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2. Neural Activity of Heterogeneous Inhibitory Spiking Networks with Delay

Author

Luccioli, Stefano, Garcia, David Angulo, and Torcini, Alessandro

Subjects
Condensed Matter - Disordered Systems and Neural Networks, Quantitative Biology - Neurons and Cognition
Abstract

We study a network of spiking neurons with heterogeneous excitabilities connected via inhibitory delayed pulses. For globally coupled systems the increase of the inhibitory coupling reduces the number of firing neurons by following a Winner Takes All mechanism. For sufficiently large transmission delay we observe the emergence of collective oscillations in the system beyond a critical coupling value. Heterogeneity promotes neural inactivation and asynchronous dynamics and its effect can be counteracted by considering longer time delays. In sparse networks, inhibition has the counterintuitive effect of promoting neural reactivation of silent neurons for sufficiently large coupling. In this regime, current fluctuations are on one side responsible for neural firing of sub-threshold neurons and on the other side for their desynchronization. Therefore, collective oscillations are present only in a limited range of coupling values, which remains finite in the thermodynamic limit. Out of this range the dynamics is asynchronous and for very large inhibition neurons display a bursting behaviour alternating periods of silence with periods where they fire freely in absence of any inhibition., Comment: 13 pages, 13 Figures, submitted to Physical review E

Published
2019
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3. Death and rebirth of neural activity in sparse inhibitory networks

Author

Angulo-Garcia, David, Luccioli, Stefano, Olmi, Simona, and Torcini, Alessandro

Subjects
Quantitative Biology - Neurons and Cognition, Condensed Matter - Disordered Systems and Neural Networks, Nonlinear Sciences - Chaotic Dynamics
Abstract

In this paper, we clarify the mechanisms underlying a general phenomenon present in pulse-coupled heterogeneous inhibitory networks: inhibition can induce not only suppression of the neural activity, as expected, but it can also promote neural reactivation. In particular, for globally coupled systems, the number of firing neurons monotonically reduces upon increasing the strength of inhibition (neurons' death). However, the random pruning of the connections is able to reverse the action of inhibition, i.e. in a sparse network a sufficiently strong synaptic strength can surprisingly promote, rather than depress, the activity of the neurons (neurons' rebirth). Thus the number of firing neurons reveals a minimum at some intermediate synaptic strength. We show that this minimum signals a transition from a regime dominated by the neurons with higher firing activity to a phase where all neurons are effectively sub-threshold and their irregular firing is driven by current fluctuations. We explain the origin of the transition by deriving an analytic mean field formulation of the problem able to provide the fraction of active neurons as well as the first two moments of their firing statistics. The introduction of a synaptic time scale does not modify the main aspects of the reported phenomenon. However, for sufficiently slow synapses the transition becomes dramatic, the system passes from a perfectly regular evolution to an irregular bursting dynamics. In this latter regime the model provides predictions consistent with experimental findings for a specific class of neurons, namely the medium spiny neurons in the striatum., Comment: 19 pages, 10 figures, submitted to NJP

Published
2016
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4. Functional Cliques in Developmentally Correlated Neural Networks

Author

Luccioli, Stefano, Barzilai, Ari, Ben-Jacob, Eshel, Bonifazi, Paolo, Torcini, Alessandro, Ghione, Giovanni, Series Editor, Asinari, Pietro, Series Editor, Ridolfi, Luca, Series Editor, Carrera, Erasmo, Series Editor, Canuto, Claudio, Series Editor, Iazzi, Felice, Series Editor, Acquaviva, Andrea, Series Editor, Corinto, Fernando, editor, and Torcini, Alessandro, editor

Published
2019
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7. Clique of functional hubs orchestrates population bursts in developmentally regulated neural networks

Author

Luccioli, Stefano, Ben-Jacob, Eshel, Barzilai, Ari, Bonifazi, Paolo, and Torcini, Alessandro

Subjects
Quantitative Biology - Neurons and Cognition, Condensed Matter - Disordered Systems and Neural Networks, Physics - Biological Physics
Abstract

It has recently been discovered that single neuron stimulation can impact network dynamics in immature and adult neuronal circuits. Here we report a novel mechanism which can explain in neuronal circuits, at an early stage of development, the peculiar role played by a few specific neurons in promoting/arresting the population activity. For this purpose, we consider a standard neuronal network model, with short-term synaptic plasticity, whose population activity is characterized by bursting behavior. The addition of developmentally inspired constraints and correlations in the distribution of the neuronal connectivities and excitabilities leads to the emergence of functional hub neurons, whose stimulation/deletion is critical for the network activity. Functional hubs form a clique, where a precise sequential activation of the neurons is essential to ignite collective events without any need for a specific topological architecture. Unsupervised time-lagged firings of supra-threshold cells, in connection with coordinated entrainments of near-threshold neurons, are the key ingredients to orchestrate, Comment: 39 pages, 15 figures, to appear in PLOS Computational Biology

Published
2014
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8. Collective dynamics in sparse networks

Author

Luccioli, Stefano, Olmi, Simona, Politi, Antonio, and Torcini, Alessandro

Subjects
Condensed Matter - Disordered Systems and Neural Networks, Nonlinear Sciences - Chaotic Dynamics
Abstract

The microscopic and macroscopic dynamics of random networks is investigated in the strong-dilution limit (i.e. for sparse networks). By simulating chaotic maps, Stuart-Landau oscillators, and leaky integrate-and-fire neurons, we show that a finite connectivity (of the order of a few tens) is able to sustain a nontrivial collective dynamics even in the thermodynamic limit. Although the network structure implies a non-additive dynamics, the microscopic evolution is extensive (i.e. the number of active degrees of freedom is proportional to the number of network elements)., Comment: 5 pages, 4 figures, to appear in Physical Review Letters

Published
2012
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9. Collective behavior of heterogeneous neural networks

Author

Luccioli, Stefano and Politi, Antonio

Subjects
Quantitative Biology - Neurons and Cognition, Condensed Matter - Disordered Systems and Neural Networks
Abstract

We investigate a network of integrate-and-fire neurons characterized by a distribution of spiking frequencies. Upon increasing the coupling strength, the model exhibits a transition from an asynchronous regime to a nontrivial collective behavior. At variance with the Kuramoto model, (i) the macroscopic dynamics is irregular even in the thermodynamic limit, and (ii) the microscopic (single-neuron) evolution is linearly stable., Comment: 4 pages, 5 figures

Published
2010
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10. Unfolding times for proteins in a force clamp

Author

Luccioli, Stefano, Imparato, Alberto, Mitternacht, Simon, Irbaeck, Anders, and Torcini, Alessandro

Subjects
Condensed Matter - Statistical Mechanics, Condensed Matter - Soft Condensed Matter
Abstract

The escape process from the native valley for proteins subjected to a constant stretching force is examined using a model for a Beta-barrel. For a wide range of forces, the unfolding dynamics can be treated as one-dimensional diffusion, parametrized in terms of the end-to-end distance. In particular, the escape times can be evaluated as first passage times for a Brownian particle moving on the protein free-energy landscape, using the Smoluchowski equation. At strong forces, the unfolding process can be viewed as a diffusive drift away from the native state, while at weak forces thermal activation is the relevant mechanism. An escape-time analysis within this approach reveals a crossover from an exponential to an inverse Gaussian escape-time distribution upon passing from weak to strong forces. Moreover, a single expression valid at weak and strong forces can be devised both for the average unfolding time as well as for the corresponding variance. The analysis offers a possible explanation of recent experimental findings for ddFLN4 and ubiquitin., Comment: 6 pages, 4 figures, submitted for pubblication to Physical Review Letters

Published
2009
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11. Changing the mechanical unfolding pathway of FnIII10 by tuning the pulling strength

Author

Mitternacht, Simon, Luccioli, Stefano, Torcini, Alessandro, Imparato, Alberto, and Irbäck, Anders

Subjects
Quantitative Biology - Biomolecules, Condensed Matter - Soft Condensed Matter
Abstract

We investigate the mechanical unfolding of the tenth type III domain from fibronectin, FnIII10, both at constant force and at constant pulling velocity, by all-atom Monte Carlo simulations. We observe both apparent two-state unfolding and several unfolding pathways involving one of three major, mutually exclusive intermediate states. All the three major intermediates lack two of seven native beta-strands, and share a quite similar extension. The unfolding behavior is found to depend strongly on the pulling conditions. In particular, we observe large variations in the relative frequencies of occurrence for the intermediates. At low constant force or low constant velocity, all the three major intermediates occur with a significant frequency. At high constant force or high constant velocity, one of them, with the N- and C-terminal beta-strands detached, dominates over the other two. Using the extended Jarzynski equality, we also estimate the equilibrium free-energy landscape, calculated as a function of chain extension. The application of a constant pulling force leads to a free-energy profile with three major local minima. Two of these correspond to the native and fully unfolded states, respectively, whereas the third one can be associated with the major unfolding intermediates., Comment: 15 pages, 9 figures

Published
2008
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12. Free energy landscape of mechanically unfolded model proteins: extended Jarzinsky versus inherent structure reconstruction

Author

Luccioli, Stefano, Imparato, Alberto, and Torcini, Alessandro

Subjects
Condensed Matter - Statistical Mechanics
Abstract

The equilibrium free energy landscape of off-lattice model heteropolymers as a function of an internal coordinate, namely the end-to-end distance, is reconstructed from out-of-equilibrium steered molecular dynamics data. This task is accomplished via two independent methods: by employing an extended version of the Jarzynski equality (EJE) and the inherent structure (IS) formalism. A comparison of the free energies estimated with these two schemes with equilibrium results obtained via the umbrella sampling technique reveals a good quantitative agreement among all the approaches in a range of temperatures around the ``folding transition'' for the two examined sequences. In particular, for the sequence with good foldability properties, the mechanically induced structural transitions can be related to thermodynamical aspects of folding. Moreover, for the same sequence the knowledge of the landscape profile allows for a good estimation of the life times of the native configuration for temperatures ranging from the folding to the collapse temperature. For the random sequence, mechanical and thermal unfolding appear to follow different paths along the landscape., Comment: Latex manuscript, 20 pages, 23 figures, submitted to Physical Review E

Published
2008
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13. Reconstructing the free energy landscape of a mechanically unfolded model protein

Author

Imparato, Alberto, Luccioli, Stefano, and Torcini, Alessandro

Subjects
Condensed Matter - Statistical Mechanics, Quantitative Biology - Biomolecules
Abstract

The equilibrium free energy landscape of an off-lattice model protein as a function of an internal (reaction) coordinate is reconstructed from out-of-equilibrium mechanical unfolding manipulations. This task is accomplished via two independent methods: by employing an extended version of the Jarzynski equality (EJE) and the protein inherent structures (ISs). In a range of temperatures around the ``folding transition'' we find a good quantitative agreement between the free energies obtained via EJE and IS approaches. This indicates that the two methodologies are consistent and able to reproduce equilibrium properties of the examined system. Moreover, for the studied model the structural transitions induced by pulling can be related to thermodynamical aspects of folding.

Published
2007
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14. Double coherence resonance in neuron models driven by discrete correlated noise

Author

Kreuz, Thomas, Luccioli, Stefano, and Torcini, Alessandro

Subjects
Condensed Matter - Disordered Systems and Neural Networks
Abstract

We study the influence of correlations among discrete stochastic excitatory or inhibitory inputs on the response of the FitzHugh-Nagumo neuron model. For any level of correlation the emitted signal exhibits at some finite noise intensity a maximal degree of regularity, i.e., a coherence resonance. Furthermore, for either inhibitory or excitatory correlated stimuli a {\it Double Coherence Resonance} (DCR) is observable. DCR refers to a (absolute) maximum coherence in the output occurring for an optimal combination of noise variance and correlation. All these effects can be explained by taking advantage of the discrete nature of the correlated inputs., Comment: 4 pages, 3 figures in eps, to appear in Physical Review Letters

Published
2006
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15. Coherent response of the Hodgkin-Huxley neuron in the high-input regime

Author

Torcini, Alessandro, Luccioli, Stefano, and Kreuz, Thomas

Subjects
Condensed Matter - Disordered Systems and Neural Networks
Abstract

We analyze the response of the Hodgkin-Huxley neuron to a large number of uncorrelated stochastic inhibitory and excitatory post-synaptic spike trains. In order to clarify the various mechanisms responsible for noise-induced spike triggering we examine the model in its silent regime. We report the coexistence of two distinct coherence resonances: the first one at low noise is due to the stimulation of "correlated" subthreshold oscillations; the second one at intermediate noise variances is instead related to the regularization of the emitted spike trains., Comment: 5 pages - 5 eps figures, contribution presented to the conference CNS 2006 held in Edinburgh (UK), to appear on Neurocomputing

Published
2006
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16. Dynamical response of the Hodgkin-Huxley model in the high-input regime

Author

Luccioli, Stefano, Kreuz, Thomas, and Torcini, Alessandro

Subjects
Condensed Matter - Disordered Systems and Neural Networks, Quantitative Biology - Neurons and Cognition
Abstract

The response of the Hodgkin-Huxley neuronal model subjected to stochastic uncorrelated spike trains originating from a large number of inhibitory and excitatory post-synaptic potentials is analyzed in detail. The model is examined in its three fundamental dynamical regimes: silence, bistability and repetitive firing. Its response is characterized in terms of statistical indicators (interspike-interval distributions and their first moments) as well as of dynamical indicators (autocorrelation functions and conditional entropies). In the silent regime, the coexistence of two different coherence resonances is revealed: one occurs at quite low noise and is related to the stimulation of subthreshold oscillations around the rest state; the second one (at intermediate noise variance) is associated with the regularization of the sequence of spikes emitted by the neuron. Bistability in the low noise limit can be interpreted in terms of jumping processes across barriers activated by stochastic fluctuations. In the repetitive firing regime a maximization of incoherence is observed at finite noise variance. Finally, the mechanisms responsible for spike triggering in the various regimes are clearly identified., Comment: 14 pages, 24 figures in eps, submitted to Physical Review E

Published
2005
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24. Risk Assessment of Food Allergens. Part 1: Review and Validation of Codex Alimetarius Priority Allergen list Through Risk Assessment

Author

Baumert, Joseph, Brooke-Taylor, Simon, Che, Huilian, Chen, Hongbing, Crevel, René, Houben, Geert, Jackson, Lauren, Kyriakidis, Symeon, La Vieille, Sébastien, Lee, N Alice, López, María Cristina, Luccioli, Stefano, O’Mahony, Patrick, Polenta, Gustavo Alberto, Pöpping, Bert, Remington, Benjamin, Södergren, Eva, Srikulnath, Sirinrat, Taylor, Stephen, and Turner, Paul

Subjects
Alérgenos, Lista de Alérgenos Prioritarios, Codex Alimentarius, Food Allergies, Evaluación de Riesgos, Alergia Alimentaria, List of Priority Allergens, Allergens, Risk Assessment
Abstract

The labelling of food allergens in pre-packaged foods plays a key role in protecting food allergic individuals, as no preventative clinical treatment is currently available. The list of major foods and ingredients known to cause hypersensitivity was included into the Codex General Standard for the Labelling of Packaged Foods (GSLPF) in 1999. There have been many scientific developments in the understanding of food allergens and their management since the original drafting of the GSLPF. Thus, in response to the request from Codex for scientific advice, including current evidence of consumer understanding of allergens, FAO and WHO convened a series of three expert meetings to provide scientific advice on this subject. The purpose of the first meeting of the Ad hoc Joint FAO/WHO Expert Consultation on Risk Assessment of Food Allergens was to review and validate the Codex priority allergen list through risk assessment. This report focuses on the deliberations and conclusions of this meeting. Resumen: El etiquetado de los alérgenos alimentarios en los alimentos preenvasados ​​juega un papel clave en la protección personas alérgicas a los alimentos, ya que actualmente no se dispone de un tratamiento clínico preventivo. Se incluyó la lista de los principales alimentos e ingredientes que causan hipersensibilidad en la Norma General del Codex para el Etiquetado de Alimentos Envasados ​​(GSLPF) en 1999. Ha habido muchos avances científicos en la comprensión de alérgenos alimentarios y su gestión desde la redacción original de la GSLPF. Por lo tanto, en respuesta a la solicitud del Codex de asesoramiento científico, incluida la actual evidencia de la comprensión del consumidor de los alérgenos, la FAO y la OMS convocaron una serie de tres reuniones de expertos para proporcionar asesoramiento científico sobre este tema. El propósito de la primera reunión de la Consulta Conjunta Especial de Expertos FAO/OMS sobre evaluación de riesgos de los alérgenos alimentarios fue revisar y validar la prioridad del Codex lista de alérgenos a través de la evaluación de riesgos. Este informe se centra en las deliberaciones y conclusiones de esta reunión. Instituto de Investigación de Tecnología de Alimentos (ITA) Fil: Baumert, Joseph. Universidad de Nebraska-Lincoln. Departamento de Ciencia y Tecnología de Alimentos; Estados Unidos Fil: Brooke-Taylor, Simon. Imperial College London. Instituto Nacional del Corazón y los Pulmones; Reino Unido. Fil: Che, Huilian. Universidad de Agricultura de China. Facultad de Ciencias de la Alimentación e Ingeniería Nutricional; China. Fil: Chen, Hongbing. Nanchang Universidad. Instituto Conjunto de Investigación Chino-Alemán; China. Fil: Crevel, René W.R. René Crevel Consulting Limited; Reino Unido. Fil: Houben, Geert F. Alergia alimentaria e inmunotoxicología. Científico principal de TNO; Países Bajos. Fil: Jackson, Lauren. Administración de Alimentos y Medicamentos. División de Ciencia y Tecnología del Procesamiento de Alimentos. Ingeniería de Procesos; Estados Unidos Fil: Kyriakidis, Symeon. Autoridad Independiente de Ingresos Públicos. Laboratorio Estatal de Química General; Grecia. Fil: La Vieille, Sébastien. Salud Canadá. Dirección de Alimentos; Canadá. Fil: Lee, N Alice. Universidad de Nueva Gales del Sur. Escuela de Química e Ingeniería. Ciencia e ingeniería de los alimentos; Australia. Fil: López, María Cristina. Universidad Nacional de San Martín. Ingeniería de Alimentos; Argentina. Fil: Luccioli, Stefano. Administración de Alimentos y Medicamentos. Centro de Seguridad Alimentaria y Nutrición Aplicada; Estados Unidos Fil: O’Mahony, Patrick. Autoridad de Seguridad Alimentaria de Irlanda . Ciencia y Tecnología de los Alimentos; Irlanda. Fil: Polenta, Gustavo Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Investigación Tecnología de Alimentos; Argentina. Fil: Pöpping, Bert. Food Consulting Strategically (FOCO); Alemania. Fil: Remington, Benjamin C. Grupo BV. Consultoría Remington; Holanda. Fil: Södergren, Eva. Agencia Sueca de Alimentos. Equipo de Encuestas Dietéticas y Departamento de Nutrición para Beneficio de Riesgo Evaluación; Suecia. Fil: Srikulnath, Sirinrat. Universidad de Kasetsart (UKaset). Instituto de Investigación y Desarrollo de Productos Alimentarios. Centro de Servicio de Aseguramiento de la Calidad de los Alimentos. Unidad de Alérgenos Alimentarios; Tailandia. Fil: Taylor, Stephen L. Universidad de Nebraska-Lincoln. Departamento de Ciencia y Tecnología de Alimentos; Estados Unidos Fil: Turner, Paul J. Colegio Imperial de Ciencia, Tecnología y Medicina. Alergia e Inmunología Pediátricas; Inglaterra.

Published
2022

25. Guidelines for the diagnosis and management of food allergy in the United States: Summary of the NIAID-Sponsored Expert Panel Report

Author

Boyce, Joshua A., Assa'a, Amal, Burks, A. Wesley, Jones, Stacie M., Sampson, Hugh A., Wood, Robert A., Plaut, Marshall, Cooper, Susan F., Fenton, Matthew J., Arshad, S. Hasan, Bahna, Sami L., Beck, Lisa A., Byrd-Bredbenner, Carol, Camargo, Carlos A., Jr., Eichenfield, Lawrence, Furuta, Glenn T., Hanifin, Jon M., Jones, Carol, Kraft, Monica, Levy, Bruce D., Lieberman, Phil, Luccioli, Stefano, McCall, Kathleen M., Schneider, Lynda C., Simon, Ronald A., Simons, F. Estelle R., Teach, Stephen J., Yawn, Barbara P., and Schwaninger, Julie M.

Published
2011
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26. Guidelines for the Diagnosis and Management of Food Allergy in the United States: Summary of the NIAID-Sponsored Expert Panel Report

Author

Boyce, Joshua A., Assa'ad, Amal, Burks, A. Wesley, Jones, Stacie M., Sampson, Hugh A., Wood, Robert A., Plaut, Marshall, Cooper, Susan F., Fenton, Matthew J., Arshad, S. Hasan, Bahna, Sami L., Beck, Lisa A., Byrd-Bredbenner, Carol, Camargo, Carlos A., Jr., Eichenfield, Lawrence, Furuta, Glenn T., Hanifin, Jon M., Jones, Carol, Kraft, Monica, Levy, Bruce D., Lieberman, Phil, Luccioli, Stefano, McCall, Kathleen M., Schneider, Lynda C., Simon, Ronald A., Simons, F. Estelle R., Teach, Stephen J., Yawn, Barbara P., and Schwaninger, Julie M.

Published
2010
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31. Maternally reported food allergies and other food-related health problems in infants: characteristics and associated factors

Author

Luccioli, Stefano, Ross, Marianne, Labiner-Wolfe, Judith, and Fein, Sara B.

Subjects
Food allergy -- Reports, Food allergy -- Demographic aspects, Food allergy -- Diagnosis, Food allergy -- Prevention, Infants (Newborn) -- Diseases, Infants (Newborn) -- Reports, Infants (Newborn) -- Demographic aspects, Infants (Newborn) -- Diagnosis, Infants (Newborn) -- Prevention
Published
2008

36. F(ab)'2-mediated neutralization of C3a and C5a anaphylatoxins: a novel effector function of immunoglobulins

Author

Basta, Milan, Van Goor, Fredric, Luccioli, Stefano, Billings, Eric M., Vortmeyer, Alexander O., Baranyi, Lajos, Szebeni, Janos, Alving, Carl R., Carroll, Michael C., Berkower, Ira, Stojilkovic, Stanko S., and Metcalfe, Dean D.

Abstract

High-dose intravenous immunoglobulin (IVIG) prevents immune damage by scavenging complement fragments C3b and C4b. We tested the hypothesis that exogenous immunoglobulin molecules also bind anaphylatoxins C3a and C5a, thereby neutralizing their pro-inflammatory effects. Single-cell calcium measurements in HMC-1 human mast cells showed that a rise in intracellular calcium caused by C3a and C5a was inhibited in a concentration-dependent manner by IVIG, F(ab)'[sub.2]-IVIG and irrelevant human monoclonal antibody. C3a- and C5a-induced thromboxane (TXB[sub.2]) generation and histamine release from HMC-1 cells and whole-blood basophils were also suppressed by exogenous immunoglobulins. In a mouse model of asthma, immunoglobulin treatment reduced cellular migration to the lung. Lethal C5a-mediated circulatory collapse in pigs was prevented by pretreatment with F(ab)'[sub.2]-IVIG. Molecular modeling, surface plasmon resonance (SPR) and western blot analyses suggested a physical association between anaphylatoxins and the constant region of F(ab)'[sub.2]. This binding could interfere with the role of C3a and C5a in inflammation., Author(s): Milan Basta (corresponding author) [1]; Fredric Van Goor [2]; Stefano Luccioli [3]; Eric M. Billings [4]; Alexander O. Vortmeyer [5]; Lajos Baranyi [6]; Janos Szebeni [6]; Carl R. Alving [...]

Published
2003
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37. The Current State of Data to Estimate Prevalence and Severity of Food Allergies in the United States

Author

Ruzante, Juliana M., Rains, Caroline, Viator, Catherine, Liao, Dan, Creel, Darryl, Luccioli, Stefano, Anic, Gabriella, Wolpert, Beverly J., Warren, Christopher, and DiGrande, Laura

Abstract

•Data on the burden of food allergies are critical for evidence-based policies.•No recent data to estimate the burden of food allergies in the United States.•Lack of consistency across years makes trend analysis difficult.•Need a comprehensive surveillance program to improve food allergy management.

Published
2025
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41. Modeling driver cells in developing neuronal networks

Author

Luccioli, Stefano, primary, Angulo-Garcia, David, additional, Cossart, Rosa, additional, Malvache, Arnaud, additional, Módol, Laura, additional, Sousa, Vitor Hugo, additional, Bonifazi, Paolo, additional, and Torcini, Alessandro, additional

Published
2018
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42. Abstracts from the Food Allergy and Anaphylaxis Meeting 2016

Author

Pouessel, Guillaume, Claverie, Claire, Labreuche, Julien, Renaudin, Jean-Marie, Dorkenoo, Aimée, Eb, Mireille, Moneret-Vautrin, Anne, Deschildre, Antoine, Leteurtre, Stephane, Grabenhenrich, Linus, Worm, Margitta, Dölle, Sabine, Scherer, Kathrin, Hutteger, Isidor, Christensen, Morten, Bindslev-Jensen, Carsten, Mortz, Charlotte, Eller, Esben, Kjaer, Henrik F, Carneiro-Leão, Leonor, Badas, Jenny, Coimbra, Alice, Levy, Dikla P, Ben-Shoshan, Moshe, Rimon, Ayelet, Benor, Shira, Arends, Nicolette J T, Edelbroek, Nikki, de Groot, Hans, Emons, Joyce A M, Brand, H. K A, Verhoeven, Dirk, van Veen, Leonieke N, de Jong, Nicolette W, Noh, Geunwoong, Jang, Eun H, Pascal, Mariona, Dominguez, Olga, Piquer, Mònica, Alvaro, Montserrat, Jimenez-Feijoo, Rosa, Lozano, Jaime, Machinena, Adriana, del Mar Folqué, Maria, Giner, Maria T, Plaza, Ana M, Turner, Paul, Patel, Nandinee, Vazquez-Ortiz, Marta, Lindsley, Sarah, Walker, Lucy, Rosenberg, Simon, Mari, Adriano, Alessandri, Claudia, Giangrieco, Ivana, Tuppo, Lisa, Rafaiani, Chiara, Mitterer, Georg, Ciancamerla, Michela, Ferrara, Rosetta, Bernardi, Maria L, Zennaro, Danila, Tamburrini, Maurizio, Ciardiello, Maria A, Harwanegg, Christian, Fernandez, Antonio, Selb, Regina, Egenmann, Philippe, Epstein, Michelle, Hoffmann-Sommergruber, Karin, Koning, Frits, Lovik, Martinus, Clare Mills, E. N, Moreno, Javier, van Loveren, Henk, Wal, Jean-Michel, Diesner, Susanne, Bergmayr, Cornelia, Pfitzner, Barbara, Assmann, Vera E, Starkl, Philipp, Endesfelder, David, Eiwegger, Thomas, Szepfalusi, Zsolt, Fehrenbach, Heinz, Jensen-Jarolim, Erika, Hartmann, Anton, Pali-Schöll, Isabella, Untersmayr, Eva, Wille, Soren, Meyer, Peter, Klingebiel, Caroline, Lidholm, Jonas, Ehrenberg, Angelica, Östling, Jonas, Cleach, Isabelle, Mège, Jean-Louis, Vitte, Joana, Aina, Roberta, Dubiela, Pawel, Pfeifer, Sabine, Bublin, Merima, Radauer, Christian, Humeniuk, Piotr, Kabasser, Stefan, Asero, Riccardo, Bogas, Gador, Gomez, Francisca, Campo, Paloma, Salas, Maria, Doña, Inmaculada, Barrionuevo, Esther, Guerrero, Maria A, Mayorga, Cristobalina, Prieto, Ana, Barber, Domingo, Torres, Maria J, Jamin, Annette, Wangorsch, Andrea, Ballmer, Barbara, Vieths, Stefan, Scheurer, Stephan, Apostolovic, Danijela, Mihailovic, Jelena, Krstic, Maja, Starkhammar, Maria, Velickovic, Tanja C, Hamsten, Carl, van Hage, Marianne, van Erp, Francine C, Knol, Edward F, Kansen, Hannah M, Pontoppidan, Bo, Meijer, Yolanda, van der Ent, Cornelis K, Knulst, André C, Sayers, Rebekah, Brown, Helen, Custovic, Adnan, Simpson, Angela, Mills, Claire, Schulz, Juliane, Akkerdaas, Jaap, Totis, Muriel, Capt, Annabelle, Herouet-Guicheney, Corinne, van Ree, Ronald, Banerjee, Tushar, Banerjee, Antima, Claude, Mathilde, Bouchaud, Grégory, Lupi, Roberta, Castan, Laure, Tranquet, Olivier, Denery-Papini, Sandra, Bodinier, Marie, Brossard, Chantal, De Poi, Rosella, Gritti, Elisa, De Dominicis, Emiliano, Popping, Bert, de Laureto, Patrizia P, Palosuo, Kati, Kukkonen, Anna K, Pelkonen, Anna, Mäkelä, Mika, Lee, Nanju A, Rost, Johanna, Muralidharan, Sridevi, Campbell, Dianne, Mehr, Sam, Nock, Catherine, Baumert, Joseph, Taylor, Steve, Mastrorilli, Carla, Tripodi, Salvatore, Caffarelli, Carlo, Perna, Serena, Di Rienzo Businco, Andrea, Sfika, Ifigenia, Dondi, Arianna, Bianchi, Annamaria, Dascola, Carlotta P, Ricci, Giampaolo, 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L, Vereda, Andrea, Ippolito, Clara, Traversa, Amaranta, Adriano, Daniela, Bianchi, Daniela M, Gallina, Silvia, Decastelli, Lucia, Makatsori, Melina, Miles, Anne, Devetak, Sonja P, Devetak, Iztok, Tabet, Soraya A, Trandbohus, Jeanette F, Winther, Pernille, Malling, Hans-Jørgen, Hansen, Kirsten S, Garvey, Lene H, Wang, Chia-Chi, Cheng, Yin-Hua, Tung, Chun-Wei, Dietrich, Mariola, Marenholz, Ingo, Kalb, Birgit, Grosche, Sarah, Blümchen, Katharina, Schlags, Rupert, Price, Mareike, Rietz, Sylke, Esparza-Gordillo, Jorge, Lau, Susanne, Lee, Young-Ae, Almontasheri, Ali, Bahkali, Mohammad A, Elshorbagi, Sahar, Alfhaid, Abdullah, Altamimi, Mashary, Madbouly, Eman, Al-Dhekri, Hassan, Arnaout, Rand K, Basagaña, Maria, Miquel, Sira, Bartolomé, Borja, Brix, Bettina, Rohwer, Stefanie, Brandhoff, Sandra, Berger, Alena, Suer, Waltraud, Weimann, Alf, Bueno, Cristina, Martín-Pedraza, Laura, Abián, Sara, Segundo-Acosta, Pablo S, López-Rodríguez, Juan C, Barderas, Rodrigo, Batanero, Eva, Cuesta-Herranz, Javier, Villalba, María T, Correia, Magna, Benito-Garcia, Filipe, Arêde, Cristina, Piedade, Susana, Morais-Almeida, Mário, Hindley, James, Yarham, Ross, Kuklinska-Pijanka, Anna, Gillick, David, Patient, Karine, Chapman, Martin D, Miranda, Ana, Matos, Eugénia, Sokolova, Anna, Rao, Huan, Baricevic-Jones, Ivona, Smith, Frances, Xue, Wentong, Magnusdottir, Helga, Vidarsdottir, Anna G, Lund, Sigrun, Jensen, Anders B, Ludviksson, Bjorn R, Simon, Reyna, Elfont, Robert, Bennett, Sean, Voyksner, Robert, de Lurdes Torre, Maria, Yürek, Songül, Faber, Margaretha A, Bastiaensen, Annick, Mangodt, Evelyne, van Gasse, Athina, Decuyper, Ine, Sabato, Vito, Hagendorens, Margo M, Bridts, Chris H, De Clerck, Luc S, Ebo, Didier, Schwarz, Susanne, Ziegert, Mandy, Albroscheit, Saskia, Schwager, Christian, Kull, Skadi, Behrends, Jochen, Röckendorf, Niels, Schocker, Frauke, Frey, Andreas, Homann, Arne, Becker, Wolf-Meinhard, Jappe, Uta, Zaabat, Nesrine, Osscini, Sylvia, Agabriel, Chantal, Sterling, Benoît, Carsin, Ania, Liabeuf, Valérie, Maćków, Monica, Zbróg, Alina, Bronkowska, Monica, Courtois, Justine, Gadisseur, Romy, Bertholet, Catherine, Lukas, Pierre, Cavalier, Etienne, Delahaut, Philippe, Quinting, Birgit, Gertmo, Margareta B, Hasseus, Ewa T, Barzylovych, Vladyslava, Oliveira, Júlio, Ensina, Luis F, Aranda, Carolina S, Dopazo, Leire, Lopez, Rebeca, Perez, Raquel, Santos-Diez, Laura, Bilbao, Agurtzane, Garcia, Juan M, Núñez, Ignacio G, Mármol, María Á A, Villarejo, María J B, Martos, José A B, Vergara, Marina S, García, José M I, Michalska, Agata, Sergiejko, Grzegorz, Zacniewski, Robert, Ghiordanescu, Ileana-Maria, Deaconu, Cristina, Popescu, Mihaela, Bumbacea, Roxana S, Ibranji, Alkerta, Nikolla, Elida, Loloci, Gjustina, Juel-Berg, Nanna, Larsen, Lau F, Poulsen, Lars K, Marcelino, João, Prata, Ricardo, Costa, Ana C, Duarte, Fátima, Neto, Marta, Santos, Jennifer, Pestana, Luís C, Sampaio, Daniel, Minale, Paola, Dignetti, Paola, Bignardi, Donatella, Nedelea, Irena, Popescu, Florin-Dan, Vieru, Mariana, Secureanu, Florin-Adrian, Ganea, Carmen S, Vieira, Miguel, Silva, José P M, Watts, Timothy, Watts, Sophia, Lomikovska, Marta, Peredelskaya, Marina, Nenasheva, Natalia, Filipovic, Ivana, Zivkovic, Zorica, Filipovic, Djordje, Higgs, Jennette, Warner, Amena, and Jones, Carla

Published
2017

43. Neurons' death and rebirth in sparse heterogeneous inhibitory networks

Author

Angulo-Garcia, David, Luccioli, Stefano, Olmi, Simona, and Torcini, Alessandro

Subjects
05.45.Xt, Pulse-coupled heterogeneous inhibitory neural networks, nervous system, Quantitative Biology::Neurons and Cognition, 87.19.lm, 87.19.lj
Abstract

Inhibition is a key aspect of neural dynamics playing a fundamental role for the emergence of neural rhythms and the implementation of various information coding strategies. Inhibitory populations are present in several brain structures and the comprehension of their dynamics is strategical for the understanding of neural processing. In this paper, we discuss a general mechanism present in pulse-coupled heterogeneous inhibitory networks: inhibition can induce not only suppression of the neural activity, as expected, but it can also promote neural reactivation. In particular, for globally coupled systems, the number of firing neurons monotonically reduces upon increasing the strength of inhibition (neurons? death). The introduction of a sparse connectivity in the network is able to reverse the action of inhibition, i.e. a sufficiently strong synaptic strength can surprisingly promote, rather than depress, the activity of the neurons (neurons? rebirth). Specifically, for small synaptic strengths, one observes an asynchronous activity of nearly independent supra-threshold neurons. By increasing the inhibition, a transition occurs towards a regime where the neurons are all effectively sub-threshold and their irregular firing is driven by current fluctuations. We explain this transition from a mean-driven to a fluctuation-driven regime by deriving an analytic mean field approach able to provide the fraction of active neurons together with the first two moments of the firing time distribution. We show that, by varying the synaptic time scale, the mechanism underlying the reported phenomenon remains unchanged. However, for sufficiently slow synapses the effect becomes dramatic. For small synaptic coupling the fraction of active neurons is frozen over long times and their firing activity is perfectly regular. For larger inhibition the active neurons display an irregular bursting behaviour induced by the emergence of correlations in the current fluctuations. In this latter regime the model gives predictions consistent with experimental findings for a specific class of neurons, namely the medium spiny neurons in the striatum.

Published
2016
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49. Discrete breathers in a realistic coarse-grained model of proteins

Author

Luccioli Stefano

Subjects
Quantitative Biology::Biomolecules
Abstract

We report the results of molecular dynamics simulations of an off-lattice protein model featuring a physical force-field and amino-acid sequence. We show that localized modes of nonlinear origin, discrete breathers (DB), emerge naturally as continuations of a subset of high-frequency normal modes residing at specific sites dictated by the native fold. In the case of the small beta-barrel structure that we consider, DB-mediated localization occurs on the turns connecting the strands. At high energies, discrete breathers stabilise the structure by concentrating energy on few sites, while their collapse marks the onset of large-amplitude fluctuations of the protein. Furthermore, we show how breathers develop as energy-accumulating centres following perturbations even at distant locations, thus mediating efficient and irreversible energy transfers. Remarkably, due to the presence of angular potentials, the breather induces a local static distortion of the native fold. Altogether, the combination of this two nonlinear effects may provide a ready means for remotely controlling local conformational changes in proteins.

Published
2011

50. Discrete breathers as energy-accumulating centres in a protein model

Author

Luccioli Stefano

Abstract

We report the results of molecular dynamics simulations of an off-lattice protein model featuring a physical force-field and amino-acid sequence. We show that localised modes of nonlinear origin, discrete breathers (DB), emerge naturally as continuations of a subset of high-frequency normal modes residing at specific sites dictated by the native fold. In the case of the small beta-barrel structure that we consider, DB-mediated localization occurs on the turns connecting the strands. At high energies, discrete breathers stabilise the structure by concentrating energy on few sites, while their collapse marks the onset of large-amplitude fluctuations of the protein. Furthermore, we show how breathers develop as energy-accumulating centres following perturbations even at distant locations, thus mediating efficient and irreversible energy transfers. Remarkably, due to the presence of angular potentials, the breather induces a local static distortion of the native fold. Altogether, the combination of this two nonlinear effects may provide a ready means for remotely controlling local conformational changes in proteins. Ref: S. Luccioli, A. Imparato, S. Lepri, F. Piazza and A. Torcini, "Discrete breathers in a realistic coarse-grained model of proteins", to appear in Physical Biology 2011.

Published
2011

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