1
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Normand F, Gajwani M, Côté DC, Allard A. NBS-SNI, an extension of the network-based statistic: Abnormal functional connections between important structural actors. Netw Neurosci 2024; 8:44-80. [PMID: 38562286 PMCID: PMC10861162 DOI: 10.1162/netn_a_00344] [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: 02/27/2023] [Accepted: 10/11/2023] [Indexed: 04/04/2024] Open
Abstract
Elucidating the coupling between the structure and the function of the brain and its development across maturation has attracted a lot of interest in the field of network neuroscience in the last 15 years. Mounting evidence supports the hypothesis that the onset of certain brain disorders is linked with the interplay between the structural architecture of the brain and its functional processes, often accompanied with unusual connectivity features. This paper introduces a method called the network-based statistic-simultaneous node investigation (NBS-SNI) that integrates both representations into a single framework, and identifies connectivity abnormalities in case-control studies. With this method, significance is given to the properties of the nodes, as well as to their connections. This approach builds on the well-established network-based statistic (NBS) proposed in 2010. We uncover and identify the regimes in which NBS-SNI offers a gain in statistical resolution to identify a contrast of interest using synthetic data. We also apply our method on two real case-control studies, one consisting of individuals diagnosed with autism and the other consisting of individuals diagnosed with early psychosis. Using NBS-SNI and node properties such as the closeness centrality and local information dimension, we found hypo- and hyperconnected subnetworks and show that our method can offer a 9 percentage points gain in prediction power over the standard NBS.
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Affiliation(s)
- Francis Normand
- Centre de Recherche CERVO, Québec, Canada
- Centre Interdisciplinaire en Modélisation Mathématique, Université Laval, Québec, Canada
- The Turner Institute for Brain and Mental Health and Monash Biomedical Imaging, Monash University, Melbourne, Australia
| | - Mehul Gajwani
- The Turner Institute for Brain and Mental Health and Monash Biomedical Imaging, Monash University, Melbourne, Australia
| | - Daniel C. Côté
- Centre de Recherche CERVO, Québec, Canada
- Département de Physique, de Génie Physique et d’Optique, Université Laval, Québec, Canada
| | - Antoine Allard
- Centre Interdisciplinaire en Modélisation Mathématique, Université Laval, Québec, Canada
- Département de Physique, de Génie Physique et d’Optique, Université Laval, Québec, Canada
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2
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Boudreau MC, Allen AJ, Roberts NJ, Allard A, Hébert-Dufresne L. Temporal and probabilistic comparisons of epidemic interventions. ArXiv 2024:arXiv:2302.03210v2. [PMID: 36798454 PMCID: PMC9934727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Forecasting disease spread is a critical tool to help public health officials design and plan public health interventions.However, the expected future state of an epidemic is not necessarily well defined as disease spread is inherently stochastic, contact patterns within a population are heterogeneous, and behaviors change. In this work, we use time-dependent probability generating functions (PGFs) to capture these characteristics by modeling a stochastic branching process of the spread of a disease over a network of contacts in which public health interventions are introduced over time. To achieve this, we define a general transmissibility equation to account for varying transmission rates (e.g. masking), recovery rates (e.g. treatment), contact patterns (e.g. social distancing) and percentage of the population immunized (e.g. vaccination). The resulting framework allows for a temporal and probabilistic analysis of an intervention's impact on disease spread, which match continuous-time stochastic simulations that are much more computationally expensive.To aid policy making, we then define several metrics over which temporal and probabilistic intervention forecasts can be compared: Looking at the expected number of cases and the worst-case scenario over time, as well as the probability of reaching a critical level of cases and of not seeing any improvement following an intervention.Given that epidemics do not always follow their average expected trajectories and that the underlying dynamics can change over time, our work paves the way for more detailed short-term forecasts of disease spread and more informed comparison of intervention strategies.
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3
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Labadie G, Bouderbala I, Boulanger Y, Béland JM, Hébert C, Allard A, Hebblewhite M, Fortin D. The umbrella value of caribou management strategies for biodiversity conservation in boreal forests under global change. Sci Total Environ 2024; 907:168087. [PMID: 37879475 DOI: 10.1016/j.scitotenv.2023.168087] [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] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/02/2023] [Accepted: 10/22/2023] [Indexed: 10/27/2023]
Abstract
Single-species conservation management is often proposed to preserve biodiversity in human-disturbed landscapes. How global change will impact the umbrella value of single-species management strategies remains an open question of critical conservation importance. We assessed the effectiveness of threatened boreal caribou as an umbrella for bird and beetle conservation under global change. We combined mechanistic, spatially explicit models of forest dynamics and predator-prey interactions to forecast the impact of management strategies on the survival of boreal caribou in boreal forest. We then used predictive models of species occupancy to characterize concurrent impacts on bird and beetle diversity. Landscapes were simulated based on three scenarios of climate change and four of forest management. We found that strategies that best mitigate human impact on boreal caribou were an effective umbrella for maintaining bird and beetle assemblages. While we detected a stronger effect of land-use change compared to climate change, the umbrella value of management strategies for caribou habitat conservation were still impacted by the severity of climate change. Our results showed an interplay among changes in forest attributes, boreal caribou mortality, as well as bird and beetle species assemblages. The conservation status of some species mandates the development of recovery strategies, highlighting the importance of our study which shows that single-species conservation can have important umbrella benefits despite global change.
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Affiliation(s)
- Guillemette Labadie
- Centre d'Étude de la Forêt, Département de biologie, Université Laval, Québec, QC G1V 0A6, Canada.
| | - Ilhem Bouderbala
- Département de biologie, Université Laval, Québec, QC G1V 0A6, Canada; Département de physique, de génie physique et d'optique, Université Laval, Québec, QC G1V 0A6, Canada
| | - Yan Boulanger
- Canadian Forest Service, Natural Resources Canada, Quebec City, QC G1V4C7, Canada
| | - Jean-Michel Béland
- Canadian Forest Service, Natural Resources Canada, Quebec City, QC G1V4C7, Canada
| | - Christian Hébert
- Canadian Forest Service, Natural Resources Canada, Quebec City, QC G1V4C7, Canada
| | - Antoine Allard
- Département de physique, de génie physique et d'optique, Université Laval, Québec, QC G1V 0A6, Canada
| | - Mark Hebblewhite
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, Franke College of Forestry and Conservation, University of Montana, Missoula, MT 59812, USA
| | - Daniel Fortin
- Centre d'Étude de la Forêt, Département de biologie, Université Laval, Québec, QC G1V 0A6, Canada
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4
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Dion MB, Shah SA, Deng L, Thorsen J, Stokholm J, Krogfelt KA, Schjørring S, Horvath P, Allard A, Nielsen DS, Petit MA, Moineau S. Escherichia coli CRISPR arrays from early life fecal samples preferentially target prophages. ISME J 2024; 18:wrae005. [PMID: 38366192 PMCID: PMC10910852 DOI: 10.1093/ismejo/wrae005] [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] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/18/2024]
Abstract
CRISPR-Cas systems are defense mechanisms against phages and other nucleic acids that invade bacteria and archaea. In Escherichia coli, it is generally accepted that CRISPR-Cas systems are inactive in laboratory conditions due to a transcriptional repressor. In natural isolates, it has been shown that CRISPR arrays remain stable over the years and that most spacer targets (protospacers) remain unknown. Here, we re-examine CRISPR arrays in natural E. coli isolates and investigate viral and bacterial genomes for spacer targets using a bioinformatics approach coupled to a unique biological dataset. We first sequenced the CRISPR1 array of 1769 E. coli isolates from the fecal samples of 639 children obtained during their first year of life. We built a network with edges between isolates that reflect the number of shared spacers. The isolates grouped into 34 modules. A search for matching spacers in bacterial genomes showed that E. coli spacers almost exclusively target prophages. While we found instances of self-targeting spacers, those involving a prophage and a spacer within the same bacterial genome were rare. The extensive search for matching spacers also expanded the library of known E. coli protospacers to 60%. Altogether, these results favor the concept that E. coli's CRISPR-Cas is an antiprophage system and highlight the importance of reconsidering the criteria use to deem CRISPR-Cas systems active.
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Affiliation(s)
- Moïra B Dion
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
| | - Ling Deng
- Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Denmark
| | - Jonathan Thorsen
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
- Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Denmark
| | - Karen A Krogfelt
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300S Copenhagen, Denmark
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
| | - Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300S Copenhagen, Denmark
| | - Philippe Horvath
- IFF Danisco, Health & Biosciences, Dangé-Saint-Romain 86220, France
| | - Antoine Allard
- Département de physique, de génie physique et d’optique, Université Laval, Québec, QC G1V 0A6, Canada
- Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec, QC G1V 0A6, Canada
| | - Dennis S Nielsen
- Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Denmark
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Micalis, Jouy-en-Josas 78350, France
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada
- Félix d’Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada
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5
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St-Onge G, Hébert-Dufresne L, Allard A. Nonlinear bias toward complex contagion in uncertain transmission settings. Proc Natl Acad Sci U S A 2024; 121:e2312202121. [PMID: 38154065 PMCID: PMC10769855 DOI: 10.1073/pnas.2312202121] [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: 07/18/2023] [Accepted: 11/24/2023] [Indexed: 12/30/2023] Open
Abstract
Current epidemics in the biological and social domains are challenging the standard assumptions of mathematical contagion models. Chief among them are the complex patterns of transmission caused by heterogeneous group sizes and infection risk varying by orders of magnitude in different settings, like indoor versus outdoor gatherings in the COVID-19 pandemic or different moderation practices in social media communities. However, quantifying these heterogeneous levels of risk is difficult, and most models typically ignore them. Here, we include these features in an epidemic model on weighted hypergraphs to capture group-specific transmission rates. We study analytically the consequences of ignoring the heterogeneous transmissibility and find an induced superlinear infection rate during the emergence of a new outbreak, even though the underlying mechanism is a simple, linear contagion. The dynamics produced at the individual and group levels are therefore more similar to complex, nonlinear contagions, thus blurring the line between simple and complex contagions in realistic settings. We support this claim by introducing a Bayesian inference framework to quantify the nonlinearity of contagion processes. We show that simple contagions on real weighted hypergraphs are systematically biased toward the superlinear regime if the heterogeneity of the weights is ignored, greatly increasing the risk of erroneous classification as complex contagions. Our results provide an important cautionary tale for the challenging task of inferring transmission mechanisms from incidence data. Yet, it also paves the way for effective models that capture complex features of epidemics through nonlinear infection rates.
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Affiliation(s)
- Guillaume St-Onge
- Laboratory for the Modeling of Biological and Socio-Technical Systems, Northeastern University, Boston, MA02115
| | - Laurent Hébert-Dufresne
- Vermont Complex Systems Center, University of Vermont, Burlington, VT05401
- Department of Computer Science, University of Vermont, Burlington, VT05401
- Département de physique, de génie physique et d’optique, Université Laval, Québec, QCG1V 0A6, Canada
| | - Antoine Allard
- Vermont Complex Systems Center, University of Vermont, Burlington, VT05401
- Département de physique, de génie physique et d’optique, Université Laval, Québec, QCG1V 0A6, Canada
- Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec, QCG1V 0A6, Canada
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6
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Lizotte S, Young JG, Allard A. Hypergraph reconstruction from uncertain pairwise observations. Sci Rep 2023; 13:21364. [PMID: 38049512 PMCID: PMC10695935 DOI: 10.1038/s41598-023-48081-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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 11/22/2023] [Indexed: 12/06/2023] Open
Abstract
The network reconstruction task aims to estimate a complex system's structure from various data sources such as time series, snapshots, or interaction counts. Recent work has examined this problem in networks whose relationships involve precisely two entities-the pairwise case. Here, using Bayesian inference, we investigate the general problem of reconstructing a network in which higher-order interactions are also present. We study a minimal example of this problem, focusing on the case of hypergraphs with interactions between pairs and triplets of vertices, measured imperfectly and indirectly. We derive a Metropolis-Hastings-within-Gibbs algorithm for this model to highlight the unique challenges that come with estimating higher-order models. We show that this approach tends to reconstruct empirical and synthetic networks more accurately than an equivalent graph model without higher-order interactions.
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Affiliation(s)
- Simon Lizotte
- Département de Physique, de génie Physique et d'optique, Université Laval, Québec, G1V 0A6, Canada
- Centre Interdisciplinaire en Modélisation Mathématique, Université Laval, Québec, G1V 0A6, Canada
| | - Jean-Gabriel Young
- Département de Physique, de génie Physique et d'optique, Université Laval, Québec, G1V 0A6, Canada
- Department of Mathematics and Statistics, University of Vermont, Burlington, VT, 05405, USA
- Vermont Complex Systems Center, University of Vermont, Burlington, VT, 05405, USA
| | - Antoine Allard
- Département de Physique, de génie Physique et d'optique, Université Laval, Québec, G1V 0A6, Canada.
- Centre Interdisciplinaire en Modélisation Mathématique, Université Laval, Québec, G1V 0A6, Canada.
- Vermont Complex Systems Center, University of Vermont, Burlington, VT, 05405, USA.
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7
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Jankowski R, Allard A, Boguñá M, Serrano MÁ. The D-Mercator method for the multidimensional hyperbolic embedding of real networks. Nat Commun 2023; 14:7585. [PMID: 37990019 PMCID: PMC10663512 DOI: 10.1038/s41467-023-43337-5] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
One of the pillars of the geometric approach to networks has been the development of model-based mapping tools that embed real networks in its latent geometry. In particular, the tool Mercator embeds networks into the hyperbolic plane. However, some real networks are better described by the multidimensional formulation of the underlying geometric model. Here, we introduce D-Mercator, a model-based embedding method that produces multidimensional maps of real networks into the (D + 1)-hyperbolic space, where the similarity subspace is represented as a D-sphere. We used D-Mercator to produce multidimensional hyperbolic maps of real networks and estimated their intrinsic dimensionality in terms of navigability and community structure. Multidimensional representations of real networks are instrumental in the identification of factors that determine connectivity and in elucidating fundamental issues that hinge on dimensionality, such as the presence of universality in critical behavior.
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Affiliation(s)
- Robert Jankowski
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, Barcelona, Spain
| | - Antoine Allard
- Département de Physique, de Génie Physique et d'optique, Université Laval, Québec, Québec, G1V 0A6, Canada
- Centre Interdisciplinaire en Modélisation Mathématique, Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Marián Boguñá
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, Barcelona, Spain
| | - M Ángeles Serrano
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain.
- Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, Barcelona, Spain.
- ICREA, Pg. Lluís Companys 23, E-08010, Barcelona, Spain.
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8
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Boudreau MC, Allen AJ, Roberts NJ, Allard A, Hébert-Dufresne L. Temporal and Probabilistic Comparisons of Epidemic Interventions. Bull Math Biol 2023; 85:118. [PMID: 37857996 DOI: 10.1007/s11538-023-01220-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: 03/08/2023] [Accepted: 09/26/2023] [Indexed: 10/21/2023]
Abstract
Forecasting disease spread is a critical tool to help public health officials design and plan public health interventions. However, the expected future state of an epidemic is not necessarily well defined as disease spread is inherently stochastic, contact patterns within a population are heterogeneous, and behaviors change. In this work, we use time-dependent probability generating functions (PGFs) to capture these characteristics by modeling a stochastic branching process of the spread of a disease over a network of contacts in which public health interventions are introduced over time. To achieve this, we define a general transmissibility equation to account for varying transmission rates (e.g. masking), recovery rates (e.g. treatment), contact patterns (e.g. social distancing) and percentage of the population immunized (e.g. vaccination). The resulting framework allows for a temporal and probabilistic analysis of an intervention's impact on disease spread, which match continuous-time stochastic simulations that are much more computationally expensive. To aid policy making, we then define several metrics over which temporal and probabilistic intervention forecasts can be compared: Looking at the expected number of cases and the worst-case scenario over time, as well as the probability of reaching a critical level of cases and of not seeing any improvement following an intervention. Given that epidemics do not always follow their average expected trajectories and that the underlying dynamics can change over time, our work paves the way for more detailed short-term forecasts of disease spread and more informed comparison of intervention strategies.
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Affiliation(s)
- Mariah C Boudreau
- Vermont Complex Systems Center, University of Vermont, Burlington, VT, USA.
- Department of Mathematics & Statistics, University of Vermont, Burlington, VT, USA.
| | - Andrea J Allen
- Vermont Complex Systems Center, University of Vermont, Burlington, VT, USA
- Children's Hospital of Philadelphia, Applied Clinical Research Center, Philadelphia, PA, USA
| | - Nicholas J Roberts
- Vermont Complex Systems Center, University of Vermont, Burlington, VT, USA
| | - Antoine Allard
- Vermont Complex Systems Center, University of Vermont, Burlington, VT, USA
- Départment de Physique, de génie physique et d'optique, Université Laval, Québec, Québec, G1V 0A6, Canada
- Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Laurent Hébert-Dufresne
- Vermont Complex Systems Center, University of Vermont, Burlington, VT, USA
- Department of Mathematics & Statistics, University of Vermont, Burlington, VT, USA
- Départment de Physique, de génie physique et d'optique, Université Laval, Québec, Québec, G1V 0A6, Canada
- Department of Computer Science, University of Vermont, Burlington, VT, USA
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9
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Liboz M, Allard A, Malo M, Lamour G, Letort G, Thiébot B, Labdi S, Pelta J, Campillo C. Using Adhesive Micropatterns and AFM to Assess Cancer Cell Morphology and Mechanics. ACS Appl Mater Interfaces 2023; 15:43403-43413. [PMID: 37682772 DOI: 10.1021/acsami.3c07785] [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] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
The mechanical properties of living cells reflect their physiological and pathological state. In particular, cancer cells undergo cytoskeletal modifications that typically make them softer than healthy cells, a property that could be used as a diagnostic tool. However, this is challenging because cells are complex structures displaying a broad range of morphologies when cultured in standard 2D culture dishes. Here, we use adhesive micropatterns to impose the cell geometry and thus standardize the mechanics and morphologies of cancer cells, which we measure by atomic force microscopy (AFM), mechanical nanomapping, and membrane nanotube pulling. We show that micropatterning cancer cells leads to distinct morphological and mechanical changes for different cell lines. Micropatterns did not systematically lower the variability in cell elastic modulus distribution. These effects emerge from a variable cell spreading rate associated with differences in the organization of the cytoskeleton, thus providing detailed insights into the structure-mechanics relationship of cancer cells cultured on micropatterns. Combining AFM with micropatterns reveals new mechanical and morphological observables applicable to cancer cells and possibly other cell types.
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Affiliation(s)
- Maxime Liboz
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
| | - Antoine Allard
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
- Department of Physics, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, U.K
| | - Michel Malo
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
| | - Guillaume Lamour
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
| | - Gaelle Letort
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, 75231 Paris, France
| | - Bénédicte Thiébot
- CY Cergy Paris Université, Université d'Evry, Université Paris-Saclay, CNRS, LAMBE, F-95000 Cergy, France
| | - Sid Labdi
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
| | - Juan Pelta
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
| | - Clément Campillo
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
- Institut Universitaire de France (IUF), 75231 Paris, France
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10
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Désy B, Desrosiers P, Allard A. Dimension matters when modeling network communities in hyperbolic spaces. PNAS Nexus 2023; 2:pgad136. [PMID: 37181048 PMCID: PMC10167553 DOI: 10.1093/pnasnexus/pgad136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/17/2023] [Accepted: 03/30/2023] [Indexed: 05/16/2023]
Abstract
Over the last decade, random hyperbolic graphs have proved successful in providing geometric explanations for many key properties of real-world networks, including strong clustering, high navigability, and heterogeneous degree distributions. These properties are ubiquitous in systems as varied as the internet, transportation, brain or epidemic networks, which are thus unified under the hyperbolic network interpretation on a surface of constant negative curvature. Although a few studies have shown that hyperbolic models can generate community structures, another salient feature observed in real networks, we argue that the current models are overlooking the choice of the latent space dimensionality that is required to adequately represent clustered networked data. We show that there is an important qualitative difference between the lowest-dimensional model and its higher-dimensional counterparts with respect to how similarity between nodes restricts connection probabilities. Since more dimensions also increase the number of nearest neighbors for angular clusters representing communities, considering only one more dimension allows us to generate more realistic and diverse community structures.
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Affiliation(s)
- Béatrice Désy
- School of Information Management, Victoria University of Wellington, Wellington 6140, New Zealand
- Antarctic Research Centre, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Patrick Desrosiers
- Département de physique, de génie physique et d’optique, Université Laval, Québec, QC, Canada G1V 0A6
- Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec, QC, Canada G1V 0A6
- Centre de recherche CERVO, Québec, QC, Canada G1J 2G3
| | - Antoine Allard
- Département de physique, de génie physique et d’optique, Université Laval, Québec, QC, Canada G1V 0A6
- Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec, QC, Canada G1V 0A6
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11
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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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12
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Grégoire A, Allard A, Huamán Fuertes E, León Trinidad S, Buff S, Berard M, Joly T. 53 Vitrification of guinea pig (. Reprod Fertil Dev 2022. [DOI: 10.1071/rdv35n2ab53] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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13
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Allard A, Moore C, Scarpino SV, Althouse BM, Hébert-Dufresne L. The role of directionality, heterogeneity and correlations in epidemic risk and spread. ArXiv 2022:arXiv:2005.11283v3. [PMID: 35169597 PMCID: PMC8845507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Revised: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Most models of epidemic spread, including many designed specifically for COVID-19, implicitly assume mass-action contact patterns and undirected contact networks, meaning that the individuals most likely to spread the disease are also the most at risk to receive it from others. Here, we review results from the theory of random directed graphs which show that many important quantities, including the reproduction number and the epidemic size, depend sensitively on the joint distribution of in- and out-degrees ("risk" and "spread"), including their heterogeneity and the correlation between them. By considering joint distributions of various kinds, we elucidate why some types of heterogeneity cause a deviation from the standard Kermack-McKendrick analysis of SIR models, i.e., so-called mass-action models where contacts are homogeneous and random, and some do not. We also show that some structured SIR models informed by realistic complex contact patterns among types of individuals (age or activity) are simply mixtures of Poisson processes and tend not to deviate significantly from the simplest mass-action model. Finally, we point out some possible policy implications of this directed structure, both for contact tracing strategy and for interventions designed to prevent superspreading events. In particular, directed graphs have a forward and backward version of the classic "friendship paradox" -- forward edges tend to lead to individuals with high risk, while backward edges lead to individuals with high spread -- such that a combination of both forward and backward contact tracing is necessary to find superspreading events and prevent future cascades of infection.
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14
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St-Onge G, Sun H, Allard A, Hébert-Dufresne L, Bianconi G. Universal Nonlinear Infection Kernel from Heterogeneous Exposure on Higher-Order Networks. Phys Rev Lett 2021; 127:158301. [PMID: 34678024 PMCID: PMC9199393 DOI: 10.1103/physrevlett.127.158301] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 07/26/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
The collocation of individuals in different environments is an important prerequisite for exposure to infectious diseases on a social network. Standard epidemic models fail to capture the potential complexity of this scenario by (1) neglecting the higher-order structure of contacts that typically occur through environments like workplaces, restaurants, and households, and (2) assuming a linear relationship between the exposure to infected contacts and the risk of infection. Here, we leverage a hypergraph model to embrace the heterogeneity of environments and the heterogeneity of individual participation in these environments. We find that combining heterogeneous exposure with the concept of minimal infective dose induces a universal nonlinear relationship between infected contacts and infection risk. Under nonlinear infection kernels, conventional epidemic wisdom breaks down with the emergence of discontinuous transitions, superexponential spread, and hysteresis.
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Affiliation(s)
- Guillaume St-Onge
- Département de physique, de génie physique et d’optique, Université Laval, Québec (Québec) G1V 0A6, Canada
- Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec (Québec) G1V 0A6, Canada
| | - Hanlin Sun
- School of Mathematical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Antoine Allard
- Département de physique, de génie physique et d’optique, Université Laval, Québec (Québec) G1V 0A6, Canada
- Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec (Québec) G1V 0A6, Canada
- Vermont Complex Systems Center, University of Vermont, Burlington, Vermont 05405, USA
| | - Laurent Hébert-Dufresne
- Département de physique, de génie physique et d’optique, Université Laval, Québec (Québec) G1V 0A6, Canada
- Vermont Complex Systems Center, University of Vermont, Burlington, Vermont 05405, USA
- Department of Computer Science, University of Vermont, Burlington, Vermont 05405, USA
| | - Ginestra Bianconi
- School of Mathematical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
- The Alan Turing Institute, 96 Euston Road, London NW1 2DB, United Kingdom
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15
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Abstract
Forecasting the evolution of contagion dynamics is still an open problem to which mechanistic models only offer a partial answer. To remain mathematically or computationally tractable, these models must rely on simplifying assumptions, thereby limiting the quantitative accuracy of their predictions and the complexity of the dynamics they can model. Here, we propose a complementary approach based on deep learning where effective local mechanisms governing a dynamic on a network are learned from time series data. Our graph neural network architecture makes very few assumptions about the dynamics, and we demonstrate its accuracy using different contagion dynamics of increasing complexity. By allowing simulations on arbitrary network structures, our approach makes it possible to explore the properties of the learned dynamics beyond the training data. Finally, we illustrate the applicability of our approach using real data of the COVID-19 outbreak in Spain. Our results demonstrate how deep learning offers a new and complementary perspective to build effective models of contagion dynamics on networks.
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Affiliation(s)
- Charles Murphy
- Département de physique, de génie physique et d'optique, Université Laval, Québec, Québec, Canada
- Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec, Québec, Canada
| | - Edward Laurence
- Département de physique, de génie physique et d'optique, Université Laval, Québec, Québec, Canada
- Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec, Québec, Canada
| | - Antoine Allard
- Département de physique, de génie physique et d'optique, Université Laval, Québec, Québec, Canada.
- Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec, Québec, Canada.
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16
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Allard A, Lopes Dos Santos R, Campillo C. Remodelling of membrane tubules by the actin cytoskeleton. Biol Cell 2021; 113:329-343. [PMID: 33826772 DOI: 10.1111/boc.202000148] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/25/2021] [Accepted: 03/27/2021] [Indexed: 12/14/2022]
Abstract
Inside living cells, the remodelling of membrane tubules by actomyosin networks is crucial for processes such as intracellular trafficking or organelle reshaping. In this review, we first present various in vivo situations in which actin affects membrane tubule remodelling, then we recall some results on force production by actin dynamics and on membrane tubules physics. Finally, we show that our knowledge of the underlying mechanisms by which actomyosin dynamics affect tubule morphology has recently been moved forward. This is thanks to in vitro experiments that mimic cellular membranes and actin dynamics and allow deciphering the physics of tubule remodelling in biochemically controlled conditions, and shed new light on tubule shape regulation.
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Affiliation(s)
- Antoine Allard
- LAMBE, Université d'Évry, CNRS, CEA, Université Paris-Saclay, Évry-Courcouronnes, 91025, France.,Sorbonne Université, UPMC, Paris 06, Paris, France.,Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France.,Department of Physics, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | | | - Clément Campillo
- LAMBE, Université d'Évry, CNRS, CEA, Université Paris-Saclay, Évry-Courcouronnes, 91025, France
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17
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Hébert-Dufresne L, Althouse BM, Scarpino SV, Allard A. Corrigendum to 'Beyond R0: heterogeneity in secondary infections and probabilistic epidemic forecasting'. J R Soc Interface 2021; 18:20210168. [PMID: 33757292 DOI: 10.1098/rsif.2021.0168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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18
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St-Onge G, Thibeault V, Allard A, Dubé LJ, Hébert-Dufresne L. Social Confinement and Mesoscopic Localization of Epidemics on Networks. Phys Rev Lett 2021; 126:098301. [PMID: 33750152 PMCID: PMC8082412 DOI: 10.1103/physrevlett.126.098301] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 11/02/2020] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
Recommendations around epidemics tend to focus on individual behaviors, with much less efforts attempting to guide event cancellations and other collective behaviors since most models lack the higher-order structure necessary to describe large gatherings. Through a higher-order description of contagions on networks, we model the impact of a blanket cancellation of events larger than a critical size and find that epidemics can suddenly collapse when interventions operate over groups of individuals rather than at the level of individuals. We relate this phenomenon to the onset of mesoscopic localization, where contagions concentrate around dominant groups.
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Affiliation(s)
- Guillaume St-Onge
- Département de physique, de génie physique et d’optique, Université Laval, Québec (Québec), Canada G1V 0A6
- Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec (Québec), Canada G1V 0A6
| | - Vincent Thibeault
- Département de physique, de génie physique et d’optique, Université Laval, Québec (Québec), Canada G1V 0A6
- Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec (Québec), Canada G1V 0A6
| | - Antoine Allard
- Département de physique, de génie physique et d’optique, Université Laval, Québec (Québec), Canada G1V 0A6
- Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec (Québec), Canada G1V 0A6
| | - Louis J. Dubé
- Département de physique, de génie physique et d’optique, Université Laval, Québec (Québec), Canada G1V 0A6
- Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec (Québec), Canada G1V 0A6
| | - Laurent Hébert-Dufresne
- Département de physique, de génie physique et d’optique, Université Laval, Québec (Québec), Canada G1V 0A6
- Department of Computer Science & Vermont Complex Systems Center, University of Vermont, Burlington, Vermont 05405, USA
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19
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St-Onge G, Thibeault V, Allard A, Dubé LJ, Hébert-Dufresne L. Master equation analysis of mesoscopic localization in contagion dynamics on higher-order networks. Phys Rev E 2021; 103:032301. [PMID: 33862710 DOI: 10.1103/physreve.103.032301] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 01/04/2021] [Indexed: 12/19/2022]
Abstract
Simple models of infectious diseases tend to assume random mixing of individuals, but real interactions are not random pairwise encounters: they occur within various types of gatherings such as workplaces, households, schools, and concerts, best described by a higher-order network structure. We model contagions on higher-order networks using group-based approximate master equations, in which we track all states and interactions within a group of nodes and assume a mean-field coupling between them. Using the susceptible-infected-susceptible dynamics, our approach reveals the existence of a mesoscopic localization regime, where a disease can concentrate and self-sustain only around large groups in the network overall organization. In this regime, the phase transition is smeared, characterized by an inhomogeneous activation of the groups. At the mesoscopic level, we observe that the distribution of infected nodes within groups of the same size can be very dispersed, even bimodal. When considering heterogeneous networks, both at the level of nodes and at the level of groups, we characterize analytically the region associated with mesoscopic localization in the structural parameter space. We put in perspective this phenomenon with eigenvector localization and discuss how a focus on higher-order structures is needed to discern the more subtle localization at the mesoscopic level. Finally, we discuss how mesoscopic localization affects the response to structural interventions and how this framework could provide important insights for a broad range of dynamics.
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Affiliation(s)
- Guillaume St-Onge
- Département de physique, de génie physique et d'optique, Université Laval, Québec (Québec), Canada G1V 0A6.,Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec (Québec), Canada G1V 0A6
| | - Vincent Thibeault
- Département de physique, de génie physique et d'optique, Université Laval, Québec (Québec), Canada G1V 0A6.,Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec (Québec), Canada G1V 0A6
| | - Antoine Allard
- Département de physique, de génie physique et d'optique, Université Laval, Québec (Québec), Canada G1V 0A6.,Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec (Québec), Canada G1V 0A6
| | - Louis J Dubé
- Département de physique, de génie physique et d'optique, Université Laval, Québec (Québec), Canada G1V 0A6.,Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec (Québec), Canada G1V 0A6
| | - Laurent Hébert-Dufresne
- Département de physique, de génie physique et d'optique, Université Laval, Québec (Québec), Canada G1V 0A6.,Vermont Complex Systems Center, University of Vermont, Burlington, Vermont 05405, USA.,Department of Computer Science, University of Vermont, Burlington, Vermont 05405, USA
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20
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St-Onge G, Thibeault V, Allard A, Dubé LJ, Hébert-Dufresne L. Social confinement and mesoscopic localization of epidemics on networks. ArXiv 2021:arXiv:2003.05924v4. [PMID: 33173802 PMCID: PMC7654871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Revised: 01/29/2021] [Indexed: 06/11/2023]
Abstract
Recommendations around epidemics tend to focus on individual behaviors, with much less efforts attempting to guide event cancellations and other collective behaviors since most models lack the higher-order structure necessary to describe large gatherings. Through a higher-order description of contagions on networks, we model the impact of a blanket cancellation of events larger than a critical size and find that epidemics can suddenly collapse when interventions operate over groups of individuals rather than at the level of individuals. We relate this phenomenon to the onset of mesoscopic localization, where contagions concentrate around dominant groups.
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21
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Hébert-Dufresne L, Althouse BM, Scarpino SV, Allard A. Beyond R0: heterogeneity in secondary infections and probabilistic epidemic forecasting. J R Soc Interface 2020; 17:20200393. [PMID: 33143594 PMCID: PMC7729039 DOI: 10.1098/rsif.2020.0393] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/12/2020] [Indexed: 01/02/2023] Open
Abstract
The basic reproductive number, R0, is one of the most common and most commonly misapplied numbers in public health. Often used to compare outbreaks and forecast pandemic risk, this single number belies the complexity that different epidemics can exhibit, even when they have the same R0. Here, we reformulate and extend a classic result from random network theory to forecast the size of an epidemic using estimates of the distribution of secondary infections, leveraging both its average R0 and the underlying heterogeneity. Importantly, epidemics with lower R0 can be larger if they spread more homogeneously (and are therefore more robust to stochastic fluctuations). We illustrate the potential of this approach using different real epidemics with known estimates for R0, heterogeneity and epidemic size in the absence of significant intervention. Further, we discuss the different ways in which this framework can be implemented in the data-scarce reality of emerging pathogens. Lastly, we demonstrate that without data on the heterogeneity in secondary infections for emerging infectious diseases like COVID-19 the uncertainty in outbreak size ranges dramatically. Taken together, our work highlights the critical need for contact tracing during emerging infectious disease outbreaks and the need to look beyond R0.
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Affiliation(s)
- Laurent Hébert-Dufresne
- Vermont Complex Systems Center, University of Vermont, Burlington, VT 05405, USA
- Department of Computer Science, University of Vermont, Burlington, VT 05405, USA
- Département de physique, de génie physique et d’optique, Université Laval, Québec, Canada G1V 0A6
| | - Benjamin M. Althouse
- Institute for Disease Modeling, Bellevue, WA 98005, USA
- Information School, University of Washington, Seattle, WA 98195-2840, USA
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
| | - Samuel V. Scarpino
- Network Science Institute, Northeastern University, Boston, MA 02115, USA
- Department of Marine and Environmental Sciences, Northeastern University, Boston, MA 02115, USA
- Department of Physics, Northeastern University, Boston, MA 02115, USA
- Department of Health Sciences, Northeastern University, Boston, MA 02115, USA
- ISI Foundation, Turin 10126, Italy
- Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Antoine Allard
- Département de physique, de génie physique et d’optique, Université Laval, Québec, Canada G1V 0A6
- Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec, Canada G1V 0A6
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22
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Althouse BM, Wenger EA, Miller JC, Scarpino SV, Allard A, Hébert-Dufresne L, Hu H. Superspreading events in the transmission dynamics of SARS-CoV-2: Opportunities for interventions and control. PLoS Biol 2020; 18:e3000897. [PMID: 33180773 PMCID: PMC7685463 DOI: 10.1371/journal.pbio.3000897] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 11/24/2020] [Indexed: 12/20/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiological agent of the Coronavirus Disease 2019 (COVID-19) disease, has moved rapidly around the globe, infecting millions and killing hundreds of thousands. The basic reproduction number, which has been widely used-appropriately and less appropriately-to characterize the transmissibility of the virus, hides the fact that transmission is stochastic, often dominated by a small number of individuals, and heavily influenced by superspreading events (SSEs). The distinct transmission features of SARS-CoV-2, e.g., high stochasticity under low prevalence (as compared to other pathogens, such as influenza), and the central role played by SSEs on transmission dynamics cannot be overlooked. Many explosive SSEs have occurred in indoor settings, stoking the pandemic and shaping its spread, such as long-term care facilities, prisons, meat-packing plants, produce processing facilities, fish factories, cruise ships, family gatherings, parties, and nightclubs. These SSEs demonstrate the urgent need to understand routes of transmission, while posing an opportunity to effectively contain outbreaks with targeted interventions to eliminate SSEs. Here, we describe the different types of SSEs, how they influence transmission, empirical evidence for their role in the COVID-19 pandemic, and give recommendations for control of SARS-CoV-2.
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Affiliation(s)
- Benjamin M. Althouse
- Institute for Disease Modeling, Bellevue, Washington, United States of America
- University of Washington, Seattle, Washington, United States of America
- New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Edward A. Wenger
- Institute for Disease Modeling, Bellevue, Washington, United States of America
| | - Joel C. Miller
- School of Engineering and Mathematical Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Samuel V. Scarpino
- Network Science Institute, Northeastern University, Boston, Massachusetts, United States of America
- Department of Marine & Environmental Sciences, Northeastern University, Boston, Massachusetts, United States of America
- Department of Physics, Northeastern University, Boston, Massachusetts, United States of America
- Department of Health Sciences, Northeastern University, Boston, Massachusetts, United States of America
- ISI Foundation, Turin, Italy
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Antoine Allard
- Département de Physique, de Génie Physique et d’Optique, Université Laval, Québec, Québec, Canada
- Centre Interdisciplinaire en Modélisation Mathématique, Université Laval, Québec, Québec, Canada
| | - Laurent Hébert-Dufresne
- Département de Physique, de Génie Physique et d’Optique, Université Laval, Québec, Québec, Canada
- Vermont Complex Systems Center, University of Vermont, Burlington, Vermont, United States of America
- Department of Computer Science, University of Vermont, Burlington, Vermont, United States of America
| | - Hao Hu
- Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
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23
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Allard A, Valentino F, Sykes C, Betz T, Campillo C. Fluctuations of a membrane nanotube covered with an actin sleeve. Phys Rev E 2020; 102:052402. [PMID: 33327147 DOI: 10.1103/physreve.102.052402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/11/2020] [Indexed: 06/12/2023]
Abstract
Many biological functions rely on the reshaping of cell membranes, in particular into nanotubes, which are covered in vivo by dynamic actin networks. Nanotubes are subject to thermal fluctuations, but the effect of these on cell functions is unknown. Here, we form nanotubes from liposomes using an optically trapped bead adhering to the liposome membrane. From the power spectral density of this bead, we study the nanotube fluctuations in the range of membrane tensions measured in vivo. We show that an actin sleeve covering the nanotube damps its high-frequency fluctuations because of the network viscoelasticity. Our work paves the way for further studies of the effect of nanotube fluctuations on cellular functions.
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Affiliation(s)
- A Allard
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
- Sorbonne Université, UPMC, Paris 06, Paris, France
- LAMBE, Université d'Évry, CNRS, CEA, Université Paris-Saclay, 91025 Évry-Courcouronnes, France
| | - F Valentino
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
- Sorbonne Université, UPMC, Paris 06, Paris, France
| | - C Sykes
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
- Sorbonne Université, UPMC, Paris 06, Paris, France
| | - T Betz
- Institute of Cell Biology, Cells in Motion Interfaculty Center, Centre for Molecular Biology of Inflammation, 48149 Münster, Germany
| | - C Campillo
- LAMBE, Université d'Évry, CNRS, CEA, Université Paris-Saclay, 91025 Évry-Courcouronnes, France
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24
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Althouse BM, Wallace B, Case B, Scarpino SV, Allard A, Berdahl AM, White ER, Hebert-Dufresné L. The unintended consequences of inconsistent pandemic control policies. medRxiv 2020. [PMID: 32869043 PMCID: PMC7457624 DOI: 10.1101/2020.08.21.20179473] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Controlling the spread of COVID-19 - even after a licensed vaccine is available - requires the effective use of non-pharmaceutical interventions, e.g., physical distancing, limits on group sizes, mask wearing, etc1–7. To date, such interventions have not been uniformly and/or systematically implemented across the United States of America (US)8. For example, even when under strict stay-at-home orders, numerous jurisdictions in the US granted exceptions and/or were in close proximity to locations with entirely different regulations in place. Here, we investigate the impact of such geographic inconsistencies in epidemic control policies by coupling high-resolution mobility, search, and COVID case data to a mathematical model of SARS-CoV-2 transmission. Our results show that while stay-at-home orders decrease contacts in most areas of the US, some specific activities and venues often see an increase in attendance. As an example, over the month of March 2020, between 10 and 30% of churches in the US saw increases in attendance; even as the total number of visits to churches declined nationally. This heterogeneity, where certain venues see substantial increases in attendance while others close, suggests that closure can cause individuals to find an open venue, even if that requires longer-distance travel. And, indeed, the average distance travelled to churches in the US rose by 13% over the same period, and over the summer, churches with more than 50 average weekly visitors saw an increase of 81% in distance visitors had to travel to attend. Strikingly, our mathematical model reveals that, across a broad range of model parameters, partial measures can often be worse than no measures at all. In the most severe cases, individuals not complying with policies by traveling to neighboring jurisdictions can create epidemics when the outbreak would otherwise have been contained. Indeed, using county-level COVID-19 data, we show that mobility from high-incidence to low-incidence associated with travel for venues like churches, parks, and gyms consistently precedes rising case numbers in the low-incidence counties. Taken together, our data analysis of nearly 120 million church visitors across 184,677 churches, 14 million grocery visitors across 7,662 grocery stores, 13.5 million gym visitors across 5,483 gyms, 7.7 million cases across 3,195 counties, and modeling results highlight the potential unintended consequences of inconsistent epidemic control policies and stress the importance of balancing the societal needs of a population with the risk of an outbreak growing into a large epidemic, and the urgent need for centralized implementation and enforcement of non-pharmaceutical interventions.
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Affiliation(s)
- Benjamin M Althouse
- Institute for Disease Modeling, Global Health, Bill & Melinda Gates Foundation, Seattle, WA.,University of Washington, Seattle, WA 98105.,New Mexico State University, Las Cruces, NM 88003
| | - Brendan Wallace
- Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA
| | - Brendan Case
- Department of Computer Science, University of Vermont, Burlington, VT 05405, USA.,Vermont Complex Systems Center, University of Vermont, Burlington, VT 05405, USA
| | - Samuel V Scarpino
- Network Science Institute, Northeastern University, Boston, MA, USA.,Roux Institute, Northeastern University, Portland, ME, USA.,Santa Fe Institute, Santa Fe, NM, USA
| | - Antoine Allard
- Département de physique, de génie physique et d'optique, Université Laval, Québec (Québec), Canada G1V 0A6.,Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec (Québec), Canada G1V 0A6
| | - Andrew M Berdahl
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, WA 98195, USA
| | - Easton R White
- Department of Biology, University of Vermont, Burlington, VT 05405, USA.,Gund Institute for Environment, University of Vermont, Burlington, VT 05405, USA
| | - Laurent Hebert-Dufresné
- Department of Computer Science, University of Vermont, Burlington, VT 05405, USA.,Vermont Complex Systems Center, University of Vermont, Burlington, VT 05405, USA.,Département de physique, de génie physique et d'optique, Université Laval, Québec (Québec), Canada G1V 0A6
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Zheng M, Allard A, Hagmann P, Alemán-Gómez Y, Serrano MÁ. Geometric renormalization unravels self-similarity of the multiscale human connectome. Proc Natl Acad Sci U S A 2020; 117:20244-20253. [PMID: 32759211 PMCID: PMC7443937 DOI: 10.1073/pnas.1922248117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 12/19/2022] Open
Abstract
Structural connectivity in the brain is typically studied by reducing its observation to a single spatial resolution. However, the brain possesses a rich architecture organized over multiple scales linked to one another. We explored the multiscale organization of human connectomes using datasets of healthy subjects reconstructed at five different resolutions. We found that the structure of the human brain remains self-similar when the resolution of observation is progressively decreased by hierarchical coarse-graining of the anatomical regions. Strikingly, a geometric network model, where distances are not Euclidean, predicts the multiscale properties of connectomes, including self-similarity. The model relies on the application of a geometric renormalization protocol which decreases the resolution by coarse-graining and averaging over short similarity distances. Our results suggest that simple organizing principles underlie the multiscale architecture of human structural brain networks, where the same connectivity law dictates short- and long-range connections between different brain regions over many resolutions. The implications are varied and can be substantial for fundamental debates, such as whether the brain is working near a critical point, as well as for applications including advanced tools to simplify the digital reconstruction and simulation of the brain.
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Affiliation(s)
- Muhua Zheng
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, 08028 Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Antoine Allard
- Département de Physique, de Génie Physique et d'Optique, Université Laval, Québec, QC G1V 0A6, Canada
- Centre Interdisciplinaire de Modélisation Mathématique, Université Laval, Québec, QC G1V 0A6, Canada
| | - Patric Hagmann
- Connectomics Lab, Department of Radiology, Lausanne University Hospital and University of Lausanne (CHUV-UNIL), 1011 Lausanne, Switzerland
| | - Yasser Alemán-Gómez
- Connectomics Lab, Department of Radiology, Lausanne University Hospital and University of Lausanne (CHUV-UNIL), 1011 Lausanne, Switzerland
- Center for Psychiatric Neurosciences, Department of Psychiatry, Lausanne University Hospital and University of Lausanne (CHUV-UNIL), 1008 Prilly, Switzerland
- Medical Image Analysis Laboratory, Lausanne University Hospital and University of Lausanne (CHUV-UNIL), 1011 Lausanne, Switzerland
| | - M Ángeles Serrano
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, 08028 Barcelona, Spain;
- Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
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Holm A, Allard A, Eriksson I, Laurell G, Nylander K, Olofsson K. Absence of high-risk human papilloma virus in p16 positive inverted sinonasal papilloma. Eur Ann Otorhinolaryngol Head Neck Dis 2020; 137:201-206. [DOI: 10.1016/j.anorl.2017.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 09/19/2017] [Accepted: 10/01/2017] [Indexed: 10/25/2022]
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Allard A, Bouzid M, Betz T, Simon C, Abou-Ghali M, Lemière J, Valentino F, Manzi J, Brochard-Wyart F, Guevorkian K, Plastino J, Lenz M, Campillo C, Sykes C. Actin modulates shape and mechanics of tubular membranes. Sci Adv 2020; 6:eaaz3050. [PMID: 32494637 PMCID: PMC7176416 DOI: 10.1126/sciadv.aaz3050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/21/2020] [Indexed: 05/22/2023]
Abstract
The actin cytoskeleton shapes cells and also organizes internal membranous compartments. In particular, it interacts with membranes for intracellular transport of material in mammalian cells, yeast, or plant cells. Tubular membrane intermediates, pulled along microtubule tracks, are formed during this process and destabilize into vesicles. While the role of actin in tubule destabilization through scission is suggested, literature also provides examples of actin-mediated stabilization of membranous structures. To directly address this apparent contradiction, we mimic the geometry of tubular intermediates with preformed membrane tubes. The growth of an actin sleeve at the tube surface is monitored spatiotemporally. Depending on network cohesiveness, actin is able to entirely stabilize or locally maintain membrane tubes under pulling. On a single tube, thicker portions correlate with the presence of actin. These structures relax over several minutes and may provide enough time and curvature geometries for other proteins to act on tube stability.
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Affiliation(s)
- A. Allard
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
- LAMBE, Université Évry Val d’Essonne, CNRS, CEA, Université Paris-Saclay, Évry, France
| | - M. Bouzid
- LPTMS, CNRS, University of Paris-Sud, Universit Paris-Saclay, 91405 Orsay, France
| | - T. Betz
- Institute of Cell Biology, Center for Molecular Biology of Inflammation, Cells in Motion Cluster of Excellence, Münster University, Von-Esmarch-Strasse 56, D-48149 Münster, Germany
| | - C. Simon
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
| | - M. Abou-Ghali
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
| | - J. Lemière
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
| | - F. Valentino
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
| | - J. Manzi
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
| | - F. Brochard-Wyart
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
| | - K. Guevorkian
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
| | - J. Plastino
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
| | - M. Lenz
- LPTMS, CNRS, University of Paris-Sud, Universit Paris-Saclay, 91405 Orsay, France
- Laboratoire de Physique et Mécanique des Milieux Hétérogènes, UMR 7636, CNRS, ESPCI Paris, PSL Research University, Université Paris Diderot, Sorbonne Université, Paris 75005, France
| | - C. Campillo
- LAMBE, Université Évry Val d’Essonne, CNRS, CEA, Université Paris-Saclay, Évry, France
- Corresponding author. (C.C.); (C.Sy.)
| | - C. Sykes
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
- Corresponding author. (C.C.); (C.Sy.)
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Lavoie M, Saint-Béat B, Strauss J, Guérin S, Allard A, V. Hardy S, Falciatore A, Lavaud J. Genome-Scale Metabolic Reconstruction and in Silico Perturbation Analysis of the Polar Diatom Fragilariopsis cylindrus Predicts High Metabolic Robustness. Biology (Basel) 2020; 9:biology9020030. [PMID: 32079178 PMCID: PMC7168318 DOI: 10.3390/biology9020030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 01/31/2020] [Accepted: 02/08/2020] [Indexed: 12/15/2022]
Abstract
Diatoms are major primary producers in polar environments where they can actively grow under extremely variable conditions. Integrative modeling using a genome-scale model (GSM) is a powerful approach to decipher the complex interactions between components of diatom metabolism and can provide insights into metabolic mechanisms underlying their evolutionary success in polar ecosystems. We developed the first GSM for a polar diatom, Fragilariopsis cylindrus, which enabled us to study its metabolic robustness using sensitivity analysis. We find that the predicted growth rate was robust to changes in all model parameters (i.e., cell biochemical composition) except the carbon uptake rate. Constraints on total cellular carbon buffer the effect of changes in the input parameters on reaction fluxes and growth rate. We also show that single reaction deletion of 20% to 32% of active (nonzero flux) reactions and single gene deletion of 44% to 55% of genes associated with active reactions affected the growth rate, as well as the production fluxes of total protein, lipid, carbohydrate, DNA, RNA, and pigments by less than 1%, which was due to the activation of compensatory reactions (e.g., analogous enzymes and alternative pathways) with more highly connected metabolites involved in the reactions that were robust to deletion. Interestingly, including highly divergent alleles unique for F. cylindrus increased its metabolic robustness to cellular perturbations even more. Overall, our results underscore the high robustness of metabolism in F. cylindrus, a feature that likely helps to maintain cell homeostasis under polar conditions.
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Affiliation(s)
- Michel Lavoie
- Unité Mixte Internationale 3376 Takuvik, CNRS-ULaval, Département de Biologie and Québec-Océan, Université Laval, Québec, QC G1V 0A6, Canada; (B.S.-B.); (S.G.); (J.L.)
- Correspondence:
| | - Blanche Saint-Béat
- Unité Mixte Internationale 3376 Takuvik, CNRS-ULaval, Département de Biologie and Québec-Océan, Université Laval, Québec, QC G1V 0A6, Canada; (B.S.-B.); (S.G.); (J.L.)
| | - Jan Strauss
- Department of Biology, University of Hamburg, D-22607 Hamburg, Germany;
- CSSB Centre for Structural Systems Biology, c/o Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, D-22607 Hamburg, Germany
| | - Sébastien Guérin
- Unité Mixte Internationale 3376 Takuvik, CNRS-ULaval, Département de Biologie and Québec-Océan, Université Laval, Québec, QC G1V 0A6, Canada; (B.S.-B.); (S.G.); (J.L.)
| | - Antoine Allard
- Département de physique, de génie physique et d’optique, Université Laval, Québec, QC G1V 0A6, Canada;
- Centre interdisciplinaire de modélisation mathématique, Université Laval, Québec, QC G1V 0A6, Canada
| | - Simon V. Hardy
- Département d’informatique et génie logiciel, Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, QC G1V 0A6, Canada;
- Unité des Neurosciences cellulaires et moléculaires, Centre de recherche CERVO, Québec, QC G1V 0A6, Canada
| | - Angela Falciatore
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141, Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France;
| | - Johann Lavaud
- Unité Mixte Internationale 3376 Takuvik, CNRS-ULaval, Département de Biologie and Québec-Océan, Université Laval, Québec, QC G1V 0A6, Canada; (B.S.-B.); (S.G.); (J.L.)
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Abstract
Connectomes are spatially embedded networks whose architecture has been shaped by physical constraints and communication needs throughout evolution. Using a decentralized navigation protocol, we investigate the relationship between the structure of the connectomes of different species and their spatial layout. As a navigation strategy, we use greedy routing where nearest neighbors, in terms of geometric distance, are visited. We measure the fraction of successful greedy paths and their length as compared to shortest paths in the topology of connectomes. In Euclidean space, we find a striking difference between the navigability properties of mammalian and non-mammalian species, which implies the inability of Euclidean distances to fully explain the structural organization of their connectomes. In contrast, we find that hyperbolic space, the effective geometry of complex networks, provides almost perfectly navigable maps of connectomes for all species, meaning that hyperbolic distances are exceptionally congruent with the structure of connectomes. Hyperbolic maps therefore offer a quantitative meaningful representation of connectomes that suggests a new cartography of the brain based on the combination of its connectivity with its effective geometry rather than on its anatomy only. Hyperbolic maps also provide a universal framework to study decentralized communication processes in connectomes of different species and at different scales on an equal footing.
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Affiliation(s)
- Antoine Allard
- Département de physique, de génie physique et d’optique, Université Laval, Québec, Canada
- Centre interdisciplinaire de modélisation mathématique, Université Laval, Québec, Canada
| | - M. Ángeles Serrano
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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Hay B, Zarr R, Stacey C, Sokolov N, Lira-Cortes L, Zhang J, Hammerschmidt U, Filtz JR, Allard A. Report on the CCT Supplementary comparison S2 on thermal conductivity measurements of insulating materials by guarded hot plate. Metrologia 2020; 57:10.1088/0026-1394/57/1a/03003. [PMID: 36451686 PMCID: PMC9706684 DOI: 10.1088/0026-1394/57/1a/03003] [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] [Indexed: 06/17/2023]
Abstract
Seven National Metrology Institutes (NMIs) from France, United States, United Kingdom, Russia, Mexico, China and Germany participated in an inter-laboratory comparison on thermal conductivity measurements by the Guarded Hot Plate method. This action was part of a series of supplementary inter-laboratory comparisons (including infrared spectral emittance and thermal diffusivity) sponsored by the Consultative Committee on Thermometry (CCT) Task Group on Thermophysical Quantities (TG-ThQ). The objective of this collaborative work was to strengthen the consistency of thermal conductivity measurements carried out worldwide on low conductive materials. Measurements were conducted successively by all participants on the same sets of specimens of insulating materials (mineral wool and expanded polystyrene) at temperatures ranging from 10 °C to 40 °C, according to the International Standard ISO 8302. This protocol aimed to minimize issues of material variability by circulating the same pairs of specimens among the laboratories following the strict format of a round-robin test program. More than 120 data points (combinations of material, thickness and temperature) were compared. 92 % of the data points were in agreement, with differences to weighted mean values less than the expanded uncertainties calculated from the individual NMI uncertainties and uncertainties related to the comparison process.
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Affiliation(s)
- B. Hay
- Laboratoire National de Métrologie et d’Essais (LNE), Scientific and Industrial Metrology Centre, Paris, France
| | - R. Zarr
- National Institute of Standards and Technology (NIST), Engineering Laboratory, Gaithersburg, MD, United States
| | - C. Stacey
- National Physical Laboratory (NPL), Materials Division, Teddington, England
| | - N. Sokolov
- D.I. Mendeleyev Institute for Metrology (VNIIM), St. Petersburg, Russia
| | - L. Lira-Cortes
- Centro Nacional de Metrología (CENAM), Division de Termometría, Queretaro, Mexico
| | - J. Zhang
- National Institute of Metrology (NIM), Heat Division, Beijing, China
| | - U. Hammerschmidt
- Physikalisch-Technische Bundesanstalt (PTB), Braunschweig, Germany
| | - J.-R. Filtz
- Laboratoire National de Métrologie et d’Essais (LNE), Scientific and Industrial Metrology Centre, Paris, France
| | - A. Allard
- Laboratoire National de Métrologie et d’Essais (LNE), Scientific and Industrial Metrology Centre, Paris, France
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31
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Murphy C, Allard A, Laurence E, St-Onge G, Dubé LJ. Geometric evolution of complex networks with degree correlations. Phys Rev E 2018; 97:032309. [PMID: 29776179 DOI: 10.1103/physreve.97.032309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Indexed: 06/08/2023]
Abstract
We present a general class of geometric network growth mechanisms by homogeneous attachment in which the links created at a given time t are distributed homogeneously between a new node and the existing nodes selected uniformly. This is achieved by creating links between nodes uniformly distributed in a homogeneous metric space according to a Fermi-Dirac connection probability with inverse temperature β and general time-dependent chemical potential μ(t). The chemical potential limits the spatial extent of newly created links. Using a hidden variable framework, we obtain an analytical expression for the degree sequence and show that μ(t) can be fixed to yield any given degree distributions, including a scale-free degree distribution. Additionally, we find that depending on the order in which nodes appear in the network-its history-the degree-degree correlations can be tuned to be assortative or disassortative. The effect of the geometry on the structure is investigated through the average clustering coefficient 〈c〉. In the thermodynamic limit, we identify a phase transition between a random regime where 〈c〉→0 when β<β_{c} and a geometric regime where 〈c〉>0 when β>β_{c}.
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Affiliation(s)
- Charles Murphy
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec City, Québec, Canada G1V 0A6
| | - Antoine Allard
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec City, Québec, Canada G1V 0A6
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Martí i Franquès 1, E-08028 Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems, Universitat de Barcelona, Barcelona, Spain
| | - Edward Laurence
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec City, Québec, Canada G1V 0A6
| | - Guillaume St-Onge
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec City, Québec, Canada G1V 0A6
| | - Louis J Dubé
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec City, Québec, Canada G1V 0A6
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Allard A, Althouse BM, Hébert-Dufresne L, Scarpino SV. The risk of sustained sexual transmission of Zika is underestimated. PLoS Pathog 2017; 13:e1006633. [PMID: 28934370 PMCID: PMC5626499 DOI: 10.1371/journal.ppat.1006633] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 10/03/2017] [Accepted: 09/07/2017] [Indexed: 12/18/2022] Open
Abstract
Pathogens often follow more than one transmission route during outbreaks-from needle sharing plus sexual transmission of HIV to small droplet aerosol plus fomite transmission of influenza. Thus, controlling an infectious disease outbreak often requires characterizing the risk associated with multiple mechanisms of transmission. For example, during the Ebola virus outbreak in West Africa, weighing the relative importance of funeral versus health care worker transmission was essential to stopping disease spread. As a result, strategic policy decisions regarding interventions must rely on accurately characterizing risks associated with multiple transmission routes. The ongoing Zika virus (ZIKV) outbreak challenges our conventional methodologies for translating case-counts into route-specific transmission risk. Critically, most approaches will fail to accurately estimate the risk of sustained sexual transmission of a pathogen that is primarily vectored by a mosquito-such as the risk of sustained sexual transmission of ZIKV. By computationally investigating a novel mathematical approach for multi-route pathogens, our results suggest that previous epidemic threshold estimates could under-estimate the risk of sustained sexual transmission by at least an order of magnitude. This result, coupled with emerging clinical, epidemiological, and experimental evidence for an increased risk of sexual transmission, would strongly support recent calls to classify ZIKV as a sexually transmitted infection.
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Affiliation(s)
- Antoine Allard
- Centre de Recerca Matemàtica, Edifici C, Campus Bellaterra, Bellaterra, Barcelona, Spain
| | - Benjamin M. Althouse
- Institute for Disease Modeling, Bellevue, Washington, United States of America
- University of Washington, Seattle, Washington, United States of America
- New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Laurent Hébert-Dufresne
- Institute for Disease Modeling, Bellevue, Washington, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- University of Vermont, Burlington, Vermont, United States of America
| | - Samuel V. Scarpino
- Northeastern University, Boston, Massasschusetts, United States of America
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Valentino F, Sens P, Lemière J, Allard A, Betz T, Campillo C, Sykes C. Fluctuations of a membrane nanotube revealed by high-resolution force measurements. Soft Matter 2016; 12:9429-9435. [PMID: 27830219 DOI: 10.1039/c6sm02117d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Pulling membrane nanotubes from liposomes presents a powerful method to gain access to membrane mechanics. Here we extend classical optical tweezers studies to infer membrane nanotube dynamics with high spatial and temporal resolution. We first validate our force measurement setup by accurately measuring the bending modulus of EPC membrane in tube pulling experiments. Then we record the position signal of a trapped bead when it is connected, or not, to a tube. We derive the fluctuation spectrum of these signals and find that the presence of a membrane nanotube induces higher fluctuations, especially at low frequencies (10-1000 Hz). We analyse these spectra by taking into account the peristaltic modes of nanotube fluctuations. This analysis provides a new experimental framework for a quantitative study of the fluctuations of nanotubular membrane structures that are present in living cells, and now classically used for in vitro biomimetic approaches.
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Affiliation(s)
- F Valentino
- Institut Curie, PSL Research University, CNRS, UMR 168, 75005 Paris, France. and Sorbonne Universités, UPMC Univ Paris 06, 4 place Jussieu, 75005 Paris, France and Univ Paris Diderot, Sorbonne Paris Cité, 5 rue Thomas-Mann, 75205 Paris, France
| | - P Sens
- Institut Curie, PSL Research University, CNRS, UMR 168, 75005 Paris, France. and Sorbonne Universités, UPMC Univ Paris 06, 4 place Jussieu, 75005 Paris, France
| | - J Lemière
- Institut Curie, PSL Research University, CNRS, UMR 168, 75005 Paris, France. and Sorbonne Universités, UPMC Univ Paris 06, 4 place Jussieu, 75005 Paris, France and Univ Paris Diderot, Sorbonne Paris Cité, 5 rue Thomas-Mann, 75205 Paris, France
| | - A Allard
- Institut Curie, PSL Research University, CNRS, UMR 168, 75005 Paris, France. and Sorbonne Universités, UPMC Univ Paris 06, 4 place Jussieu, 75005 Paris, France and Université Evry Val d'Essonne, LAMBE, Boulevard F Mitterrand, Evry 91025, France.
| | - T Betz
- Institute of Cell Biology, Center for Molecular Biology of Inflammation, Cells-in-Motion Cluster of Excellence, Münster University, Von-Esmarch-Strasse 56, D-48149 Münster, Germany
| | - C Campillo
- Université Evry Val d'Essonne, LAMBE, Boulevard F Mitterrand, Evry 91025, France.
| | - C Sykes
- Institut Curie, PSL Research University, CNRS, UMR 168, 75005 Paris, France. and Sorbonne Universités, UPMC Univ Paris 06, 4 place Jussieu, 75005 Paris, France
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García-Pérez G, Boguñá M, Allard A, Serrano MÁ. The hidden hyperbolic geometry of international trade: World Trade Atlas 1870-2013. Sci Rep 2016; 6:33441. [PMID: 27633649 PMCID: PMC5025783 DOI: 10.1038/srep33441] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 08/26/2016] [Indexed: 11/09/2022] Open
Abstract
Here, we present the World Trade Atlas 1870-2013, a collection of annual world trade maps in which distance combines economic size and the different dimensions that affect international trade beyond mere geography. Trade distances, based on a gravity model predicting the existence of significant trade channels, are such that the closer countries are in trade space, the greater their chance of becoming connected. The atlas provides us with information regarding the long-term evolution of the international trade system and demonstrates that, in terms of trade, the world is not flat but hyperbolic, as a reflection of its complex architecture. The departure from flatness has been increasing since World War I, meaning that differences in trade distances are growing and trade networks are becoming more hierarchical. Smaller-scale economies are moving away from other countries except for the largest economies; meanwhile those large economies are increasing their chances of becoming connected worldwide. At the same time, Preferential Trade Agreements do not fit in perfectly with natural communities within the trade space and have not necessarily reduced internal trade barriers. We discuss an interpretation in terms of globalization, hierarchization, and localization; three simultaneous forces that shape the international trade system.
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Affiliation(s)
- Guillermo García-Pérez
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, Barcelona, Spain
| | - Marián Boguñá
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, Barcelona, Spain
| | - Antoine Allard
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, Barcelona, Spain
| | - M. Ángeles Serrano
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, E-08010 Barcelona, Spain
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Hébert-Dufresne L, Grochow JA, Allard A. Multi-scale structure and topological anomaly detection via a new network statistic: The onion decomposition. Sci Rep 2016; 6:31708. [PMID: 27535466 PMCID: PMC4989159 DOI: 10.1038/srep31708] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/25/2016] [Indexed: 11/09/2022] Open
Abstract
We introduce a network statistic that measures structural properties at the micro-, meso-, and macroscopic scales, while still being easy to compute and interpretable at a glance. Our statistic, the onion spectrum, is based on the onion decomposition, which refines the k-core decomposition, a standard network fingerprinting method. The onion spectrum is exactly as easy to compute as the k-cores: It is based on the stages at which each vertex gets removed from a graph in the standard algorithm for computing the k-cores. Yet, the onion spectrum reveals much more information about a network, and at multiple scales; for example, it can be used to quantify node heterogeneity, degree correlations, centrality, and tree- or lattice-likeness. Furthermore, unlike the k-core decomposition, the combined degree-onion spectrum immediately gives a clear local picture of the network around each node which allows the detection of interesting subgraphs whose topological structure differs from the global network organization. This local description can also be leveraged to easily generate samples from the ensemble of networks with a given joint degree-onion distribution. We demonstrate the utility of the onion spectrum for understanding both static and dynamic properties on several standard graph models and on many real-world networks.
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Affiliation(s)
| | | | - Antoine Allard
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona 08028, Spain
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36
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Abstract
We introduce an intuitive model that describes both the emergence of community structure and the evolution of the internal structure of communities in growing social networks. The model comprises two complementary mechanisms: One mechanism accounts for the evolution of the internal link structure of a single community, and the second mechanism coordinates the growth of multiple overlapping communities. The first mechanism is based on the assumption that each node establishes links with its neighbors and introduces new nodes to the community at different rates. We demonstrate that this simple mechanism gives rise to an effective maximal degree within communities. This observation is related to the anthropological theory known as Dunbar's number, i.e., the empirical observation of a maximal number of ties which an average individual can sustain within its social groups. The second mechanism is based on a recently proposed generalization of preferential attachment to community structure, appropriately called structural preferential attachment (SPA). The combination of these two mechanisms into a single model (SPA+) allows us to reproduce a number of the global statistics of real networks: The distribution of community sizes, of node memberships, and of degrees. The SPA+ model also predicts (a) three qualitative regimes for the degree distribution within overlapping communities and (b) strong correlations between the number of communities to which a node belongs and its number of connections within each community. We present empirical evidence that support our findings in real complex networks.
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Affiliation(s)
- Jean-Gabriel Young
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec (Québec), Canada G1V 0A6
| | - Laurent Hébert-Dufresne
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec (Québec), Canada G1V 0A6
- Santa Fe Institute, Santa Fe, New Mexico 87501, USA
| | - Antoine Allard
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec (Québec), Canada G1V 0A6
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Martí i Franquès 1, E-08028 Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, Barcelona, Spain
| | - Louis J Dubé
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec (Québec), Canada G1V 0A6
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Abstract
Scale independence is a ubiquitous feature of complex systems that implies a highly skewed distribution of resources with no characteristic scale. Research has long focused on why systems as varied as protein networks, evolution, and stock actions all feature scale independence. Assuming that they simply do, we focus here on describing how this behavior emerges, in contrast to more idealized models usually considered. We arrive at the conjecture that a minimal model to explain the growth toward scale independence involves only two coupled dynamical features: the first is the well-known preferential attachment principle, and the second is a general form of delayed temporal scaling. While the first is sufficient, the second is present in all studied data and appears to maximize the speed of convergence to true scale independence. The delay in this temporal scaling acts as a coupling between population growth and individual activity. Together, these two dynamical properties appear to pave a precise evolution path, such that even an instantaneous snapshot of a distribution is enough to reconstruct the past of the system and predict its future. We validate our approach and confirm its usefulness in diverse spheres of human activities, ranging from scientific and artistic productivity to sexual relations and online traffic.
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Affiliation(s)
- Laurent Hébert-Dufresne
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec (Québec), Canada G1V 0A6.,Santa Fe Institute, Santa Fe, New Mexico 87501, USA
| | - Antoine Allard
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec (Québec), Canada G1V 0A6.,Departament de Física Fonamental, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Jean-Gabriel Young
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec (Québec), Canada G1V 0A6
| | - Louis J Dubé
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec (Québec), Canada G1V 0A6
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38
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Hébert-Dufresne L, Laurence E, Allard A, Young JG, Dubé LJ. Complex networks as an emerging property of hierarchical preferential attachment. Phys Rev E Stat Nonlin Soft Matter Phys 2015; 92:062809. [PMID: 26764746 DOI: 10.1103/physreve.92.062809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Indexed: 06/05/2023]
Abstract
Real complex systems are not rigidly structured; no clear rules or blueprints exist for their construction. Yet, amidst their apparent randomness, complex structural properties universally emerge. We propose that an important class of complex systems can be modeled as an organization of many embedded levels (potentially infinite in number), all of them following the same universal growth principle known as preferential attachment. We give examples of such hierarchy in real systems, for instance, in the pyramid of production entities of the film industry. More importantly, we show how real complex networks can be interpreted as a projection of our model, from which their scale independence, their clustering, their hierarchy, their fractality, and their navigability naturally emerge. Our results suggest that complex networks, viewed as growing systems, can be quite simple, and that the apparent complexity of their structure is largely a reflection of their unobserved hierarchical nature.
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Affiliation(s)
- Laurent Hébert-Dufresne
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec (Québec), Canada G1V 0A6
- Santa Fe Institute, Santa Fe, New Mexico 87501, USA
| | - Edward Laurence
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec (Québec), Canada G1V 0A6
| | - Antoine Allard
- Departament de Física Fonamental, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Jean-Gabriel Young
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec (Québec), Canada G1V 0A6
| | - Louis J Dubé
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec (Québec), Canada G1V 0A6
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Allard A, Hébert-Dufresne L, Young JG, Dubé LJ. General and exact approach to percolation on random graphs. Phys Rev E Stat Nonlin Soft Matter Phys 2015; 92:062807. [PMID: 26764744 DOI: 10.1103/physreve.92.062807] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Indexed: 06/05/2023]
Abstract
We present a comprehensive and versatile theoretical framework to study site and bond percolation on clustered and correlated random graphs. Our contribution can be summarized in three main points. (i) We introduce a set of iterative equations that solve the exact distribution of the size and composition of components in finite-size quenched or random multitype graphs. (ii) We define a very general random graph ensemble that encompasses most of the models published to this day and also makes it possible to model structural properties not yet included in a theoretical framework. Site and bond percolation on this ensemble is solved exactly in the infinite-size limit using probability generating functions [i.e., the percolation threshold, the size, and the composition of the giant (extensive) and small components]. Several examples and applications are also provided. (iii) Our approach can be adapted to model interdependent graphs-whose most striking feature is the emergence of an extensive component via a discontinuous phase transition-in an equally general fashion. We show how a graph can successively undergo a continuous then a discontinuous phase transition, and preliminary results suggest that clustering increases the amplitude of the discontinuity at the transition.
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Affiliation(s)
- Antoine Allard
- Département de physique, de génie physique, et d'optique, Université Laval, Québec, Québec, Canada G1V 0A6
| | - Laurent Hébert-Dufresne
- Département de physique, de génie physique, et d'optique, Université Laval, Québec, Québec, Canada G1V 0A6
| | - Jean-Gabriel Young
- Département de physique, de génie physique, et d'optique, Université Laval, Québec, Québec, Canada G1V 0A6
| | - Louis J Dubé
- Département de physique, de génie physique, et d'optique, Université Laval, Québec, Québec, Canada G1V 0A6
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40
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Swartling L, Allard A, Törlen J, Ljungman P, Mattsson J, Sparrelid E. Prolonged outbreak of adenovirus A31 in allogeneic stem cell transplant recipients. Transpl Infect Dis 2015; 17:785-94. [PMID: 26284461 DOI: 10.1111/tid.12443] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [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: 02/19/2015] [Revised: 06/02/2015] [Accepted: 08/02/2015] [Indexed: 11/29/2022]
Abstract
BACKGROUND An outbreak of human adenovirus (HAdV) A31 occurred from December 2011 to March 2012 at the Center for Allogeneic Stem Cell Transplantation (CAST), Karolinska University Hospital in Sweden. We analyzed the outbreak, the routes of transmission, and report the medical consequences. METHODS The medical records of all patients admitted to CAST during the outbreak period were studied. Phylogenetic analysis of the patient HAdV strains was performed by sequencing the hexon gene and the more variable E3 gene. RESULTS We identified 9 cases of HAdV A31. Hygiene measures were implemented, but transmission continued for 2 months. All 9 patients had been admitted to the ward, but 2 had no connection in time to other known HAdV A31 cases. DNA sequencing of the patient strains strongly suggested nosocomial transmission. Transplantation was postponed and then cancelled in 1 patient, and 5 patients were treated with cidofovir because of high levels of viremia. In 7 patients, concomitant graft-versus-host disease (GVHD) grade II-V complicated the clinical picture, as it was difficult to distinguish symptoms of GVHD from those of HAdV infection. CONCLUSION An outbreak of HAdV in HSCT recipients can be difficult to control. Although none of the patients had severe disease, the medical consequences were significant. It is possible that unidentified cases with mild symptoms may have caused continuous transmission at the unit. Regular testing of all patients several weeks beyond the last case identified may be an important measure to control transmission.
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Affiliation(s)
- L Swartling
- Division of Infectious Diseases, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - A Allard
- Department of Virology, Umeå University, Umeå, Sweden
| | - J Törlen
- Center for Allogeneic Stem Cell Transplantation, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - P Ljungman
- Center for Allogeneic Stem Cell Transplantation, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Department of Hematology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - J Mattsson
- Center for Allogeneic Stem Cell Transplantation, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - E Sparrelid
- Division of Infectious Diseases, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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41
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Ziros PG, Kokkinos PA, Allard A, Vantarakis A. Development and Evaluation of a Loop-Mediated Isothermal Amplification Assay for the Detection of Adenovirus 40 and 41. Food Environ Virol 2015; 7:276-285. [PMID: 25649029 DOI: 10.1007/s12560-015-9182-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 01/28/2015] [Indexed: 06/04/2023]
Abstract
Human adenoviruses (hAdVs) of subgroup F (enteric serotypes 40 and 41) display characteristic gut tropism, in vivo, fastidious growth characteristics in cell culture, and are estimated to be associated with 5-20% worldwide of acute gastroenteritis cases among infants and young children. Adequate hAdV gastroenteritis case management requires laboratory-based diagnosis. The present study aimed to the development and evaluation of a simple and cost-effective, one-step, single-tube adenovirus type 40/41 specific loop-mediated isothermal amplification (LAMP) assay for the detection of hAdV40/41 DNA in environmental and/or clinical samples, since no LAMP assay has previously been reported for the detection of these virus types. The assay targeted the hexon gene and had the advantages of being rapid, simple, specific, and sensitive. Results could be obtained within 60 min, under isothermal conditions at 69 °C. The detection limits for hAdV genomes were between 50 and 100 copies/reaction for hAdV40 and hAdV41, and no cross-reactions with other selected viruses, were found. The assay was evaluated with clinical as well as environmental samples. The developed assay is expected to provide a potential molecular tool in obtaining greater knowledge of the hAdV40/41 importance in the epidemiology and clinical manifestations of gastroenteritis.
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Affiliation(s)
- P G Ziros
- Environmental Microbiology Unit, Department of Public Health, School of Medicine, University of Patras, 26504, Rion, Greece
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42
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Zem G, Tosunyan O, Hambarsoomian A, Lim K, Khatiblou K, Niamat S, Choi E, Monroy C, Chavez M, Karaan N, Basmajian M, Kim S, Kurginyan A, Sorooshiani S, Manzo L, Bahri F, Holverson A, Chacon G, Allatabakhsh N, Irikyan C, Tortorice C, Balyan S, Amer N, Shtivelman S, Vahdati V, Kaur T, Danialian S, Allard A, Jorshari L, Kazmi N, Sarkissian N, Mkhitarian K, Chavez C, Havaei M, Adzhemian A, Takakura M, Huang Y, Haritounian A, Arakelian A, Bohorquez J, Asatryan M, Herrera Y, Mayorga L, Garcia A, Oppenheimer S. Hierarchy of Anti‐Clumping Salts. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.925.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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43
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Brooks AN, Reiss DJ, Allard A, Wu WJ, Salvanha DM, Plaisier CL, Chandrasekaran S, Pan M, Kaur A, Baliga NS. A system-level model for the microbial regulatory genome. Mol Syst Biol 2014; 10:740. [PMID: 25028489 PMCID: PMC4299497 DOI: 10.15252/msb.20145160] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Microbes can tailor transcriptional responses to diverse environmental challenges despite having streamlined genomes and a limited number of regulators. Here, we present data-driven models that capture the dynamic interplay of the environment and genome-encoded regulatory programs of two types of prokaryotes: Escherichia coli (a bacterium) and Halobacterium salinarum (an archaeon). The models reveal how the genome-wide distributions of cis-acting gene regulatory elements and the conditional influences of transcription factors at each of those elements encode programs for eliciting a wide array of environment-specific responses. We demonstrate how these programs partition transcriptional regulation of genes within regulons and operons to re-organize gene-gene functional associations in each environment. The models capture fitness-relevant co-regulation by different transcriptional control mechanisms acting across the entire genome, to define a generalized, system-level organizing principle for prokaryotic gene regulatory networks that goes well beyond existing paradigms of gene regulation. An online resource (http://egrin2.systemsbiology.net) has been developed to facilitate multiscale exploration of conditional gene regulation in the two prokaryotes.
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Affiliation(s)
- Aaron N Brooks
- Institute for Systems Biology, Seattle, WA, USA Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | | | - Antoine Allard
- Département de Physique, de Génie Physique et d'Optique, Université Laval, Québec, QC, Canada
| | - Wei-Ju Wu
- Institute for Systems Biology, Seattle, WA, USA
| | - Diego M Salvanha
- Institute for Systems Biology, Seattle, WA, USA LabPIB, Department of Computing and Mathematics FFCLRP-USP, University of Sao Paulo, Ribeirao Preto, Brazil
| | | | | | - Min Pan
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Nitin S Baliga
- Institute for Systems Biology, Seattle, WA, USA Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA Departments of Microbiology and Biology, University of Washington, Seattle, WA, USA Lawrence Berkeley National Laboratories, Berkeley, CA, USA
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44
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Allard A, Hébert-Dufresne L, Young JG, Dubé LJ. Coexistence of phases and the observability of random graphs. Phys Rev E Stat Nonlin Soft Matter Phys 2014; 89:022801. [PMID: 25353528 DOI: 10.1103/physreve.89.022801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Indexed: 06/04/2023]
Abstract
In a recent Letter, Yang et al. [Phys. Rev. Lett. 109, 258701 (2012)] introduced the concept of observability transitions: the percolationlike emergence of a macroscopic observable component in graphs in which the state of a fraction of the nodes, and of their first neighbors, is monitored. We show how their concept of depth-L percolation--where the state of nodes up to a distance L of monitored nodes is known--can be mapped onto multitype random graphs, and use this mapping to exactly solve the observability problem for arbitrary L. We then demonstrate a nontrivial coexistence of an observable and of a nonobservable extensive component. This coexistence suggests that monitoring a macroscopic portion of a graph does not prevent a macroscopic event to occur unbeknown to the observer. We also show that real complex systems behave quite differently with regard to observability depending on whether they are geographically constrained or not.
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Affiliation(s)
- Antoine Allard
- Département de physique, de génie physique et d'optique, Université Laval, Québec (Québec), Canada G1V 0A6
| | - Laurent Hébert-Dufresne
- Département de physique, de génie physique et d'optique, Université Laval, Québec (Québec), Canada G1V 0A6
| | - Jean-Gabriel Young
- Département de physique, de génie physique et d'optique, Université Laval, Québec (Québec), Canada G1V 0A6
| | - Louis J Dubé
- Département de physique, de génie physique et d'optique, Université Laval, Québec (Québec), Canada G1V 0A6
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Noël PA, Allard A, Hébert-Dufresne L, Marceau V, Dubé LJ. Spreading dynamics on complex networks: a general stochastic approach. J Math Biol 2013; 69:1627-60. [PMID: 24366372 DOI: 10.1007/s00285-013-0744-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Indexed: 11/30/2022]
Abstract
Dynamics on networks is considered from the perspective of Markov stochastic processes. We partially describe the state of the system through network motifs and infer any missing data using the available information. This versatile approach is especially well adapted for modelling spreading processes and/or population dynamics. In particular, the generality of our framework and the fact that its assumptions are explicitly stated suggests that it could be used as a common ground for comparing existing epidemics models too complex for direct comparison, such as agent-based computer simulations. We provide many examples for the special cases of susceptible-infectious-susceptible and susceptible-infectious-removed dynamics (e.g., epidemics propagation) and we observe multiple situations where accurate results may be obtained at low computational cost. Our perspective reveals a subtle balance between the complex requirements of a realistic model and its basic assumptions.
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Hébert-Dufresne L, Allard A, Young JG, Dubé LJ. Percolation on random networks with arbitrary k-core structure. Phys Rev E Stat Nonlin Soft Matter Phys 2013; 88:062820. [PMID: 24483524 DOI: 10.1103/physreve.88.062820] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Indexed: 06/03/2023]
Abstract
The k-core decomposition of a network has thus far mainly served as a powerful tool for the empirical study of complex networks. We now propose its explicit integration in a theoretical model. We introduce a hard-core random network (HRN) model that generates maximally random networks with arbitrary degree distribution and arbitrary k-core structure. We then solve exactly the bond percolation problem on the HRN model and produce fast and precise analytical estimates for the corresponding real networks. Extensive comparison with real databases reveals that our approach performs better than existing models, while requiring less input information.
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Affiliation(s)
- Laurent Hébert-Dufresne
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec (Québec), Canada G1V 0A6
| | - Antoine Allard
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec (Québec), Canada G1V 0A6
| | - Jean-Gabriel Young
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec (Québec), Canada G1V 0A6
| | - Louis J Dubé
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec (Québec), Canada G1V 0A6
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47
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Hébert-Dufresne L, Allard A, Young JG, Dubé LJ. Global efficiency of local immunization on complex networks. Sci Rep 2013; 3:2171. [PMID: 23842121 PMCID: PMC3707349 DOI: 10.1038/srep02171] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 06/18/2013] [Indexed: 11/29/2022] Open
Abstract
Epidemics occur in all shapes and forms: infections propagating in our sparse sexual networks, rumours and diseases spreading through our much denser social interactions, or viruses circulating on the Internet. With the advent of large databases and efficient analysis algorithms, these processes can be better predicted and controlled. In this study, we use different characteristics of network organization to identify the influential spreaders in 17 empirical networks of diverse nature using 2 epidemic models. We find that a judicious choice of local measures, based either on the network's connectivity at a microscopic scale or on its community structure at a mesoscopic scale, compares favorably to global measures, such as betweenness centrality, in terms of efficiency, practicality and robustness. We also develop an analytical framework that highlights a transition in the characteristic scale of different epidemic regimes. This allows to decide which local measure should govern immunization in a given scenario.
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Affiliation(s)
- Laurent Hébert-Dufresne
- Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec (Québec), Canada G1V 0A6
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Pawel JV, Gorbounova V, Reck M, Kowalski DM, Allard A, Chadjaa M, Rey A, Bennouna J, Grossi F. DISRUPT: A randomized phase 2 trial of ombrabulin (AVE8062) combined with a taxane-platinum regimen in the first-line treatment of metastatic non-small cell lung cancer (NSCLC). Pneumologie 2013. [DOI: 10.1055/s-0033-1334708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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von Pawel J, Gorbounova V, Reck M, Kowalski D, Allard A, Chadjaa M, Rey A, Bennouna J, Grossi F. Disrupt: A Randomized Phase 2 Trial of Ombrabulin (AVE8062) Combined with a Taxane-Platinum Regimen in the First-Line Treatment of Metastatic Non-Small Cell Lung Cancer (NSCLC). Ann Oncol 2012. [DOI: 10.1016/s0923-7534(20)33843-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Commin L, Buff S, Rosset E, Galet C, Allard A, Bruyere P, Joly T, Guérin P, Neto V. Follicle development in cryopreserved bitch ovarian tissue grafted to immunodeficient mouse. Reprod Fertil Dev 2012; 24:461-71. [PMID: 22401278 DOI: 10.1071/rd11166] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 07/22/2011] [Indexed: 01/03/2023] Open
Abstract
The present study evaluated: (1) in vivo follicular development in canine ovarian tissue after slow freezing and xenotransplantation; and (2) the use of erythropoietin (EPO) as an angiogenic factor to optimise the transplantation procedure. Frozen-thawed ovarian tissue from five bitches was grafted into severe combined immunodeficient (SCID) mice (n=47) treated with or without EPO (500 IU kg(-1), once daily for 3 days) (Groups A and B, respectively) and analysed after 0, 1, 8 or 16 weeks. Follicle grade, follicle density, follicle morphology and stromal cells density were assessed by histological analysis, whereas vascularisation of the graft was quantified by immunohistochemistry with anti-α-smooth muscle actin antibody. Despite a massive loss of follicles after grafting, secondary follicle density was higher at 8 and 16 weeks than at 1 week regardless of EPO treatment. EPO significantly improved early follicle morphology and stromal cell density after 8 weeks and blood vessel density at 16 weeks after transplantation (P<0.05). Intact secondary follicles with more than three granulosa cells layers were observed 16 weeks after transplantation. The results suggest that canine ovarian tissue can be successfully preserved by our slow-freezing protocol because the tissue showed follicular growth after xenotransplantation. EPO treatment did not lessen the massive loss of follicles after transplantation.
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Affiliation(s)
- L Commin
- Equipe Cryobio, Unité Propre de Soutien de Programme Interaction Cellule Environnement, VetAgroSup/ISARA Lyon, Université de Lyon, VetAgro Sup, 2011.03.101, UPSP I.C.E.-Equipe CRYOBIO, F-69280 Marcy l'Etoile, France.
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