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Microtubules as a potential platform for energy transfer in biological systems: a target for implementing individualized, dynamic variability patterns to improve organ function. Mol Cell Biochem 2023; 478:375-392. [PMID: 35829870 DOI: 10.1007/s11010-022-04513-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/24/2022] [Indexed: 02/07/2023]
Abstract
Variability characterizes the complexity of biological systems and is essential for their function. Microtubules (MTs) play a role in structural integrity, cell motility, material transport, and force generation during mitosis, and dynamic instability exemplifies the variability in the proper function of MTs. MTs are a platform for energy transfer in cells. The dynamic instability of MTs manifests itself by the coexistence of growth and shortening, or polymerization and depolymerization. It results from a balance between attractive and repulsive forces between tubulin dimers. The paper reviews the current data on MTs and their potential roles as energy-transfer cellular structures and presents how variability can improve the function of biological systems in an individualized manner. The paper presents the option for targeting MTs to trigger dynamic improvement in cell plasticity, regulate energy transfer, and possibly control quantum effects in biological systems. The described system quantifies MT-dependent variability patterns combined with additional personalized signatures to improve organ function in a subject-tailored manner. The platform can regulate the use of MT-targeting drugs to improve the response to chronic therapies. Ongoing trials test the effects of this platform on various disorders.
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Larson BT, Garbus J, Pollack JB, Marshall WF. A unicellular walker controlled by a microtubule-based finite-state machine. Curr Biol 2022; 32:3745-3757.e7. [PMID: 35963241 PMCID: PMC9474717 DOI: 10.1016/j.cub.2022.07.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/20/2022] [Accepted: 07/14/2022] [Indexed: 11/21/2022]
Abstract
Cells are complex biochemical systems whose behaviors emerge from interactions among myriad molecular components. Computation is often invoked as a general framework for navigating this cellular complexity. However, it is unclear how cells might embody computational processes such that the theories of computation, including finite-state machine models, could be productively applied. Here, we demonstrate finite-state-machine-like processing embodied in cells using the walking behavior of Euplotes eurystomus, a ciliate that walks across surfaces using fourteen motile appendages (cirri). We found that cellular walking entails regulated transitions among a discrete set of gait states. The set of observed transitions decomposes into a small group of high-probability, temporally irreversible transitions and a large group of low-probability, time-symmetric transitions, thus revealing stereotypy in the sequential patterns of state transitions. Simulations and experiments suggest that the sequential logic of the gait is functionally important. Taken together, these findings implicate a finite-state-machine-like process. Cirri are connected by microtubule bundles (fibers), and we found that the dynamics of cirri involved in different state transitions are associated with the structure of the fiber system. Perturbative experiments revealed that the fibers mediate gait coordination, suggesting a mechanical basis of gait control.
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Affiliation(s)
- Ben T Larson
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Jack Garbus
- Computer Science Department, Brandeis University, Waltham, MA 02453, USA
| | - Jordan B Pollack
- Computer Science Department, Brandeis University, Waltham, MA 02453, USA
| | - Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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Nganfo WA, Kenfack-Sadem C, Fotué AJ, Ekosso MC, Wopunghwo SN, Fai LC. Dynamics of exciton polaron in microtubule. Heliyon 2022; 8:e08897. [PMID: 35265761 PMCID: PMC8899671 DOI: 10.1016/j.heliyon.2022.e08897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/19/2021] [Accepted: 01/31/2022] [Indexed: 11/16/2022] Open
Abstract
In this paper, we study the dynamical properties of the exciton-polaron in the microtubule. The study was carried out using a unitary transformation and an approximate diagonalization technique. Analytically, the modeling of exciton-polaron dynamics in microtubules is presented. From this model, the ground state energy, mobility, and entropy of the exciton-polaron are derived as a function of microtubule's parameters. Numerical results show that, depending on the three vibrational modes (protofilament, helix, antihelix) in MTs, exciton-polaron energy is anisotropic and is more present on the protofilament than the helix and absent on the antihelix. Taking into account the variation of the protofilament vibrations by fixing the helix vibrations, exciton-polaron moves between the 1st and 2nd protofilaments. It is seen that the variation of the two vibrations induces mobility of the quasiparticle between the 1st and 15th protofilament. This result points out the importance of helix vibrations on the dynamics of quasiparticles. It is observed that the mobility of the exciton polaron and the entropy of the system are strongly influenced by the vibrations through the protofilament and helix. The effects of the one through the antihelix is negligible. The entropy of the system is similar to that of mobility. Confirming that the quasiparticles move in the protofilament faster than in the helix.
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Affiliation(s)
- W A Nganfo
- Condensed Matter and Nanomaterials, Faculty of Science, Department of Physics, University of Dschang, Po Box 67, Cameroon
| | - C Kenfack-Sadem
- Condensed Matter and Nanomaterials, Faculty of Science, Department of Physics, University of Dschang, Po Box 67, Cameroon
| | - A J Fotué
- Condensed Matter and Nanomaterials, Faculty of Science, Department of Physics, University of Dschang, Po Box 67, Cameroon
| | - M C Ekosso
- Condensed Matter and Nanomaterials, Faculty of Science, Department of Physics, University of Dschang, Po Box 67, Cameroon
| | - S N Wopunghwo
- Condensed Matter and Nanomaterials, Faculty of Science, Department of Physics, University of Dschang, Po Box 67, Cameroon
| | - L C Fai
- Condensed Matter and Nanomaterials, Faculty of Science, Department of Physics, University of Dschang, Po Box 67, Cameroon
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Chiolerio A, Draper TC, Mayne R, Adamatzky A. On resistance switching and oscillations in tubulin microtubule droplets. J Colloid Interface Sci 2020; 560:589-595. [DOI: 10.1016/j.jcis.2019.10.065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/15/2019] [Accepted: 10/17/2019] [Indexed: 01/30/2023]
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5
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Barvitenko N, Lawen A, Aslam M, Pantaleo A, Saldanha C, Skverchinskaya E, Regolini M, Tuszynski JA. Integration of intracellular signaling: Biological analogues of wires, processors and memories organized by a centrosome 3D reference system. Biosystems 2018; 173:191-206. [PMID: 30142359 DOI: 10.1016/j.biosystems.2018.08.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/03/2018] [Accepted: 08/20/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND Myriads of signaling pathways in a single cell function to achieve the highest spatio-temporal integration. Data are accumulating on the role of electromechanical soliton-like waves in signal transduction processes. Theoretical studies strongly suggest feasibility of both classical and quantum computing involving microtubules. AIM A theoretical study of the role of the complex composed of the plasma membrane and the microtubule-based cytoskeleton as a system that transmits, stores and processes information. METHODS Theoretical analysis presented here refers to (i) the Penrose-Hameroff theory of consciousness (Orchestrated Objective Reduction; Orch OR), (ii) the description of the centrosome as a reference system for construction of the 3D map of the cell proposed by Regolini, (iii) the Heimburg-Jackson model of the nerve pulse propagation along axons' lipid bilayer as soliton-like electro-mechanical waves. RESULTS AND CONCLUSION The ideas presented in this paper provide a qualitative model for the decision-making processes in a living cell undergoing a differentiation process. OUTLOOK This paper paves the way for the real-time live-cell observation of information processing by microtubule-based cytoskeleton and cell fate decision making.
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Affiliation(s)
| | - Alfons Lawen
- Monash University, School of Biomedical Sciences, Department of Biochemistry and Molecular Biology, VIC, 3800, Australia
| | - Muhammad Aslam
- Medical Clininc I, Cardiology/Angiology, University Hospital, Justus-Liebig-University, Giessen, Germany
| | - Antonella Pantaleo
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Carlota Saldanha
- Instituto de Medicina Molecular, Instituto de Bioquimica, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | | | - Marco Regolini
- Department of Bioengineering and Mathematical Modeling, AudioLogic, Milan, Italy
| | - Jack A Tuszynski
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada; Department of Physics, University of Alberta, Edmonton, Alberta, Canada; Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128, Torino, Italy.
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Agnati LF, Guidolin D, Maura G, Marcoli M. Functional roles of three cues that provide nonsynaptic modes of communication in the brain: electromagnetic field, oxygen, and carbon dioxide. J Neurophysiol 2017; 119:356-368. [PMID: 29070628 DOI: 10.1152/jn.00413.2017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The integrative actions of the brain depend on the exchange of information among its computational elements. Hence, this phenomenon plays the key role in driving the complex dynamics of the central nervous system, in which true computations interact with noncomputational dynamical processes to generate brain representations of the body and of the body in the external world, and hence the finalistic behavior of the organism. In this context, it should be pointed out that, besides the intercellular interactions mediated by classical electrochemical signals, other types of interactions, namely, "cues" and "coercions," also appear to be exploited by the system to achieve its function. The present review focuses mainly on cues present in the environment and on those produced by cells of the body, which "pervade" the brain and contribute to its dynamics. These cues can also be metabolic substrates, and, in most cases, they are of fundamental importance to brain function and the survival of the entire organism. Three of these highly pervasive cues will be analyzed in greater detail, namely, oxygen, carbon dioxide, and electromagnetic fields (EMF). Special emphasis will be placed on EMF, since several authors have suggested that these highly pervasive energy fluctuations may play an important role in the global integrative actions of the brain; hence, EMF signaling may transcend classical connectionist models of brain function. Thus the new concept of "broadcasted neuroconnectomics" has been introduced, which transcends the current connectomics view of the brain.
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Affiliation(s)
- Luigi F Agnati
- Department of Diagnostics, Clinical Medicine and Public Health, University of Modena and Reggio Emilia , Modena , Italy.,Department of Neuroscience, Karolinska Institutet , Stockholm , Sweden
| | - Diego Guidolin
- Department of Neuroscience, University of Padova , Padua , Italy
| | - Guido Maura
- Department of Pharmacy and Center of Excellence for Biomedical Research, University of Genova , Genoa , Italy
| | - Manuela Marcoli
- Department of Pharmacy and Center of Excellence for Biomedical Research, University of Genova , Genoa , Italy
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Nesterov AI, Ramírez MF, Berman GP, Mavromatos NE. Nonlinear dynamics of dipoles in microtubules: Pseudospin model. Phys Rev E 2016; 93:062412. [PMID: 27415303 DOI: 10.1103/physreve.93.062412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Indexed: 06/06/2023]
Abstract
We perform a theoretical study of the dynamics of the electric field excitations in a microtubule by taking into consideration the realistic cylindrical geometry, dipole-dipole interactions of the tubulin-based protein heterodimers, the radial electric field produced by the solvent, and a possible degeneracy of energy states of individual heterodimers. The consideration is done in the frame of the classical pseudospin model. We derive the system of nonlinear dynamical partial differential equations of motion for interacting dipoles and the continuum version of these equations. We obtain the solutions of these equations in the form of snoidal waves, solitons, kinks, and localized spikes. Our results will help to achieve a better understanding of the functional properties of microtubules including the motor protein dynamics and the information transfer processes. Our considerations are based on classical dynamics. Some speculations on the role of possible quantum effects are also made.
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Affiliation(s)
- Alexander I Nesterov
- Departamento de Física, Centro Universitario de Ciencias Exactas e Ingenierias, Universidad de Guadalajara, Avenida Revolución 1500, Guadalajara, CP 44420, Jalisco, Mexico
| | - Mónica F Ramírez
- Departamento de Física, Centro Universitario de Ciencias Exactas e Ingenierias, Universidad de Guadalajara, Avenida Revolución 1500, Guadalajara, CP 44420, Jalisco, Mexico
| | - Gennady P Berman
- Bioscience Division, Los Alamos National Laboratory, and the New Mexico Consortium, Los Alamos, New Mexico 87544, USA
| | - Nick E Mavromatos
- Department of Physics, King's College London, Strand, London WC2R 2LS, United Kingdom
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Globus G. Heideggerian dynamics and the monadological role of the 'between': A crossing with quantum brain dynamics. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:324-31. [PMID: 26193172 DOI: 10.1016/j.pbiomolbio.2015.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Heideggerian theory is retrieved as a dynamics, the "Godly event" of das Ereignis ("enowning"), which is unexpectedly compatible with a version of quantum brain dynamics. In both the "between" (das Zwischen) has the fundamental role of the dis-closure that is Existenz. Heidegger's harsh critique of technology and science does not apply to revolutionary quantum brain dynamics. The crossing between Heidegger and quantum brain dynamics, as well as one fundamental ontological difference, illuminates both. To our surprise this difference turns out, contra Heidegger, to be monadological. The monadological conception is applied to long-standing problematics of measurement in quantum physics and consciousness in philosophy. Heideggerian Existenz is affirmed as fundamentally non-computational but is reformulated as a dynamical process of monadological dis-closure that radically deconstructs transcendent world.
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Scholkmann F. Two emerging topics regarding long-range physical signaling in neurosystems: Membrane nanotubes and electromagnetic fields. J Integr Neurosci 2015; 14:135-53. [DOI: 10.1142/s0219635215300115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Welcome MO, Mastorakis NE, Pereverzev VA. Sweet taste receptor signaling network: possible implication for cognitive functioning. Neurol Res Int 2015; 2015:606479. [PMID: 25653876 PMCID: PMC4306214 DOI: 10.1155/2015/606479] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/20/2014] [Indexed: 01/01/2023] Open
Abstract
Sweet taste receptors are transmembrane protein network specialized in the transmission of information from special "sweet" molecules into the intracellular domain. These receptors can sense the taste of a range of molecules and transmit the information downstream to several acceptors, modulate cell specific functions and metabolism, and mediate cell-to-cell coupling through paracrine mechanism. Recent reports indicate that sweet taste receptors are widely distributed in the body and serves specific function relative to their localization. Due to their pleiotropic signaling properties and multisubstrate ligand affinity, sweet taste receptors are able to cooperatively bind multiple substances and mediate signaling by other receptors. Based on increasing evidence about the role of these receptors in the initiation and control of absorption and metabolism, and the pivotal role of metabolic (glucose) regulation in the central nervous system functioning, we propose a possible implication of sweet taste receptor signaling in modulating cognitive functioning.
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Affiliation(s)
- Menizibeya O. Welcome
- World Scientific and Engineering Academy and Society, Ag. Ioannou Theologou 17-23, Zografou, 15773 Athens, Greece
| | - Nikos E. Mastorakis
- World Scientific and Engineering Academy and Society, Ag. Ioannou Theologou 17-23, Zografou, 15773 Athens, Greece
- Department of Industrial Engineering, Technical University of Sofia, 8 Kl. Ohridski Boulevard, 1000 Sofia, Bulgaria
| | - Vladimir A. Pereverzev
- Department of Normal Physiology, Belarusian State Medical University, Dzerzhinsky Avenue 83, 220116 Minsk, Belarus
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Friesen DE, Craddock TJA, Kalra AP, Tuszynski JA. Biological wires, communication systems, and implications for disease. Biosystems 2014; 127:14-27. [PMID: 25448891 DOI: 10.1016/j.biosystems.2014.10.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 10/30/2014] [Accepted: 10/31/2014] [Indexed: 12/14/2022]
Abstract
Microtubules, actin, and collagen are macromolecular structures that compose a large percentage of the proteins in the human body, helping form and maintain both intracellular and extracellular structure. They are biological wires and are structurally connected through various other proteins. Microtubules (MTs) have been theorized to be involved in classical and quantum information processing, and evidence continues to suggest possible semiconduction through MTs. The previous Dendritic Cytoskeleton Information Processing Model has hypothesized how MTs and actin form a communication network in neurons. Here, we review information transfer possibilities involving MTs, actin, and collagen, and the evidence of an organism-wide high-speed communication network that may regulate morphogenesis and cellular proliferation. The direct and indirect evidence in support of this hypothesis, and implications for chronic diseases such as cancer and neurodegenerative diseases are discussed.
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Affiliation(s)
- Douglas E Friesen
- Department of Oncology, University of Alberta, Edmonton, Alberta T6G 1Z2, Canada
| | - Travis J A Craddock
- Center for Psychological Studies, Graduate School of Computer and Information Sciences, College of Osteopathic Medicine, Nova Southeastern University, Ft. Lauderdale, FL 33314, USA; Clinical Systems Biology Group, Institute for Neuro-Immune Medicine, Nova Southeastern University, Ft. Lauderdale, FL 33328, USA
| | - Aarat P Kalra
- Department of Chemistry, Dayalbagh Educational Institute, Agra 282005, India
| | - Jack A Tuszynski
- Department of Oncology, University of Alberta, Edmonton, Alberta T6G 1Z2, Canada; Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada.
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Ludueña RF. A Hypothesis on the Origin and Evolution of Tubulin. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 302:41-185. [DOI: 10.1016/b978-0-12-407699-0.00002-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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13
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Saha AA, Craddock TJ, Tuszynski JA. An investigation of the plausibility of stochastic resonance in tubulin dimers. Biosystems 2012; 107:81-7. [DOI: 10.1016/j.biosystems.2011.09.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 09/09/2011] [Accepted: 09/26/2011] [Indexed: 01/23/2023]
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Lundervold A. On consciousness, resting state fMRI, and neurodynamics. NONLINEAR BIOMEDICAL PHYSICS 2010; 4 Suppl 1:S9. [PMID: 20522270 PMCID: PMC2880806 DOI: 10.1186/1753-4631-4-s1-s9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
BACKGROUND During the last years, functional magnetic resonance imaging (fMRI) of the brain has been introduced as a new tool to measure consciousness, both in a clinical setting and in a basic neurocognitive research. Moreover, advanced mathematical methods and theories have arrived the field of fMRI (e.g. computational neuroimaging), and functional and structural brain connectivity can now be assessed non-invasively. RESULTS The present work deals with a pluralistic approach to "consciousness'', where we connect theory and tools from three quite different disciplines: (1) philosophy of mind (emergentism and global workspace theory), (2) functional neuroimaging acquisitions, and (3) theory of deterministic and statistical neurodynamics - in particular the Wilson-Cowan model and stochastic resonance. CONCLUSIONS Based on recent experimental and theoretical work, we believe that the study of large-scale neuronal processes (activity fluctuations, state transitions) that goes on in the living human brain while examined with functional MRI during "resting state", can deepen our understanding of graded consciousness in a clinical setting, and clarify the concept of "consiousness" in neurocognitive and neurophilosophy research.
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Affiliation(s)
- Arvid Lundervold
- Department of Biomedicine, Neuroinformatics and Image Analysis Laboratory, University of Bergen Jonas Lies vei 91, N-5009 Bergen, Norway.
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