Mary, Williamsburg, VA 23185
| | - Gregory D. Conradi Smith
- Applied Science and Neuroscience, William & Mary, Williamsburg, VA 23185
- Conradi Smith and Del Negro contributed equally
| | - Christopher A. Del Negro
- Applied Science and Neuroscience, William & Mary, Williamsburg, VA 23185
- Conradi Smith and Del Negro contributed equally
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Jæger KH, Charwat V, Wall S, Healy KE, Tveito A. Do calcium channel blockers applied to cardiomyocytes cause increased channel expression resulting in reduced efficacy? NPJ Syst Biol Appl 2024; 10:22. [PMID: 38429306 PMCID: PMC10907638 DOI: 10.1038/s41540-024-00347-3] [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: 10/10/2023] [Accepted: 02/08/2024] [Indexed: 03/03/2024] Open
Abstract
In the initial hours following the application of the calcium channel blocker (CCB) nifedipine to microtissues consisting of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), we observe notable variations in the drug's efficacy. Here, we investigate the possibility that these temporal changes in CCB effects are associated with adaptations in the expression of calcium ion channels in cardiomyocyte membranes. To explore this, we employ a recently developed mathematical model that delineates the regulation of calcium ion channel expression by intracellular calcium concentrations. According to the model, a decline in intracellular calcium levels below a certain target level triggers an upregulation of calcium ion channels. Such an upregulation, if instigated by a CCB, would then counteract the drug's inhibitory effect on calcium currents. We assess this hypothesis using time-dependent measurements of hiPSC-CMs dynamics and by refining an existing mathematical model of myocyte action potentials incorporating the dynamic nature of the number of calcium ion channels. The revised model forecasts that the CCB-induced reduction in intracellular calcium concentrations leads to a subsequent increase in calcium ion channel expression, thereby attenuating the drug's overall efficacy. The data and fit models suggest that dynamic changes in cardiac cells in the presence of CCBs may be explainable by induced changes in protein expression, and that this may lead to challenges in understanding calcium based drug effects on the heart unless timings of applications are carefully considered.
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Affiliation(s)
| | | | - Samuel Wall
- Simula Research Laboratory, Oslo, Norway
- Organos Inc., Berkeley, CA, USA
| | - Kevin E Healy
- Department of Bioengineering, University of California, Berkeley, CA, USA
- Department of Material Science and Engineering, University of California, Berkeley, CA, USA
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8
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Alcan V. Effects of Sensory Input Interactions on Components of Nonlinear Dynamics of Postural Sway in Aging. J Mot Behav 2024; 56:356-372. [PMID: 38423521 DOI: 10.1080/00222895.2024.2317759] [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: 09/19/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024]
Abstract
Postural control involves complex nonlinear dynamics influenced by the interaction and adaptation of different sensory inputs. However, it is not how these inputs interact with one another due to the complex complications associated with aging, particularly concerning the nonlinear dynamics of postural sway. This study aimed to examine how different sensory inputs, surface conditions, and aging factors to influence postural control mechanisms between young and older by investigating the nonlinear dynamics of postural control using the stabilogram diffusion analysis (SDA) and entropy methods. SDA parameters were much greater on foam surfaces than on firm surfaces for both groups in eyes-open and eyes-closed conditions (p ≤ 0.05). For older subjects, there were significant differences in entropy values between firm and foam surfaces (p ≤ 0.05) but no significant difference between eyes conditions (p > 0.05). For both SDA and entropy parameters, surface and age interaction potentially revealed significant differences between young and older subjects (p ≤ 0.05) than eyes and age interaction. The present study provided insight into uncovering the complex relationships between sensory inputs, surface conditions, age, and their potential interaction effects on postural control mechanisms that could mitigate falls and alleviate the fear of falling, particularly in older populations.
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Affiliation(s)
- Veysel Alcan
- Department of Electrical and Electronics Engineering, Tarsus University, Tarsus, Turkiye
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Cartwright JHE, Čejková J, Fimmel E, Giannerini S, Gonzalez DL, Goracci G, Grácio C, Houwing-Duistermaat J, Matić D, Mišić N, Mulder FAA, Piro O. Information, Coding, and Biological Function: The Dynamics of Life. Artif Life 2024:1-12. [PMID: 38358121 DOI: 10.1162/artl_a_00432] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
In the mid-20th century, two new scientific disciplines emerged forcefully: molecular biology and information-communication theory. At the beginning, cross-fertilization was so deep that the term genetic code was universally accepted for describing the meaning of triplets of mRNA (codons) as amino acids. However, today, such synergy has not taken advantage of the vertiginous advances in the two disciplines and presents more challenges than answers. These challenges not only are of great theoretical relevance but also represent unavoidable milestones for next-generation biology: from personalized genetic therapy and diagnosis to Artificial Life to the production of biologically active proteins. Moreover, the matter is intimately connected to a paradigm shift needed in theoretical biology, pioneered a long time ago, that requires combined contributions from disciplines well beyond the biological realm. The use of information as a conceptual metaphor needs to be turned into quantitative and predictive models that can be tested empirically and integrated in a unified view. Successfully achieving these tasks requires a wide multidisciplinary approach, including Artificial Life researchers, to address such an endeavour.
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Affiliation(s)
- Julyan H E Cartwright
- CSIC-Universidad de Granada, Instituto Andaluz de Ciencias de la Tierra, Department of Chemical Engineering, Instituto Carlos I de Física Teórica y Computacional
| | | | - Elena Fimmel
- Mannheim University of Applied Sciences, Institute of Mathematical Biology
| | | | - Diego Luis Gonzalez
- University of Bologna, Department of Statistical Science CNR, Area della Ricerca di Bologna
| | - Greta Goracci
- Free University of Bozen-Bolzano, Institute of Mathematical Biology
| | - Clara Grácio
- Universidade de Évora, CIMA Faculty of Economics and Management
| | | | - Dragan Matić
- University of Banja Luka, Faculty of Natural Science and Mathematics
| | | | | | - Oreste Piro
- Universitat de les Illes Balears, Department of Physics, Mediterranean Institute for Advanced Studies
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10
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Liu Z, Qin B, Shi Z, Wang X, Lv Q, Wei X, Huan R. Nonlinearity-Induced Asymmetric Synchronization Region in Micromechanical Oscillators. Micromachines (Basel) 2024; 15:238. [PMID: 38398967 PMCID: PMC10891831 DOI: 10.3390/mi15020238] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024]
Abstract
Synchronization in microstructures is a widely explored domain due to its diverse dynamic traits and promising practical applications. Within synchronization analysis, the synchronization bandwidth serves as a pivotal metric. While current research predominantly focuses on symmetric evaluations of synchronization bandwidth, the investigation into potential asymmetries within nonlinear oscillators remains unexplored, carrying implications for sensor application performance. This paper conducts a comprehensive exploration employing straight and arch beams capable of demonstrating linear, hardening, and softening characteristics to thoroughly scrutinize potential asymmetry within the synchronization region. Through the introduction of weak harmonic forces to induce synchronization within the oscillator, we observe distinct asymmetry within its synchronization range. Additionally, we present a robust theoretical model capable of fully capturing the linear, hardening, and softening traits of resonators synchronized to external perturbation. Further investigation into the effects of feedback strength and phase delay on synchronization region asymmetry, conducted through analytical and experimental approaches, reveals a consistent alignment between theoretical predictions and experimental outcomes. These findings hold promise in providing crucial technical insights to enhance resonator performance and broaden the application landscape of MEMS (Micro-Electro-Mechanical Systems) technology.
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Affiliation(s)
- Zhonghua Liu
- Department of Civil Engineering, Xiamen University, Xiamen 361005, China; (Z.L.); (B.Q.)
| | - Bingchan Qin
- Department of Civil Engineering, Xiamen University, Xiamen 361005, China; (Z.L.); (B.Q.)
| | - Zhan Shi
- Department of Mechanics, Key Laboratory of Soft Machines and Smart Devices of Zhejiang Province, Zhejiang University, Hangzhou 310027, China;
| | - Xuefeng Wang
- Department of Engineering Mechanics, MIIT Key Laboratory of Dynamics and Control of Complex Systems, Northwestern Polytechnical University, Xi’an 710072, China;
| | - Qiangfeng Lv
- Department of Mechanics, Key Laboratory of Soft Machines and Smart Devices of Zhejiang Province, Zhejiang University, Hangzhou 310027, China;
- Huanjiang Laboratory, Zhuji 311800, China
| | - Xueyong Wei
- State Key Laboratory for Manufacturing Systems Engineering, Xi’an Jiaotong University, Xi’an 710049, China;
| | - Ronghua Huan
- Department of Mechanics, Key Laboratory of Soft Machines and Smart Devices of Zhejiang Province, Zhejiang University, Hangzhou 310027, China;
- Huanjiang Laboratory, Zhuji 311800, China
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11
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Neumeier L, Ciampini MA, Romero-Isart O, Aspelmeyer M, Kiesel N. Fast quantum interference of a nanoparticle via optical potential control. Proc Natl Acad Sci U S A 2024; 121:e2306953121. [PMID: 38227651 PMCID: PMC10823235 DOI: 10.1073/pnas.2306953121] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 12/08/2023] [Indexed: 01/18/2024] Open
Abstract
We introduce and theoretically analyze a scheme to prepare and detect non-Gaussian quantum states of an optically levitated particle via the interaction with light pulses that generate cubic and inverted potentials. We show that this approach allows to operate on sufficiently short time- and length scales to beat decoherence in a regime accessible in state-of-the-art experiments. Specifically, we predict the observation of single-particle interference of a nanoparticle with a mass above 108 atomic mass units delocalized by several nanometers, on timescales of milliseconds. The proposed experiment uses only optical and electrostatic control, and can be performed at about 10-10 mbar and at room temperature. We discuss the prospect of this method for coherently splitting the wavepacket of massive dielectric objects without using either projective measurements or an internal level structure.
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Affiliation(s)
- Lukas Neumeier
- Vienna Center for Quantum Science and Technology, Faculty of Physics, University of Vienna, ViennaA-1090, Austria
| | - Mario A. Ciampini
- Vienna Center for Quantum Science and Technology, Faculty of Physics, University of Vienna, ViennaA-1090, Austria
| | - Oriol Romero-Isart
- Institute for Quantum Optics and Quantum Information (IQOQI) Innsbruck, Austrian Academy of Sciences, InnsbruckA-6020, Austria
- Institute for Theoretical Physics, School of Mathematics, Computer Science and Physics, University of Innsbruck, InnsbruckA-6020, Austria
| | - Markus Aspelmeyer
- Vienna Center for Quantum Science and Technology, Faculty of Physics, University of Vienna, ViennaA-1090, Austria
- Institute for Quantum Optics and Quantum Information (IQOQI) Vienna, Austrian Academy of Sciences, ViennaA-1090, Austria
| | - Nikolai Kiesel
- Vienna Center for Quantum Science and Technology, Faculty of Physics, University of Vienna, ViennaA-1090, Austria
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12
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Guralnik T, Moulder RG, Merom D, Zilcha-Mano S. A multi-modality and multi-dyad approach to measuring flexibility in psychotherapy. Psychother Res 2024:1-17. [PMID: 38252916 DOI: 10.1080/10503307.2023.2292746] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/05/2023] [Indexed: 01/24/2024] Open
Abstract
INTRODUCTION Flexibility, the ability of an individual to adapt to environmental changes in ways that facilitate goal attainment, has been proposed as a potential mechanism underlying psychopathology and psychotherapy. In psychotherapy, most findings are based on self-report measures that have important limitations. We propose a multimodal, multi-dyad approach based on a nonlinear dynamical systems framework to capture the complexity of this concept. METHOD A new research paradigm was designed to explore the validity of the proposed conceptual model. The paradigm includes a psychotherapy-like social interaction, during which body movement and facial expressiveness data were collected. We analyzed the data using Hankel Alternative View of Koopmann analysis to reconstruct attractors of the observed behaviors and compare them. RESULTS The patterns of behavior in the two cases differ, and differences in the reconstructed attractors correspond with differences in self-report measures and behavior in the interactions. CONCLUSIONS The case studies show that information provided by a single modality is not enough to provide the full picture, and multiple modalities are needed. These observations can serve as an initial support for our claims that a multi-modal and multi-dyad approach to flexibility can address some of the issues of measurement in the field.
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Affiliation(s)
- Timur Guralnik
- The Department of Psychology, University of Haifa, Haifa, Israel
| | - Robert G Moulder
- Institute of Cognitive Science, University of Colorado, Boulder, CO, USA
| | - Daniel Merom
- The Department of Psychology, University of Haifa, Haifa, Israel
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13
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Khorasani N, Sadeghi M. A computational model of stem cells' internal mechanism to recapitulate spatial patterning and maintain the self-organized pattern in the homeostasis state. Sci Rep 2024; 14:1528. [PMID: 38233402 PMCID: PMC10794714 DOI: 10.1038/s41598-024-51386-z] [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: 03/08/2023] [Accepted: 01/04/2024] [Indexed: 01/19/2024] Open
Abstract
The complex functioning of multi-cellular tissue development relies on proper cell production rates to replace dead or differentiated specialized cells. Stem cells are critical for tissue development and maintenance, as they produce specialized cells to meet the tissues' demands. In this study, we propose a computational model to investigate the stem cell's mechanism, which generates the appropriate proportion of specialized cells, and distributes them to their correct position to form and maintain the organized structure in the population through intercellular reactions. Our computational model focuses on early development, where the populations overall behavior is determined by stem cells and signaling molecules. The model does not include complicated factors such as movement of specialized cells or outside signaling sources. The results indicate that in our model, the stem cells can organize the population into a desired spatial pattern, which demonstrates their ability to self-organize as long as the corresponding leading signal is present. We also investigate the impact of stochasticity, which provides desired non-genetic diversity; however, it can also break the proper boundaries of the desired spatial pattern. We further examine the role of the death rate in maintaining the system's steady state. Overall, our study sheds light on the strategies employed by stem cells to organize specialized cells and maintain proper functionality. Our findings provide insight into the complex mechanisms involved in tissue development and maintenance, which could lead to new approaches in regenerative medicine and tissue engineering.
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Affiliation(s)
- Najme Khorasani
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran.
| | - Mehdi Sadeghi
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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14
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Hong Y, Zhong Z, Shore KA. Time-delay signature suppression in delayed-feedback semiconductor lasers as a paradigm for feedback control in complex physiological networks. Front Netw Physiol 2024; 3:1330375. [PMID: 38274037 PMCID: PMC10808580 DOI: 10.3389/fnetp.2023.1330375] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/04/2023] [Indexed: 01/27/2024]
Abstract
Physiological networks, as observed in the human organism, involve multi-component systems with feedback loops that contribute to self-regulation. Physiological phenomena accompanied by time-delay effects may lead to oscillatory and even chaotic dynamics in their behaviors. Analogous dynamics are found in semiconductor lasers subjected to delayed optical feedback, where the dynamics typically include a time-delay signature. In many applications of semiconductor lasers, the suppression of the time-delay signature is essential, and hence several approaches have been adopted for that purpose. In this paper, experimental results are presented wherein photonic filters utilized in order to suppress time-delay signatures in semiconductor lasers subjected to delayed optical feedback effects. Two types of semiconductor lasers are used: discrete-mode semiconductor lasers and vertical-cavity surface-emitting lasers (VCSELs). It is shown that with the use of photonic filters, a complete suppression of the time-delay signature may be affected in discrete-mode semiconductor lasers, but a remnant of the signature persists in VCSELs. These results contribute to the broader understanding of time-delay effects in complex systems. The exploration of photonic filters as a means to suppress time-delay signatures opens avenues for potential applications in diverse fields, extending the interdisciplinary nature of this study.
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Affiliation(s)
- Yanhua Hong
- School of Computer Science and Engineering, Bangor University, Bangor, United Kingdom
| | - Zhuqiang Zhong
- College of Science, Chongqing University of Technology, Chongqing, China
| | - K. Alan Shore
- School of Computer Science and Engineering, Bangor University, Bangor, United Kingdom
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15
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Rosenberg MC, Proctor JL, Steele KM. Quantifying changes in individual-specific template-based representations of center-of-mass dynamics during walking with ankle exoskeletons using Hybrid-SINDy. Sci Rep 2024; 14:1031. [PMID: 38200078 PMCID: PMC10781730 DOI: 10.1038/s41598-023-50999-0] [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: 06/02/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Ankle exoskeletons alter whole-body walking mechanics, energetics, and stability by altering center-of-mass (CoM) motion. Controlling the dynamics governing CoM motion is, therefore, critical for maintaining efficient and stable gait. However, how CoM dynamics change with ankle exoskeletons is unknown, and how to optimally model individual-specific CoM dynamics, especially in individuals with neurological injuries, remains a challenge. Here, we evaluated individual-specific changes in CoM dynamics in unimpaired adults and one individual with post-stroke hemiparesis while walking in shoes-only and with zero-stiffness and high-stiffness passive ankle exoskeletons. To identify optimal sets of physically interpretable mechanisms describing CoM dynamics, termed template signatures, we leveraged hybrid sparse identification of nonlinear dynamics (Hybrid-SINDy), an equation-free data-driven method for inferring sparse hybrid dynamics from a library of candidate functional forms. In unimpaired adults, Hybrid-SINDy automatically identified spring-loaded inverted pendulum-like template signatures, which did not change with exoskeletons (p > 0.16), except for small changes in leg resting length (p < 0.001). Conversely, post-stroke paretic-leg rotary stiffness mechanisms increased by 37-50% with zero-stiffness exoskeletons. While unimpaired CoM dynamics appear robust to passive ankle exoskeletons, how neurological injuries alter exoskeleton impacts on CoM dynamics merits further investigation. Our findings support Hybrid-SINDy's potential to discover mechanisms describing individual-specific CoM dynamics with assistive devices.
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Affiliation(s)
- Michael C Rosenberg
- Department of Mechanical Engineering, University of Washington, Seattle, USA.
| | - Joshua L Proctor
- Department of Mechanical Engineering, University of Washington, Seattle, USA
- Department of Applied Mathematics, University of Washington, Seattle, USA
| | - Katherine M Steele
- Department of Mechanical Engineering, University of Washington, Seattle, USA
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16
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Snellman JE, Barreiro NL, Barrio RA, Ventura CI, Govezensky T, Kaski KK, Korpi-Lagg MJ. Socio-economic pandemic modelling: case of Spain. Sci Rep 2024; 14:817. [PMID: 38191603 PMCID: PMC10774333 DOI: 10.1038/s41598-023-44637-y] [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: 08/04/2023] [Accepted: 10/10/2023] [Indexed: 01/10/2024] Open
Abstract
A global disaster, such as the recent Covid-19 pandemic, affects every aspect of our lives and there is a need to investigate these highly complex phenomena if one aims to diminish their impact in the health of the population, as well as their socio-economic stability. In this paper we present an attempt to understand the role of the governmental authorities and the response of the rest of the population facing such emergencies. We present a mathematical model that takes into account the epidemiological features of the pandemic and also the actions of people responding to it, focusing only on three aspects of the system, namely, the fear of catching this serious disease, the impact on the economic activities and the compliance of the people to the mitigating measures adopted by the authorities. We apply the model to the specific case of Spain, since there are accurate data available about these three features. We focused on tourism as an example of the economic activity, since this sector of economy is one of the most likely to be affected by the restrictions imposed by the authorities, and because it represents an important part of Spanish economy. The results of numerical calculations agree with the empirical data in such a way that we can acquire a better insight of the different processes at play in such a complex situation, and also in other different circumstances.
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Affiliation(s)
- Jan E Snellman
- Department of Computer Science, Aalto University School of Science, 00076, Aalto, Finland
| | - Nadia L Barreiro
- Instituto de Investigaciones Científicas y Técnicas para la Defensa (CITEDEF), 1603, Buenos Aires, Argentina
| | - Rafael A Barrio
- Instituto de Física, Universidad Nacional Autónoma de México, 04510, CDMX, Mexico
| | - Cecilia I Ventura
- (CONICET) Centro Atómico Bariloche-CNEA, 8400, Bariloche, Argentina
- Universidad Nacional de Río Negro, 8400, Bariloche, Argentina
| | - Tzipe Govezensky
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, CDMX, Mexico
| | - Kimmo K Kaski
- Department of Computer Science, Aalto University School of Science, 00076, Aalto, Finland
- The Alan Turing Institute, 96 Euston Rd, Kings Cross, London, NW1 2DB, UK
| | - Maarit J Korpi-Lagg
- Department of Computer Science, Aalto University School of Science, 00076, Aalto, Finland.
- Max-Planck-Institut für Sonnensystemforschung, Justus-von-Liebig-Weg 3, 37077, Göttingen, Germany.
- Nordita, KTH Royal Institute of Technology, Stockholm University, Hannes Alfvéns väg 12, 11419, Stockholm, Sweden.
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17
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Camacho-Vidales LJ, Robledo A. A Nonlinear Dynamical View of Kleiber's Law on the Metabolism of Plants and Animals. Entropy (Basel) 2023; 26:32. [PMID: 38248158 DOI: 10.3390/e26010032] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/18/2023] [Accepted: 12/25/2023] [Indexed: 01/23/2024]
Abstract
Kleiber's empirical law, which describes that metabolism increases as the mass to the power 3/4, has arguably remained life sciences' enigma since its formal uncovering in 1930. Why is this behavior sustained over many orders of magnitude? There have been quantitative rationalizations put forward for both plants and animals based on realistic mechanisms. However, universality in scaling laws of this kind, like in critical phenomena, has not yet received substantiation. Here, we provide an account, with quantitative reproduction of the available data, of the metabolism for these two biology kingdoms by means of broad arguments based on statistical mechanics and nonlinear dynamics. We consider iterated renormalization group (RG) fixed-point maps that are associated with an extensive generalized (Tsallis) entropy. We find two unique universality classes that satisfy the 3/4 power law. One corresponds to preferential attachment processes-rich gets richer-and the other to critical processes that suppress the effort for motion. We discuss and generalize our findings to other empirical laws that exhibit similar situations, using data based on general but different concepts that form a conjugate pair that gives rise to the same power-law exponents.
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Affiliation(s)
| | - Alberto Robledo
- Instituto de Física, Universidad Nacional Autónoma de México, Apartado Postal 20-364, Mexico City 01000, Mexico
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18
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Panahi S, Do Y, Hastings A, Lai YC. Rate-induced tipping in complex high-dimensional ecological networks. Proc Natl Acad Sci U S A 2023; 120:e2308820120. [PMID: 38091288 PMCID: PMC10743502 DOI: 10.1073/pnas.2308820120] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/15/2023] [Indexed: 12/24/2023] Open
Abstract
In an ecosystem, environmental changes as a result of natural and human processes can cause some key parameters of the system to change with time. Depending on how fast such a parameter changes, a tipping point can occur. Existing works on rate-induced tipping, or R-tipping, offered a theoretical way to study this phenomenon but from a local dynamical point of view, revealing, e.g., the existence of a critical rate for some specific initial condition above which a tipping point will occur. As ecosystems are subject to constant disturbances and can drift away from their equilibrium point, it is necessary to study R-tipping from a global perspective in terms of the initial conditions in the entire relevant phase space region. In particular, we introduce the notion of the probability of R-tipping defined for initial conditions taken from the whole relevant phase space. Using a number of real-world, complex mutualistic networks as a paradigm, we find a scaling law between this probability and the rate of parameter change and provide a geometric theory to explain the law. The real-world implication is that even a slow parameter change can lead to a system collapse with catastrophic consequences. In fact, to mitigate the environmental changes by merely slowing down the parameter drift may not always be effective: Only when the rate of parameter change is reduced to practically zero would the tipping be avoided. Our global dynamics approach offers a more complete and physically meaningful way to understand the important phenomenon of R-tipping.
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Affiliation(s)
- Shirin Panahi
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ85287
| | - Younghae Do
- Department of Mathematics, Nonlinear Dynamics Mathematical Application Center, Kyungpook National University, Daegu41566, Republic of Korea
| | - Alan Hastings
- Department of Environmental Science and Policy, University of California, Davis, CA95616
- Santa Fe Institute, Santa Fe, NM87501
| | - Ying-Cheng Lai
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ85287
- Department of Physics, Arizona State University, Tempe, AZ85287
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19
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Takeshita A, Madrid J, Granillo E, Abdelkefi A. Insights on the Impacts of Accelerometer Location on the Dynamics and Characteristics of Complex Structures. Sensors (Basel) 2023; 23:9830. [PMID: 38139676 PMCID: PMC10747832 DOI: 10.3390/s23249830] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/04/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023]
Abstract
There exists a high level of difficulty in understanding the physical responses of complex dynamical systems. To this end, researchers have previously used different measurement techniques, such as displacement sensors or accelerometers, in the laboratory to capture a system's dynamics. A well-known structure in the literature is the Box Assembly with Removable Component (BARC) whose purpose is to gain a deep understanding of testing complex systems. Further breaking down the structure, the Removable Component (RC) portion is often used as a relatively simplified version which retains significant complexity from the original system. However, the placement of accelerometers on the RC have varied greatly throughout the literature which presents a challenge in comparing results and may not accurately represent the system's dynamics. Finite Element Analysis (FEA) is performed for three common accelerometer locations to determine how their placement affects the frequencies and mode shapes for the RC and results are compared against those without accelerometers. Free vibration experiments are carried out to understand the variation of frequencies and damping for each accelerometer location to obtain the overall response for the first mode of vibration. Next, random vibration experiments are run to gain insight on the interaction between linear and nonlinear responses based on excitation level, while showing the influence of an accelerometer's location on system dynamics. The results demonstrate that the location of the accelerometer is highly influential on the linear and nonlinear characteristics of the system. It is proved that for the first mode of vibration, nonlinear softening and nonlinear damping behaviors may take place due to the interaction between the location of accelerometers, direction of excitation, and response axis analyzed.
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Affiliation(s)
| | | | | | - Abdessattar Abdelkefi
- Department of Mechanical and Aerospace Engineering, New Mexico State University, Las Cruces, NM 88003, USA; (A.T.); (J.M.); (E.G.)
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20
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Demos AP, Palmer C. Musical synchrony, dynamical systems and information processing: Merger or redundancy? Trends Cogn Sci 2023; 27:1107-1108. [PMID: 37739922 DOI: 10.1016/j.tics.2023.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 08/23/2023] [Indexed: 09/24/2023]
Affiliation(s)
- Alexander P Demos
- Department of Psychology, University of Illinois Chicago, Chicago, IL 60612, USA.
| | - Caroline Palmer
- Department of Psychology, McGill University, Montreal, QC, Canada H3A 1B1.
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21
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Jordão S, Stergiou N, Brandão R, Pezarat-Correia P, Oliveira R, Cortes N, Vaz JR. Muscle activity variability patterns and stride to stride fluctuations of older adults are positively correlated during walking. Sci Rep 2023; 13:20721. [PMID: 38007498 PMCID: PMC10676363 DOI: 10.1038/s41598-023-47828-9] [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: 04/03/2023] [Accepted: 11/18/2023] [Indexed: 11/27/2023] Open
Abstract
It has been found that fractal-like patterns are present in the temporal structure of the variability of healthy biological rhythms, while pathology and disease lead to their deterioration. Interestingly, it has recently been suggested that these patterns in biological rhythms are related with each other, reflecting overall health or lack of it, due to their interaction. However, the underlying neurophysiological mechanisms responsible for such dependency remain unknown. In addition, this relationship between different elements needs to be first verified before we even pursue understanding their interaction. This study aimed to investigate the relationship between two elements of the neuromuscular system, gait and muscle activity variability patterns in older adults. Twenty-one older adults walked at their preferred walking speed on a treadmill. Inter-stride intervals were obtained through an accelerometer placed on the lateral malleoli to assess the temporal structure of variability of stride-to-stride fluctuations. Inter muscle peak intervals were obtained through the electromyographic signal of the gastrocnemius to assess the temporal structure of the variability of the simultaneous muscle activity. The temporal structure of variability from both signals was evaluated through the detrended fluctuation analysis, while their magnitude of variability was evaluated using the coefficient of variation. The Pearson's Correlation coefficient was used to identify the relationship between the two dependent variables. A significant strong positive correlation was found between the temporal structure of gait and muscle activity patterns. This result suggests that there is an interdependency between biological rhythms that compose the human neuromuscular system.
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Affiliation(s)
- Sofia Jordão
- CIPER, Neuromuscular Research Lab, Faculty of Human Kinetics, University of Lisbon, Lisbon, Portugal
- Egas Moniz Center for Interdisciplinary Research (CiiEM), Egas Moniz School of Health & Science, Campus Universitário, Quinta da Granja, Monte da Caparica, 2829 - 511, Caparica, Portugal
- Hospital da Ordem Terceira Chiado, Lisbon, Portugal
| | - Nick Stergiou
- Department of Biomechanics, University of Nebraska at Omaha, Omaha, NE, USA
- Department of Physical Education and Sport Science, Aristotle University, Thessaloniki, Greece
| | - Rita Brandão
- CIPER, Neuromuscular Research Lab, Faculty of Human Kinetics, University of Lisbon, Lisbon, Portugal
| | - Pedro Pezarat-Correia
- CIPER, Neuromuscular Research Lab, Faculty of Human Kinetics, University of Lisbon, Lisbon, Portugal
| | - Raúl Oliveira
- CIPER, Neuromuscular Research Lab, Faculty of Human Kinetics, University of Lisbon, Lisbon, Portugal
| | - Nelson Cortes
- School of Sport, Rehabilitation and Exercise Sciences, University of Essex, Colchester, UK
- Department of Bioengineering, George Mason University, Fairfax, VA, USA
| | - João R Vaz
- CIPER, Neuromuscular Research Lab, Faculty of Human Kinetics, University of Lisbon, Lisbon, Portugal.
- Egas Moniz Center for Interdisciplinary Research (CiiEM), Egas Moniz School of Health & Science, Campus Universitário, Quinta da Granja, Monte da Caparica, 2829 - 511, Caparica, Portugal.
- Department of Biomechanics, University of Nebraska at Omaha, Omaha, NE, USA.
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22
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Zhang L, Zhang H, Li X, Qiao N, Gao X, Ji Y. The Nonlinear Dynamics of a MEMS Resonator with a Triangular Tuning Comb. Micromachines (Basel) 2023; 14:2109. [PMID: 38004966 PMCID: PMC10673572 DOI: 10.3390/mi14112109] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/01/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023]
Abstract
The nonlinear dynamic response of a MEMS resonator with a triangular tuning comb is studied. The motion equation with dis-smooth tuning electrostatic force is derived according to Newton's second law. The analytical solution of the periodic response is obtained using the harmonic balance method and section integral method. The singularity theory is then applied to investigate the bifurcation of the periodic response of the untuned system. The transition sets on the DC-AC voltage plane dividing the planes into several persistent regions are obtained. The bifurcation diagrams' topological structures and jump phenomena corresponding to different parameter regions are analyzed. We explore the effects of tuning voltage on the response. This demonstrates that the amplitude-frequency curves present more hardening characteristics with increased tuning voltage. Many twists, bifurcation points, and unstable solutions appear, leading to complicated jump phenomena. Two bifurcation points exist on the response curves: the smooth and dis-smooth bifurcation points, with the latter occurring on the switching plane of non-uniform fingers.
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Affiliation(s)
- Lijuan Zhang
- School of Automobile and Transportation, Tianjin University of Technology and Education, Tianjin 300222, China; (N.Q.); (X.G.)
| | - Huabiao Zhang
- School of Mechanical Engineering, Tianjin University of Commerce, Tianjin 300134, China;
| | - Xinye Li
- School of Mechanical Engineering, Hebei University of Technology, Tianjin 300401, China;
| | - Ningguo Qiao
- School of Automobile and Transportation, Tianjin University of Technology and Education, Tianjin 300222, China; (N.Q.); (X.G.)
| | - Xianping Gao
- School of Automobile and Transportation, Tianjin University of Technology and Education, Tianjin 300222, China; (N.Q.); (X.G.)
| | - Yunxiao Ji
- Tianjin Juxinhongtai Metal Material Company Ltd., Tianjin 300112, China;
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23
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Wuyts B, Sieber J. Emergent structure and dynamics of tropical forest-grassland landscapes. Proc Natl Acad Sci U S A 2023; 120:e2211853120. [PMID: 37903268 PMCID: PMC10636392 DOI: 10.1073/pnas.2211853120] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/06/2023] [Indexed: 11/01/2023] Open
Abstract
Previous work indicates that tropical forest can exist as an alternative stable state to savanna. Therefore, perturbation by climate change or human impact may lead to crossing of a tipping point beyond which there is rapid forest dieback that is not easily reversed. A hypothesized mechanism for such bistability is feedback between fire and vegetation, where fire spreads as a contagion process on grass patches. Theoretical models have largely implemented this mechanism implicitly, by assuming a threshold dependence of fire spread on flammable vegetation. Here, we show how the nonlinear dynamics and bistability emerge spontaneously, without assuming equations or thresholds for fire spread. We find that the forest geometry causes the nonlinearity that induces bistability. We demonstrate this in three steps. First, we model forest and fire as interacting contagion processes on grass patches, showing that spatial structure emerges due to two counteracting effects on the forest perimeter: forest expansion by dispersal and forest erosion by fires originating in adjacent grassland. Then, we derive a landscape-scale balance equation in which these two effects link forest geometry and dynamics: Forest expands proportionally to its perimeter, while it shrinks proportionally to its perimeter weighted by adjacent grassland area. Finally, we show that these perimeter quantities introduce nonlinearity in our balance equation and lead to bistability. Relying on the link between structure and dynamics, we propose a forest resilience indicator that could be used for targeted conservation or restoration.
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Affiliation(s)
- Bert Wuyts
- Centre for Systems, Dynamics and Control, Department of Mathematics and Statistics, University of Exeter, EX4 4QF, United Kingdom
| | - Jan Sieber
- Centre for Systems, Dynamics and Control, Department of Mathematics and Statistics, University of Exeter, EX4 4QF, United Kingdom
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24
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Demos AP, Palmer C. Social and nonlinear dynamics unite: musical group synchrony. Trends Cogn Sci 2023; 27:1008-1018. [PMID: 37277276 DOI: 10.1016/j.tics.2023.05.005] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 06/07/2023]
Abstract
Synchronization, the human tendency to align behaviors in time with others, is necessary for many survival skills. The ability to synchronize actions with rhythmic (predictable) sound patterns is especially well developed in music making. Recent models of synchrony in musical ensembles rely on pairwise comparisons between group members. This pairwise approach to synchrony has hampered theory development, given current findings from social dynamics indicating shifts in members' influence within larger groups. We draw on social theory and nonlinear dynamics to argue that emergent properties and novel roles arise in musical group synchrony that differ from individual or pairwise behaviors. This transformational shift in defining synchrony sheds light on successful outcomes as well as on disruptions that cause negative behavioral outcomes.
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Affiliation(s)
- Alexander P Demos
- Department of Psychology, University of Illinois Chicago, 1007 W Harrison St., Chicago, IL 60607, USA.
| | - Caroline Palmer
- Department of Psychology, McGill University, 1205 Dr Penfield Ave., Montreal, QC H3A 1B1, Canada.
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25
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Gómez-Lozada F, del Valle CA, Jiménez-Paz JD, Lazarov BS, Galvis J. Modelling and simulation of brinicle formation. R Soc Open Sci 2023; 10:230268. [PMID: 37885987 PMCID: PMC10598449 DOI: 10.1098/rsos.230268] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023]
Abstract
Below the Arctic sea ice, under the right conditions, a flux of icy brine flows down into the sea. The icy brine has a much lower fusion point and is denser than normal seawater. As a result, it sinks while freezing everything around it, forming an ice channel called a brinicle (also known as ice stalactite). In this paper, we develop a mathematical model for this phenomenon, assuming cylindrical symmetry. The fluid is considered to be viscous and quasi-stationary. The heat and salt transport are weakly coupled to the fluid motion and are modelled with the corresponding conservation equations, accounting for diffusive and convective effects. Finite-element discretization is employed to solve the coupled system of partial differential equations. We find that the model can capture the general behaviour of the physical system and generate brinicle-like structures while also recovering dendrite composition, which is a physically expected feature aligned with previous experimental results. This represents, to our knowledge, the first complete model proposed that captures the global structure of the physical phenomenon even though it has some discrepancies, such as brine accumulation.
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Affiliation(s)
- Felipe Gómez-Lozada
- Departamento de Física, Universidad Nacional de Colombia, Carrera 45 No. 26-85, Edificio Uriel Gutiérrez, Bogotá D.C., Colombia
| | - Carlos Andrés del Valle
- Departamento de Física, Universidad Nacional de Colombia, Carrera 45 No. 26-85, Edificio Uriel Gutiérrez, Bogotá D.C., Colombia
| | - Julián David Jiménez-Paz
- Departamento de Física, Universidad Nacional de Colombia, Carrera 45 No. 26-85, Edificio Uriel Gutiérrez, Bogotá D.C., Colombia
| | | | - Juan Galvis
- Departamento de Matemáticas, Universidad Nacional de Colombia, Carrera 45 No. 26-85, Edificio Uriel Gutiérrez, Bogotá D.C., Colombia
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Haeffner LSB, Backes DS, Hammel GDSC, de Sousa FGM, Rupolo I, Smeha LN. Social and health vulnerability of homeless people. Rev Esc Enferm USP 2023; 57:e20220379. [PMID: 37942983 PMCID: PMC10634269 DOI: 10.1590/1980-220x-reeusp-2022-0379en] [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: 10/03/2022] [Accepted: 07/19/2023] [Indexed: 11/10/2023] Open
Abstract
The objective is to conduct a theoretical reflection on the social and health vulnerability of homeless people, from the perspective of complexity thinking. Study with a theoretical and reflective approach that accessed bibliographical sources of contemporary authors who seek to understand the phenomenon of homeless populations and, at the same time, attribute theoretical support from the reference of complexity, under a critical and analytical bias. Health is conceived as a subsystem of the social system that transcends any linear and punctual diagnostic perspective. Theoretical reflection on the social and health vulnerability of homeless people sparks a unique and multidimensional apprehension of the human being - a complex unit par excellence, which demands equally complex interventions.
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Affiliation(s)
| | - Dirce Stein Backes
- Universidade Franciscana, Programa em Saúde Materno-Infantil, Santa Maria, RS, Brazil
| | | | | | - Irani Rupolo
- Universidade Franciscana, Santa Maria, RS, Brazil
| | - Luciane Najar Smeha
- Universidade Franciscana, Programa em Saúde Materno-Infantil, Santa Maria, RS, Brazil
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Kloska SM, Pałczyński K, Marciniak T, Talaśka T, Wysocki BJ, Davis P, Wysocki TA. Integrating glycolysis, citric acid cycle, pentose phosphate pathway, and fatty acid beta-oxidation into a single computational model. Sci Rep 2023; 13:14484. [PMID: 37660197 PMCID: PMC10475038 DOI: 10.1038/s41598-023-41765-3] [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: 05/09/2023] [Accepted: 08/31/2023] [Indexed: 09/04/2023] Open
Abstract
The metabolic network of a living cell is highly intricate and involves complex interactions between various pathways. In this study, we propose a computational model that integrates glycolysis, the pentose phosphate pathway (PPP), the fatty acids beta-oxidation, and the tricarboxylic acid cycle (TCA cycle) using queueing theory. The model utilizes literature data on metabolite concentrations and enzyme kinetic constants to calculate the probabilities of individual reactions occurring on a microscopic scale, which can be viewed as the reaction rates on a macroscopic scale. However, it should be noted that the model has some limitations, including not accounting for all the reactions in which the metabolites are involved. Therefore, a genetic algorithm (GA) was used to estimate the impact of these external processes. Despite these limitations, our model achieved high accuracy and stability, providing real-time observation of changes in metabolite concentrations. This type of model can help in better understanding the mechanisms of biochemical reactions in cells, which can ultimately contribute to the prevention and treatment of aging, cancer, metabolic diseases, and neurodegenerative disorders.
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Affiliation(s)
- Sylwester M Kloska
- Faculty of Medicine, Nicolaus Copernicus University Ludwik Rydygier Collegium Medicum, 85-094, Bydgoszcz, Poland.
| | - Krzysztof Pałczyński
- Faculty of Telecommunications, Computer Science and Electrical Engineering, Bydgoszcz University of Science and Technology, 85-796, Bydgoszcz, Poland
| | - Tomasz Marciniak
- Faculty of Telecommunications, Computer Science and Electrical Engineering, Bydgoszcz University of Science and Technology, 85-796, Bydgoszcz, Poland
| | - Tomasz Talaśka
- Faculty of Telecommunications, Computer Science and Electrical Engineering, Bydgoszcz University of Science and Technology, 85-796, Bydgoszcz, Poland
| | - Beata J Wysocki
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, 68182, USA
| | - Paul Davis
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, 68182, USA
| | - Tadeusz A Wysocki
- Faculty of Telecommunications, Computer Science and Electrical Engineering, Bydgoszcz University of Science and Technology, 85-796, Bydgoszcz, Poland
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Omaha, NE, 68182, USA
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Brown TD, Bohaichuk SM, Islam M, Kumar S, Pop E, Williams RS. Electro-Thermal Characterization of Dynamical VO 2 Memristors via Local Activity Modeling. Adv Mater 2023; 35:e2205451. [PMID: 36165218 DOI: 10.1002/adma.202205451] [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] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Translating the surging interest in neuromorphic electronic components, such as those based on nonlinearities near Mott transitions, into large-scale commercial deployment faces steep challenges in the current lack of means to identify and design key material parameters. These issues are exemplified by the difficulties in connecting measurable material properties to device behavior via circuit element models. Here, the principle of local activity is used to build a model of VO2 /SiN Mott threshold switches by sequentially accounting for constraints from a minimal set of quasistatic and dynamic electrical and high-spatial-resolution thermal data obtained via in situ thermoreflectance mapping. By combining independent data sets for devices with varying dimensions, the model is distilled to measurable material properties, and device scaling laws are established. The model can accurately predict electrical and thermal conductivities and capacitances and locally active dynamics (especially persistent spiking self-oscillations). The systematic procedure by which this model is developed has been a missing link in predictively connecting neuromorphic device behavior with their underlying material properties, and should enable rapid screening of material candidates before employing expensive manufacturing processes and testing procedures.
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Affiliation(s)
- Timothy D Brown
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843, USA
- Sandia National Laboratories, Livermore, CA, 94550, USA
| | | | - Mahnaz Islam
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Suhas Kumar
- Sandia National Laboratories, Livermore, CA, 94550, USA
| | - Eric Pop
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, 94305, USA
| | - R Stanley Williams
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843, USA
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Ghamari N, Ghaderpanah R, Sadrian SH, Fallah N. Effect of a visual dual task on postural stability-A comparative study using linear and nonlinear methods. Health Sci Rep 2023; 6:e1437. [PMID: 37520463 PMCID: PMC10375842 DOI: 10.1002/hsr2.1437] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023] Open
Abstract
Background and Aims The dual-task experimental paradigm is used to study the attentional demands of postural control. Postural control is impaired in poststroke patients, and dual-task balance studies address the visual needs of postural control in stroke patients. A nonlinear approach can help us understand the overall behavior of the dynamic system. Methods A total of 20 chronic stroke patients and 20 healthy subjects with similar age, height, and weight participated in this study. The stability and complexity of postural control were assessed using linear and nonlinear methods. All data and parameters (center of pressure [COP] velocity, anteroposterior and mediolateral directions displacement, length of COP path, and phase plane) were analyzed using the Kolmogorov-Smirnov test. Results When postural control was examined based on linear analysis, the results showed that the main effect of the group was not significant, but the main impact of position was significant for all parameters of the COP variation (p < 0.05). Examination of postural control based on nonlinear analysis also showed that the main effect of the group was not significant, and the main effect of status was significant only for the parameters of approximate entropy in both directions and short-term Lyapunov view in the anterior-posterior direction (p < 0.05). Conclusion According to the results of this study, the assessment of postural control and gait performance in poststroke patients, as well as the dual tasks they have to perform in daily life, is crucial for their independence in activities of daily living.
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Affiliation(s)
- Narges Ghamari
- Bone and Joint Diseases Research CenterShiraz University of Medical SciencesShirazIran
| | - Rezvan Ghaderpanah
- Department of Physical Medicine and Rehabilitation, Students Research Committee, School of MedicineShiraz University of Medical SciencesShirazIran
| | - Seyed Hassan Sadrian
- Department of Physical Medicine and Rehabilitation, Students Research Committee, School of MedicineShiraz University of Medical SciencesShirazIran
| | - Nahid Fallah
- Department of Health, Sports Physiotherapy Research CommitteeUniversity of Bath, Claverton DownBathUK
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Boudaghi M, Edwards BJ, Khomami B. Molecular Processes Leading to Shear Banding in Entangled Polymeric Solutions. Polymers (Basel) 2023; 15:3264. [PMID: 37571158 PMCID: PMC10422620 DOI: 10.3390/polym15153264] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 07/24/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
The temporal and spatial evolution of shear banding during startup and steady-state shear flow was studied for solutions of entangled, linear, monodisperse polyethylene C3000H6002 dissolved in hexadecane and benzene solvents. A high-fidelity coarse-grained dissipative particle dynamics method was developed and evaluated based on previous NEMD simulations of similar solutions. The polymeric contribution to shear stress exhibited a monotonically increasing flow curve with a broad stress plateau at intermediate shear rates. For startup shear flow, transient shear banding was observed at applied shear rates within the steady-state shear stress plateau. Shear bands were generated at strain values where the first normal stress difference exhibited a maximum, with lifetimes persisting for up to several hundred strain units. During the lifetime of the shear bands, an inhomogeneous concentration distribution was evident within the system, with higher polymer concentration in the slow bands at low effective shear rate; i.e., γ˙<τR-1, and vice versa at high shear rate. At low values of applied shear rate, a reverse flow phenomenon was observed in the hexadecane solution, which resulted from elastic recoil of the molecules within the slow band. In all cases, the shear bands dissipated at high strains and the system attained steady-state behavior, with a uniform, linear velocity profile across the simulation cell and a homogeneous concentration.
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Affiliation(s)
| | - Brian J. Edwards
- Materials Research and Innovation Laboratory, Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA;
| | - Bamin Khomami
- Materials Research and Innovation Laboratory, Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA;
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Lainscsek X, Taher L. Predicting chromosomal compartments directly from the nucleotide sequence with DNA-DDA. Brief Bioinform 2023; 24:bbad198. [PMID: 37264486 PMCID: PMC10359093 DOI: 10.1093/bib/bbad198] [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: 11/16/2022] [Revised: 04/18/2023] [Accepted: 05/08/2023] [Indexed: 06/03/2023] Open
Abstract
Three-dimensional (3D) genome architecture is characterized by multi-scale patterns and plays an essential role in gene regulation. Chromatin conformation capturing experiments have revealed many properties underlying 3D genome architecture, such as the compartmentalization of chromatin based on transcriptional states. However, they are complex, costly and time consuming, and therefore only a limited number of cell types have been examined using these techniques. Increasing effort is being directed towards deriving computational methods that can predict chromatin conformation and associated structures. Here we present DNA-delay differential analysis (DDA), a purely sequence-based method based on chaos theory to predict genome-wide A and B compartments. We show that DNA-DDA models derived from a 20 Mb sequence are sufficient to predict genome wide compartmentalization at the scale of 100 kb in four different cell types. Although this is a proof-of-concept study, our method shows promise in elucidating the mechanisms responsible for genome folding as well as modeling the impact of genetic variation on 3D genome architecture and the processes regulated thereby.
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Affiliation(s)
- Xenia Lainscsek
- Institute of Biomedical Informatics, Graz University of Technology, Austria
| | - Leila Taher
- Institute of Biomedical Informatics, Graz University of Technology, Austria
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Mahmoodi K, Kerick SE, Grigolini P, Franaszczuk PJ, West BJ. Complexity synchronization: a measure of interaction between the brain, heart and lungs. Sci Rep 2023; 13:11433. [PMID: 37454210 PMCID: PMC10349874 DOI: 10.1038/s41598-023-38622-8] [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: 11/17/2022] [Accepted: 07/11/2023] [Indexed: 07/18/2023] Open
Abstract
Herein we address the measurable consequences of the network effect (NE) on time series generated by different parts of the brain, heart, and lung organ-networks (ONs), which are directly related to their inter-network and intra-network interactions. Moreover, these same physiologic ONs have been shown to generate crucial event (CE) time series, and herein are shown, using modified diffusion entropy analysis (MDEA) to have scaling indices with quasiperiodic changes in complexity, as measured by scaling indices, over time. Such time series are generated by different parts of the brain, heart, and lung ONs, and the results do not depend on the underlying coherence properties of the associated time series but demonstrate a generalized synchronization of complexity. This high-order synchrony among the scaling indices of EEG (brain), ECG (heart), and respiratory time series is governed by the quantitative interdependence of the multifractal behavior of the various physiological ONs' dynamics. This consequence of the NE opens the door for an entirely general characterization of the dynamics of complex networks in terms of complexity synchronization (CS) independently of the scientific, engineering, or technological context. CS is truly a transdisciplinary effect.
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Affiliation(s)
- Korosh Mahmoodi
- US Combat Capabilities Command, Army Research Laboratory, Aberdeen Proving Ground, MD, 21005, USA.
- Center for Nonlinear Science, University of North Texas, P.O. Box 311427, Denton, TX, 76203, USA.
| | - Scott E Kerick
- US Combat Capabilities Command, Army Research Laboratory, Aberdeen Proving Ground, MD, 21005, USA
| | - Paolo Grigolini
- Center for Nonlinear Science, University of North Texas, P.O. Box 311427, Denton, TX, 76203, USA
| | - Piotr J Franaszczuk
- US Combat Capabilities Command, Army Research Laboratory, Aberdeen Proving Ground, MD, 21005, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Bruce J West
- Center for Nonlinear Science, University of North Texas, P.O. Box 311427, Denton, TX, 76203, USA
- Office of Research and Innovation, North Carolina State University, Raleigh, NC, 27695, USA
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Krishnamurthy D, Prakash M. Emergent programmable behavior and chaos in dynamically driven active filaments. Proc Natl Acad Sci U S A 2023; 120:e2304981120. [PMID: 37406100 PMCID: PMC10334789 DOI: 10.1073/pnas.2304981120] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/16/2023] [Indexed: 07/07/2023] Open
Abstract
How the behavior of cells emerges from their constituent subcellular biochemical and physical parts is an outstanding challenge at the intersection of biology and physics. A remarkable example of single-cell behavior occurs in the ciliate Lacrymaria olor, which hunts for its prey via rapid movements and protrusions of a slender neck, many times the size of the original cell body. The dynamics of this cell neck is powered by a coat of cilia across its length and tip. How a cell can program this active filamentous structure to produce desirable behaviors like search and homing to a target remains unknown. Here, we present an active filament model that allows us to uncover how a "program" (time sequence of active forcing) leads to "behavior" (filament shape dynamics). Our model captures two key features of this system-time-varying activity patterns (extension and compression cycles) and active stresses that are uniquely aligned with the filament geometry-a "follower force" constraint. We show that active filaments under deterministic, time-varying follower forces display rich behaviors including periodic and aperiodic dynamics over long times. We further show that aperiodicity occurs due to a transition to chaos in regions of a biologically accessible parameter space. We also identify a simple nonlinear iterated map of filament shape that approximately predicts long-term behavior suggesting simple, artificial "programs" for filament functions such as homing and searching space. Last, we directly measure the statistical properties of biological programs in L. olor, enabling comparisons between model predictions and experiments.
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Affiliation(s)
| | - Manu Prakash
- Department of Bioengineering, Stanford University, Stanford, CA94305
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Shaikh K, Hussain I, Chowdhry BS. Wheel Defect Detection Using a Hybrid Deep Learning Approach. Sensors (Basel) 2023; 23:6248. [PMID: 37514543 PMCID: PMC10383427 DOI: 10.3390/s23146248] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/02/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023]
Abstract
Defective wheels pose a significant challenge in railway transportation, impacting operational performance and safety. Excessive traction and braking forces give rise to deviations from the intended conical tread shape, resulting in amplified vibrations and noise. Moreover, these deviations contribute to the accelerated damage of track components. Detecting wheel defects at an early stage is crucial to ensure safe and comfortable operation, as well as to minimize maintenance costs. However, the presence of various vibrations, such as those induced by the track, traction motors, and other rolling stock subsystems, poses a significant challenge for onboard detection techniques. These vibrations create difficulties in accurately identifying wheel defects in real-time during operational activities, often resulting in false alarms. This research paper aims to address this issue by using a hybrid deep learning-based approach for the accurate detection of various types of wheel defects using accelerometer data. The proposed approach aims to enhance wheel defect detection accuracy while considering onboard techniques' cost-effectiveness and efficiency. A realistic simulation model of the railway wheelset is developed to generate a comprehensive dataset. To generate vibration data in various scenarios, the model is simulated for 20 s under different conditions, including one non-faulty scenario and six faulty scenarios. The simulations are conducted at different speeds and track conditions to capture a wide range of operating conditions. Within each simulation iteration, a total of 200,000 data points are generated, providing a comprehensive dataset for analysis and evaluation. The generated data are then utilized to train and evaluate a hybrid deep learning model, employing a multi-layer perceptron (MLP) as a feature extractor and multiple machine learning models (support vector machine, random forest, decision tree, and k-nearest neighbors) for performance comparison. The results demonstrate that the MLP-RF (multi-layer perceptron with random forest) model achieved an accuracy of 99%, while the MLP-DT (multi-layer perceptron with decision tree) model achieved an accuracy of 98%. These high accuracy values indicate the effectiveness of the models in accurately classifying and predicting the outcomes. The contributions of this research work include the development of a realistic simulation model, the evaluation of sensor layout effectiveness, and the application of deep learning techniques for improved wheel flat detections.
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Affiliation(s)
- Khurram Shaikh
- Department of Electronic Engineering, Mehran University of Engineering and Technology, Jamshoro 76062, Pakistan
| | - Imtiaz Hussain
- Department of Electrical Engineering, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Bhawani Shankar Chowdhry
- NCRA-Condition Monitoring Lab, Mehran University of Engineering and Technology, Jamshoro 76062, Pakistan
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Hernandez CI, Kargarnovin S, Hejazi S, Karwowski W. Examining electroencephalogram signatures of people with multiple sclerosis using a nonlinear dynamics approach: a systematic review and bibliographic analysis. Front Comput Neurosci 2023; 17:1207067. [PMID: 37457899 PMCID: PMC10344458 DOI: 10.3389/fncom.2023.1207067] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023] Open
Abstract
Background Considering that brain activity involves communication between millions of neurons in a complex network, nonlinear analysis is a viable tool for studying electroencephalography (EEG). The main objective of this review was to collate studies that utilized chaotic measures and nonlinear dynamical analysis in EEG of multiple sclerosis (MS) patients and to discuss the contributions of chaos theory techniques to understanding, diagnosing, and treating MS. Methods Using the preferred reporting items for systematic reviews and meta-analysis (PRISMA), the databases EbscoHost, IEEE, ProQuest, PubMed, Science Direct, Web of Science, and Google Scholar were searched for publications that applied chaos theory in EEG analysis of MS patients. Results A bibliographic analysis was performed using VOSviewer software keyword co-occurrence analysis indicated that MS was the focus of the research and that research on MS diagnosis has shifted from conventional methods, such as magnetic resonance imaging, to EEG techniques in recent years. A total of 17 studies were included in this review. Among the included articles, nine studies examined resting-state, and eight examined task-based conditions. Conclusion Although nonlinear EEG analysis of MS is a relatively novel area of research, the findings have been demonstrated to be informative and effective. The most frequently used nonlinear dynamics analyses were fractal dimension, recurrence quantification analysis, mutual information, and coherence. Each analysis selected provided a unique assessment to fulfill the objective of this review. While considering the limitations discussed, there is a promising path forward using nonlinear analyses with MS data.
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de Vasconcelos ASV, de Lima JS, Cardoso RTN. Multiobjective optimization to assess dengue control costs using a climate-dependent epidemiological model. Sci Rep 2023; 13:10271. [PMID: 37355697 PMCID: PMC10290689 DOI: 10.1038/s41598-023-36903-w] [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: 01/10/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023] Open
Abstract
Arboviruses, diseases transmitted by arthropods, have become a significant challenge for public health managers. The World Health Organization highlights dengue as responsible for millions of infections worldwide annually. As there is no specific treatment for the disease and no free-of-charge vaccine for mass use in Brazil, the best option is the measures to combat the vector, the Aedes aegypti mosquito. Therefore, we proposed an epidemiological model dependent on temperature, precipitation, and humidity, considering symptomatic and asymptomatic dengue infections. Through computer simulations, we aimed to minimize the amount of insecticides and the social cost demanded to treat patients. We proposed a case study in which our model is fitted with real data from symptomatic dengue-infected humans in an epidemic year in a Brazilian city. Our multiobjective optimization model considers an additional control using larvicide, adulticide, and ultra-low volume spraying. The work's main contribution is studying the monetary cost of the actions to combat the vector demand versus the hospital cost per confirmed infected, comparing approaches with and without additional control. Results showed that the additional vector control measures are cheaper than the hospital treatment without the vector control would be.
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Affiliation(s)
- Amália Soares Vieira de Vasconcelos
- Postgraduate Program in Mathematical and Computational Modeling (PPGMMC), Federal Center for Technological Education-CEFET-MG, Av. Amazonas, 7675, Nova Gameleira, Belo Horizonte, Minas Gerais, 30510-000, Brazil.
| | - Josenildo Silva de Lima
- Postgraduate Program in Mathematical and Computational Modeling (PPGMMC), Federal Center for Technological Education-CEFET-MG, Av. Amazonas, 7675, Nova Gameleira, Belo Horizonte, Minas Gerais, 30510-000, Brazil
| | - Rodrigo Tomás Nogueira Cardoso
- Department of Mathematics, Federal Center for Technological Education-CEFET-MG, Av. Amazonas, 7675, Nova Gameleira, Belo Horizonte, Minas Gerais, 30510-000, Brazil
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Walter N, Meinersen-Schmidt N, Kulla P, Loew T, Kruse J, Hinterberger T. Sensory-Processing Sensitivity Is Associated with Increased Neural Entropy. Entropy (Basel) 2023; 25:890. [PMID: 37372234 DOI: 10.3390/e25060890] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/17/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023]
Abstract
BACKGROUND This study aimed at answering the following research questions: (1) Does the self-reported level of sensory-processing sensitivity (SPS) correlate with complexity, or criticality features of the electroencephalogram (EEG)? (2) Are there significant EEG differences comparing individuals with high and low levels of SPS? METHODS One hundred fifteen participants were measured with 64-channel EEG during a task-free resting state. The data were analyzed using criticality theory tools (detrended fluctuation analysis, neuronal avalanche analysis) and complexity measures (sample entropy, Higuchi's fractal dimension). Correlations with the 'Highly Sensitive Person Scale' (HSPS-G) scores were determined. Then, the cohort's lowest and the highest 30% were contrasted as opposites. EEG features were compared between the two groups by applying a Wilcoxon signed-rank test. RESULTS During resting with eyes open, HSPS-G scores correlated significantly positively with the sample entropy and Higuchi's fractal dimension (Spearman's ρ = 0.22, p < 0.05). The highly sensitive group revealed higher sample entropy values (1.83 ± 0.10 vs. 1.77 ± 0.13, p = 0.031). The increased sample entropy in the highly sensitive group was most pronounced in the central, temporal, and parietal regions. CONCLUSION For the first time, neurophysiological complexity features associated with SPS during a task-free resting state were demonstrated. Evidence is provided that neural processes differ between low- and highly-sensitive persons, whereby the latter displayed increased neural entropy. The findings support the central theoretical assumption of enhanced information processing and could be important for developing biomarkers for clinical diagnostics.
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Affiliation(s)
- Nike Walter
- Department of Psychosomatic Medicine, University Hospital Regensburg, 93059 Regensburg, Germany
| | - Nicole Meinersen-Schmidt
- Department for Clinical Psychology and Trauma Therapy, University of the Bundeswehr Munich, 85579 Neubiberg, Germany
| | - Patricia Kulla
- Department for Clinical Psychology and Trauma Therapy, University of the Bundeswehr Munich, 85579 Neubiberg, Germany
| | - Thomas Loew
- Department of Psychosomatic Medicine, University Hospital Regensburg, 93059 Regensburg, Germany
| | - Joachim Kruse
- Department for Clinical Psychology and Trauma Therapy, University of the Bundeswehr Munich, 85579 Neubiberg, Germany
| | - Thilo Hinterberger
- Department of Psychosomatic Medicine, University Hospital Regensburg, 93059 Regensburg, Germany
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Rombouts J, Verplaetse S, Gelens L. The ups and downs of biological oscillators: a comparison of time-delayed negative feedback mechanisms. J R Soc Interface 2023; 20:20230123. [PMID: 37376871 DOI: 10.1098/rsif.2023.0123] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Many biochemical oscillators are driven by the periodic rise and fall of protein concentrations or activities. A negative feedback loop underlies such oscillations. The feedback can act on different parts of the biochemical network. Here, we mathematically compare time-delay models where the feedback affects production and degradation. We show a mathematical connection between the linear stability of the two models, and derive how both mechanisms impose different constraints on the production and degradation rates that allow oscillations. We show how oscillations are affected by the inclusion of a distributed delay, of double regulation (acting on production and degradation) and of enzymatic degradation.
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Affiliation(s)
- Jan Rombouts
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Cellular and Molecular Medicine, KU Leuven, Belgium
| | - Sarah Verplaetse
- Department of Cellular and Molecular Medicine, KU Leuven, Belgium
| | - Lendert Gelens
- Department of Cellular and Molecular Medicine, KU Leuven, Belgium
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Warshauer JA, Bustamante Lopez DA, Dong Q, Chen G, Hu W. Transient gap generation in BaFe 2As 2 driven by coherent lattice vibrations. PNAS Nexus 2023; 2:pgad164. [PMID: 37266397 PMCID: PMC10230283 DOI: 10.1093/pnasnexus/pgad164] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/02/2023] [Accepted: 05/08/2023] [Indexed: 06/03/2023]
Abstract
Iron-based superconductors provide a rich platform to investigate the interplay between unconventional superconductivity, nematicity, and magnetism. The electronic structure and the magnetic properties of iron-based superconductors are highly sensitive to the pnictogen height. Coherent excitation of the A1g phonon by femtosecond laser directly modulates the pnictogen height, which has been used to control the physical properties of iron-based superconductors. Previous studies show that the driven A1g phonon resulted in a transient increase of the pnictogen height in BaFe2As2, favoring an enhanced Fe magnetic moment. However, there are no direct observations on either the enhanced Fe magnetic moments or the enhanced spin-density wave (SDW) gap. Here, we use time-resolved broadband terahertz spectroscopy to investigate the dynamics of BaFe2As2 in the A1g phonon-driven state. Below the SDW transition temperature, we observe a transient gap generation at early-time delays. A similar transient feature is observed in the normal state up to room temperature.
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Affiliation(s)
- Jacob A Warshauer
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, 02215 MA, USA
| | | | - Qingxin Dong
- Institute of Physics and Beijing National Laboratory for Condensed Matter Physics, Chinese Academy of Sciences, 8 Zhongguancun 3rd South Street, 100190 Beijing, China
- School of Physical Sciences, University of Chinese Academy of Sciences, No. 19 A Yuquan Road, 100049 Beijing, China
| | - Genfu Chen
- Institute of Physics and Beijing National Laboratory for Condensed Matter Physics, Chinese Academy of Sciences, 8 Zhongguancun 3rd South Street, 100190 Beijing, China
- School of Physical Sciences, University of Chinese Academy of Sciences, No. 19 A Yuquan Road, 100049 Beijing, China
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40
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Tarraf W, Queiros-Condé D, Ribeiro P, Absi R. Fractal Geometric Model for Statistical Intermittency Phenomenon. Entropy (Basel) 2023; 25:e25050749. [PMID: 37238504 DOI: 10.3390/e25050749] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/25/2023] [Accepted: 04/30/2023] [Indexed: 05/28/2023]
Abstract
The phenomenon of intermittency has remained a theoretical concept without any attempts to approach it geometrically with the use of a simple visualization. In this paper, a particular geometric model of point clustering approaching the Cantor shape in 2D, with a symmetry scale θ being an intermittency parameter, is proposed. To verify its ability to describe intermittency, to this model, we applied the entropic skin theory concept. This allowed us to obtain a conceptual validation. We observed that the intermittency phenomenon in our model was adequately described with the multiscale dynamics proposed by the entropic skin theory, coupling the fluctuation levels that extended between two extremes: the bulk and the crest. We calculated the reversibility efficiency γ with two different methods: statistical and geometrical analyses. Both efficiency values, γstat and γgeo, showed equality with a low relative error margin, which actually validated our suggested fractal model for intermittency. In addition, we applied the extended self-similarity (E.S.S.) to the model. This highlighted the intermittency phenomenon as a deviation from the homogeneity assumed by Kolmogorov in turbulence.
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Affiliation(s)
- Walid Tarraf
- Laboratory of Research in Industrial Eco-Innovation and Energetic (LR2E), Ecole Supérieure d'Ingénieurs ECAM-EPMI, 13 Bd de l'Hautil, 95000 Cergy, France
- Laboratory of Energetics Mechanics and Electromagnetism (LEME), Université Paris Nanterre, Pôle de Ville d'Avray, 50 rue de Sèvres, 92410 Ville d'Avray, France
| | - Diogo Queiros-Condé
- Laboratory of Energetics Mechanics and Electromagnetism (LEME), Université Paris Nanterre, Pôle de Ville d'Avray, 50 rue de Sèvres, 92410 Ville d'Avray, France
| | - Patrick Ribeiro
- Laboratory of Energetics Mechanics and Electromagnetism (LEME), Université Paris Nanterre, Pôle de Ville d'Avray, 50 rue de Sèvres, 92410 Ville d'Avray, France
| | - Rafik Absi
- Laboratory of Research in Industrial Eco-Innovation and Energetic (LR2E), Ecole Supérieure d'Ingénieurs ECAM-EPMI, 13 Bd de l'Hautil, 95000 Cergy, France
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Vegué M, Thibeault V, Desrosiers P, Allard A. Dimension reduction of dynamics on modular and heterogeneous directed networks. PNAS Nexus 2023; 2:pgad150. [PMID: 37215634 PMCID: PMC10198746 DOI: 10.1093/pnasnexus/pgad150] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/17/2023] [Accepted: 04/12/2023] [Indexed: 05/24/2023]
Abstract
Dimension reduction is a common strategy to study nonlinear dynamical systems composed by a large number of variables. The goal is to find a smaller version of the system whose time evolution is easier to predict while preserving some of the key dynamical features of the original system. Finding such a reduced representation for complex systems is, however, a difficult task. We address this problem for dynamics on weighted directed networks, with special emphasis on modular and heterogeneous networks. We propose a two-step dimension-reduction method that takes into account the properties of the adjacency matrix. First, units are partitioned into groups of similar connectivity profiles. Each group is associated to an observable that is a weighted average of the nodes' activities within the group. Second, we derive a set of equations that must be fulfilled for these observables to properly represent the original system's behavior, together with a method for approximately solving them. The result is a reduced adjacency matrix and an approximate system of ODEs for the observables' evolution. We show that the reduced system can be used to predict some characteristic features of the complete dynamics for different types of connectivity structures, both synthetic and derived from real data, including neuronal, ecological, and social networks. Our formalism opens a way to a systematic comparison of the effect of various structural properties on the overall network dynamics. It can thus help to identify the main structural driving forces guiding the evolution of dynamical processes on networks.
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Affiliation(s)
- Marina Vegué
- Département de physique, de génie physique et d'optique, Université Laval, 2325 rue de l'Université, G1V 0A6 Québec, Canada
- Centre interdisciplinaire en modélisation mathématique, Université Laval, 2325 rue de l'Université, G1V 0A6 Québec, Canada
| | - Vincent Thibeault
- Département de physique, de génie physique et d'optique, Université Laval, 2325 rue de l'Université, G1V 0A6 Québec, Canada
- Centre interdisciplinaire en modélisation mathématique, Université Laval, 2325 rue de l'Université, G1V 0A6 Québec, Canada
| | - Patrick Desrosiers
- Département de physique, de génie physique et d'optique, Université Laval, 2325 rue de l'Université, G1V 0A6 Québec, Canada
- Centre interdisciplinaire en modélisation mathématique, Université Laval, 2325 rue de l'Université, G1V 0A6 Québec, Canada
- CERVO Brain Research Center, 2301 avenue d'Estimauville, G1E 1T2 Québec, Canada
| | - Antoine Allard
- Département de physique, de génie physique et d'optique, Université Laval, 2325 rue de l'Université, G1V 0A6 Québec, Canada
- Centre interdisciplinaire en modélisation mathématique, Université Laval, 2325 rue de l'Université, G1V 0A6 Québec, Canada
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Rodriguez J, Iniguez A, Jena N, Tata P, Liu ZY, Lander AD, Lowengrub J, Van Etten RA. Predictive nonlinear modeling of malignant myelopoiesis and tyrosine kinase inhibitor therapy. eLife 2023; 12:e84149. [PMID: 37115622 PMCID: PMC10212564 DOI: 10.7554/elife.84149] [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: 10/12/2022] [Accepted: 04/26/2023] [Indexed: 04/29/2023] Open
Abstract
Chronic myeloid leukemia (CML) is a blood cancer characterized by dysregulated production of maturing myeloid cells driven by the product of the Philadelphia chromosome, the BCR-ABL1 tyrosine kinase. Tyrosine kinase inhibitors (TKIs) have proved effective in treating CML, but there is still a cohort of patients who do not respond to TKI therapy even in the absence of mutations in the BCR-ABL1 kinase domain that mediate drug resistance. To discover novel strategies to improve TKI therapy in CML, we developed a nonlinear mathematical model of CML hematopoiesis that incorporates feedback control and lineage branching. Cell-cell interactions were constrained using an automated model selection method together with previous observations and new in vivo data from a chimeric BCR-ABL1 transgenic mouse model of CML. The resulting quantitative model captures the dynamics of normal and CML cells at various stages of the disease and exhibits variable responses to TKI treatment, consistent with those of CML patients. The model predicts that an increase in the proportion of CML stem cells in the bone marrow would decrease the tendency of the disease to respond to TKI therapy, in concordance with clinical data and confirmed experimentally in mice. The model further suggests that, under our assumed similarities between normal and leukemic cells, a key predictor of refractory response to TKI treatment is an increased maximum probability of self-renewal of normal hematopoietic stem cells. We use these insights to develop a clinical prognostic criterion to predict the efficacy of TKI treatment and design strategies to improve treatment response. The model predicts that stimulating the differentiation of leukemic stem cells while applying TKI therapy can significantly improve treatment outcomes.
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MESH Headings
- Mice
- Animals
- Tyrosine Kinase Inhibitors
- Protein Kinase Inhibitors/pharmacology
- Protein Kinase Inhibitors/therapeutic use
- Drug Resistance, Neoplasm
- Myelopoiesis
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/pharmacology
- Mice, Transgenic
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
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Affiliation(s)
- Jonathan Rodriguez
- Graduate Program in Mathematical, Computational and Systems Biology, University of California, IrvineIrvineUnited States
- Center for Complex Biological Systems, University of California, IrvineIrvineUnited States
| | - Abdon Iniguez
- Graduate Program in Mathematical, Computational and Systems Biology, University of California, IrvineIrvineUnited States
- Center for Complex Biological Systems, University of California, IrvineIrvineUnited States
| | - Nilamani Jena
- Department of Medicine, University of California, IrvineIrvineUnited States
| | - Prasanthi Tata
- Department of Medicine, University of California, IrvineIrvineUnited States
| | - Zhong-Ying Liu
- Department of Medicine, University of California, IrvineIrvineUnited States
| | - Arthur D Lander
- Center for Complex Biological Systems, University of California, IrvineIrvineUnited States
- Department of Developmental and Cell Biology, University of California, IrvineIrvineUnited States
- Chao Family Comprehensive Cancer Center, University of California, IrvineIrvineUnited States
- Department of Biomedical Engineering, University of California, IrvineIrvineUnited States
| | - John Lowengrub
- Center for Complex Biological Systems, University of California, IrvineIrvineUnited States
- Chao Family Comprehensive Cancer Center, University of California, IrvineIrvineUnited States
- Department of Biomedical Engineering, University of California, IrvineIrvineUnited States
- Department of Mathematics, University of California, IrvineIrvineUnited States
| | - Richard A Van Etten
- Center for Complex Biological Systems, University of California, IrvineIrvineUnited States
- Department of Medicine, University of California, IrvineIrvineUnited States
- Chao Family Comprehensive Cancer Center, University of California, IrvineIrvineUnited States
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43
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Nepomnyashchy A, Samoilova A. Introduction to 'New trends in pattern formation and nonlinear dynamics of extended systems'. Philos Trans A Math Phys Eng Sci 2023; 381:20220091. [PMID: 36842982 PMCID: PMC9968531 DOI: 10.1098/rsta.2022.0091] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Pattern formation is a widespread phenomenon observed in physical, chemical and biological systems. During the past decades, powerful experimental and theoretical tools for the investigation of that phenomenon have been developed. Also, the set of pattern forming system was diversified. The present issue presents a panorama of pattern formation and other nonlinear dynamical phenomena in different natural and engineering systems. Special attention is paid to nonlinear dynamics of fluids. Non-equilibrium phenomena in chemical and quantum systems are also considered. This article is part of the theme issue 'New trends in pattern formation and nonlinear dynamics of extended systems'.
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Affiliation(s)
| | - Anna Samoilova
- Institute of Continuous Media Mechanics, UB RAS, Academician Korolev Street 1, Perm 614013, Russia
- Department of Theoretical Physics, Perm State University, Bukirev Street 15, Perm 614990, Russia
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44
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Gobat G, Fresca S, Manzoni A, Frangi A. Reduced Order Modeling of Nonlinear Vibrating Multiphysics Microstructures with Deep Learning-Based Approaches. Sensors (Basel) 2023; 23:3001. [PMID: 36991715 PMCID: PMC10051645 DOI: 10.3390/s23063001] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Micro-electro-mechanical-systems are complex structures, often involving nonlinearites of geometric and multiphysics nature, that are used as sensors and actuators in countless applications. Starting from full-order representations, we apply deep learning techniques to generate accurate, efficient, and real-time reduced order models to be used for the simulation and optimization of higher-level complex systems. We extensively test the reliability of the proposed procedures on micromirrors, arches, and gyroscopes, as well as displaying intricate dynamical evolutions such as internal resonances. In particular, we discuss the accuracy of the deep learning technique and its ability to replicate and converge to the invariant manifolds predicted using the recently developed direct parametrization approach that allows the extraction of the nonlinear normal modes of large finite element models. Finally, by addressing an electromechanical gyroscope, we show that the non-intrusive deep learning approach generalizes easily to complex multiphysics problems.
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Affiliation(s)
- Giorgio Gobat
- Department of Civil and Environmental Engineering, Politecnico di Milano, Piazza Leonardo da Vinci, 32, 20133 Milano, Italy;
| | - Stefania Fresca
- MOX—Department of Mathematics, Politecnico di Milano, P.za Leonardo da Vinci 32, 20133 Milano, Italy; (S.F.); (A.M.)
| | - Andrea Manzoni
- MOX—Department of Mathematics, Politecnico di Milano, P.za Leonardo da Vinci 32, 20133 Milano, Italy; (S.F.); (A.M.)
| | - Attilio Frangi
- Department of Civil and Environmental Engineering, Politecnico di Milano, Piazza Leonardo da Vinci, 32, 20133 Milano, Italy;
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45
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Moulder RG, Martynova E, Boker SM. Extracting Nonlinear Dynamics from Psychological and Behavioral Time Series Through HAVOK Analysis. Multivariate Behav Res 2023; 58:441-465. [PMID: 35001769 DOI: 10.1080/00273171.2021.1994848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Analytical methods derived from nonlinear dynamical systems, complexity, and chaos theories offer researchers a framework for in-depth analysis of time series data. However, relatively few studies involving time series data obtained from psychological and behavioral research employ such methods. This paucity of application is due to a lack of general analysis frameworks for modeling time series data with strong nonlinear components. In this article, we describe the potential of Hankel alternative view of Koopman (HAVOK) analysis for solving this issue. HAVOK analysis is a unified framework for nonlinear dynamical systems analysis of time series data. By utilizing HAVOK analysis, researchers may model nonlinear time series data in a linear framework while simultaneously reconstructing attractor manifolds and obtaining a secondary time series representing the amount of nonlinear forcing occurring in a system at any given time. We begin by showing the mathematical underpinnings of HAVOK analysis and then show example applications of HAVOK analysis for modeling time series data derived from real psychological and behavioral studies.
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46
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Han Z, Sun LW, Wu XT, Yang X, Fan YB. Nonlinear dynamics of membrane skeleton in osteocyte. Comput Methods Biomech Biomed Engin 2023; 26:249-260. [PMID: 35363098 DOI: 10.1080/10255842.2022.2057796] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Osteocytes play an important role in mechanosensation and conduction in bone tissue, and the change of mechanical environment can affect the sensitivity of osteocytes to external stimulation. The structure of osteocytes will be changed when they are subjected to vibrations, which influence the mechanosensitivity of osteocytes and alter the regulation of bone remodeling process. As an important mechanotransduction structure in osteocytes, the membrane skeleton greatly affects the mechanosensation and conduction of osteocytes. However, the dynamic responses of membrane skeleton to the vibration and the structural changes of membrane skeleton are unclear. Therefore, we applied a nonlinear dynamics method to explain the time-dependent changes of membrane skeleton. The semi-ellipsoidal reticulate shell structure of membrane skeleton is built based on the experimental observation in our previous work. Then, the nonlinear dynamic equations of membrane skeleton are established according to the theory of plate and shell dynamics, and the displacement-time curves, phase portraits, and Poincaré maps of membrane skeleton structure were obtained. The numeration results show that under the vibration stimulation of 15 Hz, 30 Hz, 60 Hz, and 90 Hz, the membrane skeleton is destroyed after a transient equilibrium position vibration. The vibration of 15 Hz has the most destructive effect on the membrane skeleton, the natural frequency of membrane skeleton may be less than 15 Hz. In addition, the chaos phenomenon occurs to the membrane skeleton during vibration. As a damping factor, the existence of viscosity alleviates the damage of structure. This study can help us to understand the oscillation characteristic of membrane skeleton in osteocyte.
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Affiliation(s)
- Zhuang Han
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Lian-Wen Sun
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Xin-Tong Wu
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Xiao Yang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Yu-Bo Fan
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
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47
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Fortuna L, Buscarino A. Spiking Neuron Mathematical Models: A Compact Overview. Bioengineering (Basel) 2023; 10:bioengineering10020174. [PMID: 36829668 PMCID: PMC9952045 DOI: 10.3390/bioengineering10020174] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/13/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
The features of the main models of spiking neurons are discussed in this review. We focus on the dynamical behaviors of five paradigmatic spiking neuron models and present recent literature studies on the topic, classifying the contributions based on the most-studied items. The aim of this review is to provide the reader with fundamental details related to spiking neurons from a dynamical systems point-of-view.
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Affiliation(s)
- Luigi Fortuna
- Dipartimento di Ingegneria Elettrica Elettronica e Informatica, University of Catania, 95125 Catania, Italy
- IASI, Consiglio Nazionale delle Ricerche (CNR), 00185 Roma, Italy
- Correspondence: (L.F.); (A.B.)
| | - Arturo Buscarino
- Dipartimento di Ingegneria Elettrica Elettronica e Informatica, University of Catania, 95125 Catania, Italy
- IASI, Consiglio Nazionale delle Ricerche (CNR), 00185 Roma, Italy
- Correspondence: (L.F.); (A.B.)
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48
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Marrone JI, Sepulchre JA, Ventura AC. A nested bistable module within a negative feedback loop ensures different types of oscillations in signaling systems. Sci Rep 2023; 13:529. [PMID: 36631477 DOI: 10.1038/s41598-022-27047-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023] Open
Abstract
In this article, we consider a double phosphorylation cycle, a ubiquitous signaling component, having the ability to display bistability, a behavior strongly related to the existence of positive feedback loops. If this component is connected to other signaling elements, it very likely undergoes some sort of protein-protein interaction. In several cases, these interactions result in a non-explicit negative feedback effect, leading to interlinked positive and negative feedbacks. This combination was studied in the literature as a way to generate relaxation-type oscillations. Here, we show that the two feedbacks together ensure two types of oscillations, the relaxation-type ones and a smoother type of oscillations functioning in a very narrow range of frequencies, in such a way that outside that range, the amplitude of the oscillations is severely compromised. Even more, we show that the two feedbacks are essential for both oscillatory types to emerge, and it is their hierarchy what determines the type of oscillation at work. We used bifurcation analyses and amplitude vs. frequency curves to characterize and classify the oscillations. We also applied the same ideas to another simple model, with the goal of generalizing what we learned from signaling models. The results obtained display the wealth of oscillatory dynamics that exists in a system with a bistable module nested within a negative feedback loop, showing how to transition between different types of oscillations and other dynamical behaviors such as excitability. Our work provides a framework for the study of other oscillatory systems based on bistable modules, from simple two-component models to more complex examples like the MAPK cascade and experimental cases like cell cycle oscillators.
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49
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Adams J, Khan N, Morris A, Elhabian S. Learning spatiotemporal statistical shape models for non-linear dynamic anatomies. Front Bioeng Biotechnol 2023; 11:1086234. [PMID: 36777257 PMCID: PMC9911425 DOI: 10.3389/fbioe.2023.1086234] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/16/2023] [Indexed: 01/28/2023] Open
Abstract
Numerous clinical investigations require understanding changes in anatomical shape over time, such as in dynamic organ cycle characterization or longitudinal analyses (e.g., for disease progression). Spatiotemporal statistical shape modeling (SSM) allows for quantifying and evaluating dynamic shape variation with respect to a cohort or population of interest. Existing data-driven SSM approaches leverage information theory to capture population-level shape variations by learning correspondence-based (landmark) representations of shapes directly from data using entropy-based optimization schemes. These approaches assume sample independence and thus are unsuitable for sequential dynamic shape observations. Previous methods for adapting entropy-based SSM optimization schemes for the spatiotemporal case either utilize a cross-sectional design (ignoring within-subject correlation) or impose other limiting assumptions, such as the linearity of shape dynamics. Here, we present a principled approach to spatiotemporal SSM that relaxes these assumptions to correctly capture population-level shape variation over time. We propose to incorporate modeling the underlying time dependency into correspondence optimization via a regularized principal component polynomial regression. This approach is flexible enough to capture non-linear temporal dynamics while encoding population-specific spatial regularity. We demonstrate our method's efficacy on synthetic data and left atrium segmented from cardiac MRI scans. Our approach better captures the population modes of variation and a statistically significant time dependency than existing methods.
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Affiliation(s)
- Jadie Adams
- School of Computing, University of Utah, Salt Lake City, UT, United States
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, United States
- *Correspondence: Jadie Adams, ; Nawazish Khan, ; Shireen Elhabian,
| | - Nawazish Khan
- School of Computing, University of Utah, Salt Lake City, UT, United States
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, United States
- *Correspondence: Jadie Adams, ; Nawazish Khan, ; Shireen Elhabian,
| | - Alan Morris
- School of Computing, University of Utah, Salt Lake City, UT, United States
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, United States
| | - Shireen Elhabian
- School of Computing, University of Utah, Salt Lake City, UT, United States
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, United States
- *Correspondence: Jadie Adams, ; Nawazish Khan, ; Shireen Elhabian,
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Azami H, Daftarifard E, Humeau-Heurtier A, Fernandez A, Abasolo D, Rajji TK. Assessment and Comparison of Nonlinear Measures in Resting-State Magnetoencephalograms in Alzheimer's Disease and Mild Cognitive Impairment. J Alzheimers Dis 2023; 96:1151-1162. [PMID: 37980661 DOI: 10.3233/jad-230544] [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] [Indexed: 11/21/2023]
Abstract
BACKGROUND Nonlinear dynamical measures, such as fractal dimension (FD), entropy, and Lempel-Ziv complexity (LZC), have been extensively investigated individually for detecting information content in magnetoencephalograms (MEGs) from patients with Alzheimer's disease (AD). OBJECTIVE To compare systematically the performance of twenty conventional and recently introduced nonlinear dynamical measures in studying AD versus mild cognitive impairment (MCI) and healthy control (HC) subjects using MEG. METHODS We compared twenty nonlinear measures to distinguish MEG recordings from 36 AD (mean age = 74.06±6.95 years), 18 MCI (mean age = 74.89±5.57 years), and 26 HC subjects (mean age = 71.77±6.38 years) in different brain regions and also evaluated the effect of the length of MEG epochs on their performance. We also studied the correlation between these measures and cognitive performance based on the Mini-Mental State Examination (MMSE). RESULTS The results obtained by LZC, zero-crossing rate (ZCR), FD, and dispersion entropy (DispEn) measures showed significant differences among the three groups. There was no significant difference between HC and MCI. The highest Hedge's g effect sizes for HC versus AD and MCI versus AD were respectively obtained by Higuchi's FD (HFD) and fuzzy DispEn (FuzDispEn) in the whole brain and was most prominent in left lateral. The results obtained by HFD and FuzDispEn had a significant correlation with the MMSE scores. DispEn-based techniques, LZC, and ZCR, compared with HFD, were less sensitive to epoch length in distinguishing HC form AD. CONCLUSIONS FuzDispEn was the most consistent technique to distinguish MEG dynamical patterns in AD compared with HC and MCI.
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Affiliation(s)
- Hamed Azami
- Adult Neurodevelopment and Geriatric Psychiatry Division, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Elham Daftarifard
- Department of Pharmaceutics, Mazandaran University of Medical Sciences, Sari, Iran
| | | | - Alberto Fernandez
- Department of Legal Medicine, Psychiatry and Pathology, Complutense University of Madrid, Madrid, Spain
| | - Daniel Abasolo
- Centre for Biomedical Engineering, School of Mechanical Engineering Sciences, University of Surrey, Guildford, UK
| | - Tarek K Rajji
- Adult Neurodevelopment and Geriatric Psychiatry Division, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Toronto Dementia Research Alliance, University of Toronto, Toronto, ON, Canada
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