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Traversa P, Ferraz de Arruda G, Vazquez A, Moreno Y. Robustness and Complexity of Directed and Weighted Metabolic Hypergraphs. ENTROPY (BASEL, SWITZERLAND) 2023; 25:1537. [PMID: 37998229 PMCID: PMC10670216 DOI: 10.3390/e25111537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/04/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023]
Abstract
Metabolic networks are probably among the most challenging and important biological networks. Their study provides insight into how biological pathways work and how robust a specific organism is against an environment or therapy. Here, we propose a directed hypergraph with edge-dependent vertex weight as a novel framework to represent metabolic networks. This hypergraph-based representation captures higher-order interactions among metabolites and reactions, as well as the directionalities of reactions and stoichiometric weights, preserving all essential information. Within this framework, we propose the communicability and the search information as metrics to quantify the robustness and complexity of directed hypergraphs. We explore the implications of network directionality on these measures and illustrate a practical example by applying them to a small-scale E. coli core model. Additionally, we compare the robustness and the complexity of 30 different models of metabolism, connecting structural and biological properties. Our findings show that antibiotic resistance is associated with high structural robustness, while the complexity can distinguish between eukaryotic and prokaryotic organisms.
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Affiliation(s)
- Pietro Traversa
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018 Zaragoza, Spain
- Department of Theoretical Physics, University of Zaragoza, 50018 Zaragoza, Spain
- CENTAI Institute, 10138 Turin, Italy
| | | | - Alexei Vazquez
- Nodes & Links Ltd., Salisbury House, Station Road, Cambridge CB1 2LA, UK
| | - Yamir Moreno
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018 Zaragoza, Spain
- Department of Theoretical Physics, University of Zaragoza, 50018 Zaragoza, Spain
- CENTAI Institute, 10138 Turin, Italy
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Multistability, intermittency, and hybrid transitions in social contagion models on hypergraphs. Nat Commun 2023; 14:1375. [PMID: 36914645 PMCID: PMC10011415 DOI: 10.1038/s41467-023-37118-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 02/28/2023] [Indexed: 03/16/2023] Open
Abstract
Although ubiquitous, interactions in groups of individuals are not yet thoroughly studied. Frequently, single groups are modeled as critical-mass dynamics, which is a widespread concept used not only by academics but also by politicians and the media. However, less explored questions are how a collection of groups will behave and how their intersection might change the dynamics. Here, we formulate this process as binary-state dynamics on hypergraphs. We showed that our model has a rich behavior beyond discontinuous transitions. Notably, we have multistability and intermittency. We demonstrated that this phenomenology could be associated with community structures, where we might have multistability or intermittency by controlling the number or size of bridges between communities. Furthermore, we provided evidence that the observed transitions are hybrid. Our findings open new paths for research, ranging from physics, on the formal calculation of quantities of interest, to social sciences, where new experiments can be designed.
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Andrighetto G, Vriens E. A research agenda for the study of social norm change. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20200411. [PMID: 35599567 PMCID: PMC9125228 DOI: 10.1098/rsta.2020.0411] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/23/2021] [Indexed: 05/02/2023]
Abstract
Social norms have been investigated across many disciplines for many years, but until recently, studies mainly provided indirect, implicit and correlational support for the role of social norms in driving behaviour. To understand how social norms, and in particular social norm change, can generate a large-scale behavioural change to deal with some of the most pressing challenges of our current societies, such as climate change and vaccine hesitancy, we discuss and review several recent advances in social norm research that enable a more precise underpinning of the role of social norms: how to identify their existence, how to establish their causal effect on behaviour and when norm change may pass tipping points. We advocate future research on social norms to study norm change through a mechanism-based approach that integrates experimental and computational methods in theory-driven, empirically calibrated agent-based models. As such, social norm research may move beyond unequivocal praising of social norms as the missing link between self-interested behaviour and observed cooperation or as the explanation for (the lack of) social tipping. It provides the toolkit to understand explicitly where, when and how social norms can be a solution to solve large-scale problems, but also to recognize their limits. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.
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Affiliation(s)
- Giulia Andrighetto
- Institute of Cognitive Sciences and Technologies, National research Council of Italy, via Palestro 32, 00185 Rome, Italy
- School of Education, Culture and Communication, Division of Mathematics and Physics, Malardalens University, 883, 721 23 Västerås, Sweden
- Institute for Future Studies, Holländargatan 13, 111 36 Stockholm, Sweden
| | - Eva Vriens
- Institute of Cognitive Sciences and Technologies, National research Council of Italy, via Palestro 32, 00185 Rome, Italy
- Institute for Future Studies, Holländargatan 13, 111 36 Stockholm, Sweden
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Lucchini L, Aiello LM, Alessandretti L, De Francisci Morales G, Starnini M, Baronchelli A. From Reddit to Wall Street: the role of committed minorities in financial collective action. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211488. [PMID: 35425623 PMCID: PMC8984357 DOI: 10.1098/rsos.211488] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 02/22/2022] [Indexed: 05/03/2023]
Abstract
In January 2021, retail investors coordinated on Reddit to target short-selling activity by hedge funds on GameStop shares, causing a surge in the share price and triggering significant losses for the funds involved. Such an effective collective action was unprecedented in finance, and its dynamics remain unclear. Here, we analyse Reddit and financial data and rationalize the events based on recent findings describing how a small fraction of committed individuals may trigger behavioural cascades. First, we operationalize the concept of individual commitment in financial discussions. Second, we show that the increase of commitment within Reddit pre-dated the initial surge in price. Third, we reveal that initial committed users occupied a central position in the network of Reddit conversations. Finally, we show that the social identity of the broader Reddit community grew as the collective action unfolded. These findings shed light on financial collective action, as several observers anticipate it will grow in importance.
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Affiliation(s)
- Lorenzo Lucchini
- Bocconi University, Milano 20100, Italy
- FBK—Fondazione Bruno Kessler, Trento 38123, Italy
| | | | | | | | | | - Andrea Baronchelli
- Department of Mathematics, City University of London, London EC1V 0HB, UK
- The Alan Turing Institute, British Library, 96 Euston Road, London NW1 2DB, UK
- UCL Centre for Blockchain Technologies, University College London, London, UK
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Gowsalya K, Yasothamani V, Vivek R. Emerging indocyanine green-integrated nanocarriers for multimodal cancer therapy: a review. NANOSCALE ADVANCES 2021; 3:3332-3352. [PMID: 36133722 PMCID: PMC9418715 DOI: 10.1039/d1na00059d] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/03/2021] [Indexed: 05/17/2023]
Abstract
Nanotechnology is a branch of science dealing with the development of new types of nanomaterials by several methods. In the biomedical field, nanotechnology is widely used in the form of nanotherapeutics. Therefore, the current biomedical research pays much attention to nanotechnology for the development of efficient cancer treatment. Indocyanine green (ICG) is a near-infrared tricarbocyanine dye approved by the Food and Drug Administration (FDA) for human clinical use. ICG is a biologically safe photosensitizer and it can kill tumor cells by producing singlet oxygen species and photothermal heat upon NIR irradiation. ICG has some limitations such as easy aggregation, rapid aqueous degradation, and a short half-life. To address these limitations, ICG is further formulated with nanoparticles. Therefore, ICG is integrated with organic nanomaterials (polymers, micelles, liposomes, dendrimers and protein), inorganic nanomaterials (magnetic, gold, mesoporous, calcium, and LDH based), and hybrid nanomaterials. The combination of ICG with nanomaterials provides highly efficient therapeutic effects. Nowadays, ICG is used for various biomedical applications, especially in cancer therapeutics. In this review, we mainly focus on ICG-based combined cancer nanotherapeutics for advanced cancer treatment.
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Affiliation(s)
- Karunanidhi Gowsalya
- Bio-Nano Therapeutics Research Laboratory, Cancer Research Program (CRP), School of Life Sciences, Department of Zoology, Bharathiar University Coimbatore-641 046 India
| | - Vellingiri Yasothamani
- Bio-Nano Therapeutics Research Laboratory, Cancer Research Program (CRP), School of Life Sciences, Department of Zoology, Bharathiar University Coimbatore-641 046 India
| | - Raju Vivek
- Bio-Nano Therapeutics Research Laboratory, Cancer Research Program (CRP), School of Life Sciences, Department of Zoology, Bharathiar University Coimbatore-641 046 India
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Marchetti G, Patriarca M, Heinsalu E. A bird's-eye view of naming game dynamics: From trait competition to Bayesian inference. CHAOS (WOODBURY, N.Y.) 2020; 30:063119. [PMID: 32611080 DOI: 10.1063/5.0009569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/15/2020] [Indexed: 06/11/2023]
Abstract
The present contribution reviews a set of different versions of the basic naming game model, differing in the underlying topology or in the mechanisms regulating the interactions between agents. We include also a Bayesian naming game model recently introduced, which merges the social dynamics of the basic naming game model with the Bayesian learning framework introduced by Tenenbaum and co-workers. The latter model goes beyond the fixed nature of names and concepts of standard semiotic dynamics models and the corresponding one-shot learning process by describing dynamically how agents can generalize a concept from a few examples, according to principles of Bayesian inference.
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Affiliation(s)
- Gionni Marchetti
- National Institute of Chemical Physics and Biophysics, Rävala 10, 10143 Tallinn, Estonia
| | - Marco Patriarca
- National Institute of Chemical Physics and Biophysics, Rävala 10, 10143 Tallinn, Estonia
| | - Els Heinsalu
- National Institute of Chemical Physics and Biophysics, Rävala 10, 10143 Tallinn, Estonia
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Abstract
Our understanding of the dynamics of complex networked systems has increased significantly in the last two decades. However, most of our knowledge is built upon assuming pairwise relations among the system's components. This is often an oversimplification, for instance, in social interactions that occur frequently within groups. To overcome this limitation, here we study the dynamics of social contagion on hypergraphs. We develop an analytical framework and provide numerical results for arbitrary hypergraphs, which we also support with Monte Carlo simulations. Our analyses show that the model has a vast parameter space, with first- and second-order transitions, bistability, and hysteresis. Phenomenologically, we also extend the concept of latent heat to social contexts, which might help understanding oscillatory social behaviors. Our work unfolds the research line of higher-order models and the analytical treatment of hypergraphs, posing new questions and paving the way for modeling dynamical processes on higher-order structures.
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Abstract
What happens when a new social convention replaces an old one? While the possible forces favoring norm change-such as institutions or committed activists-have been identified for a long time, little is known about how a population adopts a new convention, due to the difficulties of finding representative data. Here, we address this issue by looking at changes that occurred to 2,541 orthographic and lexical norms in English and Spanish through the analysis of a large corpora of books published between the years 1800 and 2008. We detect three markedly distinct patterns in the data, depending on whether the behavioral change results from the action of a formal institution, an informal authority, or a spontaneous process of unregulated evolution. We propose a simple evolutionary model able to capture all of the observed behaviors, and we show that it reproduces quantitatively the empirical data. This work identifies general mechanisms of norm change, and we anticipate that it will be of interest to researchers investigating the cultural evolution of language and, more broadly, human collective behavior.
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Abstract
The origin of population-scale coordination has puzzled philosophers and scientists for centuries. Recently, game theory, evolutionary approaches and complex systems science have provided quantitative insights on the mechanisms of social consensus. However, the literature is vast and widely scattered across fields, making it hard for the single researcher to navigate it. This short review aims to provide a compact overview of the main dimensions over which the debate has unfolded and to discuss some representative examples. It focuses on those situations in which consensus emerges 'spontaneously' in the absence of centralized institutions and covers topics that include the macroscopic consequences of the different microscopic rules of behavioural contagion, the role of social networks and the mechanisms that prevent the formation of a consensus or alter it after it has emerged. Special attention is devoted to the recent wave of experiments on the emergence of consensus in social systems.
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