Physics of Life Reviews最新文献

{"title":"Data-driven mathematical modeling approaches for COVID-19: A survey","authors":"Jacques Demongeot ,&nbsp;Pierre Magal","doi":"10.1016/j.plrev.2024.08.004","DOIUrl":"10.1016/j.plrev.2024.08.004","url":null,"abstract":"<div><p>In this review, we successively present the methods for phenomenological modeling of the evolution of reported and unreported cases of COVID-19, both in the exponential phase of growth and then in a complete epidemic wave. After the case of an isolated wave, we present the modeling of several successive waves separated by endemic stationary periods. Then, we treat the case of multi-compartmental models without or with age structure. Eventually, we review the literature, based on 260 articles selected in 11 sections, ranging from the medical survey of hospital cases to forecasting the dynamics of new cases in the general population. This review favors the phenomenological approach over the mechanistic approach in the choice of references and provides simulations of the evolution of the number of observed cases of COVID-19 for 10 states (California, China, France, India, Israel, Japan, New York, Peru, Spain and United Kingdom).</p></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"50 ","pages":"Pages 166-208"},"PeriodicalIF":13.7,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1571064524000952/pdfft?md5=f967bce35df14fa525ec4cc5f498e8f3&pid=1-s2.0-S1571064524000952-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141979564","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Topological change of soil microbiota networks for forest resilience under global warming","authors":"Huiying Gong ,&nbsp;Hongxing Wang ,&nbsp;Yu Wang ,&nbsp;Shen Zhang ,&nbsp;Xiang Liu ,&nbsp;Jincan Che ,&nbsp;Shuang Wu ,&nbsp;Jie Wu ,&nbsp;Xiaomei Sun ,&nbsp;Shougong Zhang ,&nbsp;Shing-Tung Yau ,&nbsp;Rongling Wu","doi":"10.1016/j.plrev.2024.08.001","DOIUrl":"10.1016/j.plrev.2024.08.001","url":null,"abstract":"<div><p>Forest management by thinning can mitigate the detrimental impact of increasing drought caused by global warming. Growing evidence shows that the soil microbiota can coordinate the dynamic relationship between forest functions and drought intensity, but how they function as a cohesive whole remains elusive. We outline a statistical topology model to chart the roadmap of how each microbe acts and interacts with every other microbe to shape the dynamic changes of microbial communities under forest management. To demonstrate its utility, we analyze a soil microbiota data collected from a two-way longitudinal factorial experiment involving three stand densities and three levels of rainfall over a growing season in artificial plantations of a forest tree – larix (<em>Larix kaempferi</em>). We reconstruct the most sophisticated soil microbiota networks that code maximally informative microbial interactions and trace their dynamic trajectories across time, space, and environmental signals. By integrating GLMY homology theory, we dissect the topological architecture of these so-called omnidirectional networks and identify key microbial interaction pathways that play a pivotal role in mediating the structure and function of soil microbial communities. The statistical topological model described provides a systems tool for studying how microbial community assembly alters its structure, function and evolution under climate change.</p></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"50 ","pages":"Pages 228-251"},"PeriodicalIF":13.7,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142044526","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Parrondo's paradox reveals counterintuitive wins in biology and decision making in society","authors":"Tao Wen ,&nbsp;Kang Hao Cheong","doi":"10.1016/j.plrev.2024.08.002","DOIUrl":"10.1016/j.plrev.2024.08.002","url":null,"abstract":"<div><p>Parrondo's paradox refers to the paradoxical phenomenon of combining two losing strategies in a certain manner to obtain a winning outcome. It has been applied to uncover unexpected outcomes across various disciplines, particularly at different spatiotemporal scales within ecosystems. In this article, we provide a comprehensive review of recent developments in Parrondo's paradox within the interdisciplinary realm of the physics of life, focusing on its significant applications across biology and the broader life sciences. Specifically, we examine its relevance from genetic pathways and phenotypic regulation, to intercellular interaction within multicellular organisms, and finally to the competition between populations and species in ecosystems. This phenomenon, spanning multiple biological domains and scales, enhances our understanding of the unified characteristics of life and reveals that adaptability in a drastically changing environment, rather than the inherent excellence of a trait, underpins survival in the process of evolution. We conclude by summarizing our findings and discussing future research directions that hold promise for advancing the field.</p></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"51 ","pages":"Pages 33-59"},"PeriodicalIF":13.7,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142243904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The neural correlates of consciousness studies and the mystery of the human mind-a commentary on \"Beyond task response - Pre-stimulus activity modulates contents of consciousness\" by G. Northoff, F. Zilio & J. Zhang","authors":"Karl Erik Sandsten ,&nbsp;Josef Parnas","doi":"10.1016/j.plrev.2024.07.009","DOIUrl":"10.1016/j.plrev.2024.07.009","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"50 ","pages":"Pages 209-210"},"PeriodicalIF":13.7,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987114","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Language follows a distinct mode of extra-genomic evolution","authors":"Balthasar Bickel ,&nbsp;Anne-Lise Giraud ,&nbsp;Klaus Zuberbühler ,&nbsp;Carel P. van Schaik","doi":"10.1016/j.plrev.2024.08.003","DOIUrl":"10.1016/j.plrev.2024.08.003","url":null,"abstract":"<div><p>As one of the most specific, yet most diverse of human behaviors, language is shaped by both genomic and extra-genomic evolution. Sharing methods and models between these modes of evolution has significantly advanced our understanding of language and inspired generalized theories of its evolution. Progress is hampered, however, by the fact that the extra-genomic evolution of languages, i.e. linguistic evolution, maps only partially to other forms of evolution. Contrasting it with the biological evolution of eukaryotes and the cultural evolution of technology as the best understood models, we show that linguistic evolution is special by yielding a stationary dynamic rather than stable solutions, and that this dynamic allows the use of language change for social differentiation while maintaining its global adaptiveness. Linguistic evolution furthermore differs from technological evolution by requiring vertical transmission, allowing the reconstruction of phylogenies; and it differs from eukaryotic biological evolution by foregoing a genotype vs phenotype distinction, allowing deliberate and biased change. Recognising these differences will improve our empirical tools and open new avenues for analyzing how linguistic, cultural, and biological evolution interacted with each other when language emerged in the hominin lineage. Importantly, our framework will help to cope with unprecedented scientific and ethical challenges that presently arise from how rapid cultural evolution impacts language, most urgently from interventional clinical tools for language disorders, potential epigenetic effects of technology on language, artificial intelligence and linguistic communicators, and global losses of linguistic diversity and identity. Beyond language, the distinctions made here allow identifying variation in other forms of biological and cultural evolution, developing new perspectives for empirical research.</p></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"50 ","pages":"Pages 211-225"},"PeriodicalIF":13.7,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1571064524000939/pdfft?md5=b509f3258595a0bdab942a98d2a9941e&pid=1-s2.0-S1571064524000939-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141994989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The affective grounds of the mind. The Affective Pertinentization (APER) model","authors":"Sergio Salvatore ,&nbsp;Arianna Palmieri ,&nbsp;Raffaele De Luca Picione ,&nbsp;Vincenzo Bochicchio ,&nbsp;Matteo Reho ,&nbsp;Maria Rita Serio ,&nbsp;Giampaolo Salvatore","doi":"10.1016/j.plrev.2024.07.008","DOIUrl":"10.1016/j.plrev.2024.07.008","url":null,"abstract":"<div><p>The paper presents the Affective Pertinentization model (APER), a theory of the affect and its role it plays in meaning-making. APER views the affect as the basic form of making sense of reality. It consists of a global, bipolar pattern of neurophysiological activity through which the organism maps the instant-by-instant variation of its environment. Such a pattern of neuropsychological activity is constituted by a plurality of bipolar affective dimensions, each of which maps a component of the environmental variability. The affect has a pluri-componential structure defining a multidimensional affective landscape that foregrounds (i.e., makes pertinent) a certain pattern of facets of the environment (e.g., its pleasantness/unpleasantness) relevant to survival, while backgrounding the others. Doing so, the affect grounds the following cognitive processes. Accordingly, meaning-making can be modeled as a function of the dimensionality of the affective landscape. The greater the dimensionality of the affective landscape, the more differentiated the system of meaning is.</p><p>Following a brief review of current theories pertaining to the affect, the paper proceeds discussing the APER's core tenets – the multidimensional view of the affect, its semiotic function, and the concepts of Affective Landscape and Phase Space of Meaning. The paper then proceeds deepening the relationship between the APER model and other theories, highlighting how the APER succeeds in framing original conceptualizations of several challenging issues – the intertwinement between affect and sensory modalities, the manner in which the mind constitutes the content of the experience, the determinants of psychopathology, the intertwinement of mind and culture, and the spreading of affective forms of thinking and behaving in society. Finally, the unsolved issues and future developments of the model are briefly envisaged.</p></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"50 ","pages":"Pages 143-165"},"PeriodicalIF":13.7,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141900439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Homo erectus’ slowly broadening Zone of Bounded Surprisals opened the way to technological culture","authors":"Héctor M. Manrique ,&nbsp;Karl J. Friston ,&nbsp;Michael J. Walker","doi":"10.1016/j.plrev.2024.07.007","DOIUrl":"10.1016/j.plrev.2024.07.007","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"50 ","pages":"Pages 137-142"},"PeriodicalIF":13.7,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141847356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prestimulus alpha phase, not only power, modulates conscious perception. Comment on “Beyond task response—Pre-stimulus activity modulates contents of consciousness” by G. Northoff, F. Zilio & J. Zhang","authors":"Kristina Krasich ,&nbsp;Marty G. Woldorff ,&nbsp;Felipe De Brigard ,&nbsp;Walter Sinnott-Armstrong ,&nbsp;Liad Mudrik","doi":"10.1016/j.plrev.2024.07.006","DOIUrl":"10.1016/j.plrev.2024.07.006","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"50 ","pages":"Pages 123-125"},"PeriodicalIF":13.7,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141786948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Social pain. Comment on ‘Environmental factors and their impact on chronic pain development and maintenance’ by Morena Brazil Sant'Anna, Louise Faggionato Kimura, Willians Fernando Vieira, Vanessa Olzon Zambelli, Leonardo Santana Novaes, Natália Gabriele Hösch, Gisele Picolo","authors":"Sarah F. Allen ,&nbsp;Christina M. van der Feltz-Cornelis","doi":"10.1016/j.plrev.2024.07.004","DOIUrl":"10.1016/j.plrev.2024.07.004","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"50 ","pages":"Pages 120-122"},"PeriodicalIF":13.7,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141699842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Heritability of white matter in twins: A diffusion neuroimaging review","authors":"Giovanni Videtta ,&nbsp;Chiara Colli ,&nbsp;Letizia Squarcina ,&nbsp;Corrado Fagnani ,&nbsp;Emanuela Medda ,&nbsp;Paolo Brambilla ,&nbsp;Giuseppe Delvecchio","doi":"10.1016/j.plrev.2024.07.003","DOIUrl":"10.1016/j.plrev.2024.07.003","url":null,"abstract":"<div><p>Diffusion neuroimaging has emerged as an essential non-invasive technique to explore in vivo microstructural characteristics of white matter (WM), whose integrity allows complex behaviors and cognitive abilities. Studying the factors contributing to inter-individual variability in WM microstructure can provide valuable insight into structural and functional differences of brain among individuals. Genetic influence on this variation has been largely investigated in twin studies employing different measures derived from diffusion neuroimaging. In this context, we performed a comprehensive literature search across PubMed, Scopus and Web of Science of original twin studies focused on the heritability of WM. Overall, our results highlighted a consistent heritability of diffusion indices (i.e., fractional anisotropy, mean, axial and radial diffusivity), and network topology among twins. The genetic influence resulted prominent in frontal and occipital regions, in the limbic system, and in commissural fibers. To enhance the understanding of genetic influence on WM microstructure further studies in less heterogeneous experimental settings, encompassing all diffusion indices, are warranted.</p></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"50 ","pages":"Pages 126-136"},"PeriodicalIF":13.7,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141696442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}