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Expanding the horizon of interaction modeling in complex systems comment on “Topological change of soil microbiota networks for forest resilience under global warming” by Huiying Gong et al.
IF 13.7 1区 生物学
Physics of Life Reviews Pub Date : 2025-03-25 DOI: 10.1016/j.plrev.2025.03.016
Xiaoya Fan, Zhong Wang
{"title":"Expanding the horizon of interaction modeling in complex systems comment on “Topological change of soil microbiota networks for forest resilience under global warming” by Huiying Gong et al.","authors":"Xiaoya Fan, Zhong Wang","doi":"10.1016/j.plrev.2025.03.016","DOIUrl":"10.1016/j.plrev.2025.03.016","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"53 ","pages":"Pages 279-280"},"PeriodicalIF":13.7,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143747946","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}
引用次数: 0
Causal cognition in the wild: Is disentanglement really necessary? Comment on “disentangled representations for causal cognition” by F. Torresan & M. Baltieri
IF 13.7 1区 生物学
Physics of Life Reviews Pub Date : 2025-03-24 DOI: 10.1016/j.plrev.2025.03.021
Anna Finke , Vicente Raja
{"title":"Causal cognition in the wild: Is disentanglement really necessary? Comment on “disentangled representations for causal cognition” by F. Torresan & M. Baltieri","authors":"Anna Finke , Vicente Raja","doi":"10.1016/j.plrev.2025.03.021","DOIUrl":"10.1016/j.plrev.2025.03.021","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"53 ","pages":"Pages 260-261"},"PeriodicalIF":13.7,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143737885","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}
引用次数: 0
Unlocking the brain's code: The crucial role of post-translational modifications in neurodevelopment and neurological function
IF 13.7 1区 生物学
Physics of Life Reviews Pub Date : 2025-03-23 DOI: 10.1016/j.plrev.2025.03.011
Peng Ye , Wangzheqi Zhang , Yan Liao , Ting Hu , Chun-Lei Jiang
{"title":"Unlocking the brain's code: The crucial role of post-translational modifications in neurodevelopment and neurological function","authors":"Peng Ye ,&nbsp;Wangzheqi Zhang ,&nbsp;Yan Liao ,&nbsp;Ting Hu ,&nbsp;Chun-Lei Jiang","doi":"10.1016/j.plrev.2025.03.011","DOIUrl":"10.1016/j.plrev.2025.03.011","url":null,"abstract":"<div><div>Post-translational modifications (PTMs) represent a crucial regulatory mechanism in the brain, influencing various processes, including neurodevelopment and neurological function. This review discusses the effects of PTMs, such as phosphorylation, ubiquitination, acetylation, and glycosylation, on neurodevelopment and central nervous system functionality. Although neurodevelopmental processes linked to PTMs are complex, proteins frequently converge within shared pathways. These pathways encompass neurodevelopmental processes, signaling mechanisms, neuronal migration, and synaptic connection formation, where PTMs act as dynamic regulators, ensuring the precise execution of brain functions. A detailed investigation of the fundamental mechanisms governing these pathways will contribute to a deeper understanding of nervous system functions and facilitate the identification of potential therapeutic targets. A thorough examination of the PTM landscape holds significant potential, not only in advancing knowledge but also in developing treatments for various neurological disorders.</div></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"53 ","pages":"Pages 187-214"},"PeriodicalIF":13.7,"publicationDate":"2025-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143679140","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}
引用次数: 0
A new approach to quantify information in real-life, complex neuroscience processes. Comment on “Kinematic coding: Measuring information in naturalistic behavior” by Becchio, Pullar, Scaliti and Panzeri
IF 13.7 1区 生物学
Physics of Life Reviews Pub Date : 2025-03-21 DOI: 10.1016/j.plrev.2025.03.014
Ana Sanchez Jimenez , Enrique Fernández Serra , Rodrigo Quian Quiroga
{"title":"A new approach to quantify information in real-life, complex neuroscience processes. Comment on “Kinematic coding: Measuring information in naturalistic behavior” by Becchio, Pullar, Scaliti and Panzeri","authors":"Ana Sanchez Jimenez ,&nbsp;Enrique Fernández Serra ,&nbsp;Rodrigo Quian Quiroga","doi":"10.1016/j.plrev.2025.03.014","DOIUrl":"10.1016/j.plrev.2025.03.014","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"53 ","pages":"Pages 236-238"},"PeriodicalIF":13.7,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143705381","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}
引用次数: 0
Informational embodiment: Computational role of information structure in codes and robots
IF 13.7 1区 生物学
Physics of Life Reviews Pub Date : 2025-03-21 DOI: 10.1016/j.plrev.2025.03.018
Alexandre Pitti , Max Austin , Kohei Nakajima , Yasuo Kuniyoshi
{"title":"Informational embodiment: Computational role of information structure in codes and robots","authors":"Alexandre Pitti ,&nbsp;Max Austin ,&nbsp;Kohei Nakajima ,&nbsp;Yasuo Kuniyoshi","doi":"10.1016/j.plrev.2025.03.018","DOIUrl":"10.1016/j.plrev.2025.03.018","url":null,"abstract":"<div><div>The body morphology plays an important role in the way information is perceived and processed by an agent. We address an information theory (IT) account on how the precision of sensors, the accuracy of motors, their placement, the body geometry, shape the information structure in robots and computational codes. As an original idea, we envision the robot's body as a physical communication channel through which information is conveyed, in and out, despite intrinsic noise and material limitations. Following this, entropy, a measure of information and uncertainty, can be used to maximize the efficiency of robot design and of algorithmic codes <em>per se</em>. This is known as the principle of Entropy Maximization (PEM) introduced in biology by Barlow in 1969. The Shannon's source coding theorem provides then a framework to compare different types of bodies in terms of sensorimotor information. In line with the PEM, we introduce a special class of efficient codes used in IT that reached the Shannon limits in terms of information capacity for error correction and robustness against noise, and parsimony. These efficient codes, which exploit insightfully quantization and randomness, permit to deal with uncertainty, redundancy and compacity. These features can be used for perception and control in intelligent systems. In various examples and closing discussions, we reflect on the broader implications of our framework that we called <em>Informational Embodiment</em> to motor theory and bio-inspired robotics, touching upon concepts like motor synergies, reservoir computing, and morphological computation. These insights can contribute to a deeper understanding of how information theory intersects with the embodiment of intelligence in both natural and artificial systems.</div></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"53 ","pages":"Pages 262-276"},"PeriodicalIF":13.7,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143747944","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}
引用次数: 0
A kinetic theory approach for modeling Alzheimer's disease: Insights and challenges
IF 13.7 1区 生物学
Physics of Life Reviews Pub Date : 2025-03-21 DOI: 10.1016/j.plrev.2025.03.019
Nouamane Bakhdil
{"title":"A kinetic theory approach for modeling Alzheimer's disease: Insights and challenges","authors":"Nouamane Bakhdil","doi":"10.1016/j.plrev.2025.03.019","DOIUrl":"10.1016/j.plrev.2025.03.019","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"53 ","pages":"Pages 221-222"},"PeriodicalIF":13.7,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143679137","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}
引用次数: 0
Sirtuins as modulators of infection outcomes in the battle of host-pathogen dynamics
IF 13.7 1区 生物学
Physics of Life Reviews Pub Date : 2025-03-21 DOI: 10.1016/j.plrev.2025.03.020
Dipasree Hajra, Dipshikha Chakravortty
{"title":"Sirtuins as modulators of infection outcomes in the battle of host-pathogen dynamics","authors":"Dipasree Hajra,&nbsp;Dipshikha Chakravortty","doi":"10.1016/j.plrev.2025.03.020","DOIUrl":"10.1016/j.plrev.2025.03.020","url":null,"abstract":"<div><div>Sirtuins's central role in governing metabolic processes has been known for decades. However, over the past two decades, sirtuin functions have been linked to immune regulation and immunity. Sirtuins are NAD+ dependent protein deacylases involved in the regulation of several important biological processes ranging from energy homeostasis, metabolism, aging, apoptosis, autophagy, immunity, adipocyte, and muscle differentiation. Here, in this review, we discuss the role of sirtuins in several infectious diseases including viral, bacterial, and protozoan infections with detailed emphasis on bacterial-host interactions. We have aimed to explore both host and bacterial sirtuin functions contributing to the infection progression, host responses and their influence on the everlasting host-pathogen tug-of-war. In order to manipulate host pathways, pathogens such as intracellular bacteria have evolved parallelly and harbor bacterial sirtuins. The recent discoveries of bacterial sirtuins influencing the host-pathogen interaction outcomes pave the way for the discovery of potential therapeutic targets<strong>.</strong></div></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"53 ","pages":"Pages 225-235"},"PeriodicalIF":13.7,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143705380","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}
引用次数: 0
An AI researchers' perspective: At the crossroad of LLMs, agent-based modeling, and complex systems
IF 13.7 1区 生物学
Physics of Life Reviews Pub Date : 2025-03-20 DOI: 10.1016/j.plrev.2025.03.015
Siyue Ren , Ziyue Gan , Zhenfei Yin, Jing Shao, Shuyue Hu
{"title":"An AI researchers' perspective: At the crossroad of LLMs, agent-based modeling, and complex systems","authors":"Siyue Ren ,&nbsp;Ziyue Gan ,&nbsp;Zhenfei Yin,&nbsp;Jing Shao,&nbsp;Shuyue Hu","doi":"10.1016/j.plrev.2025.03.015","DOIUrl":"10.1016/j.plrev.2025.03.015","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"53 ","pages":"Pages 215-217"},"PeriodicalIF":13.7,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143679135","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}
引用次数: 0
Inner speech is not a simulation of language but an act of speaking: Comment on “The Sound of Thought: Form Matters – The Prosody of Inner Speech” by Hamutal Kreiner, Zohar Eviatar
IF 13.7 1区 生物学
Physics of Life Reviews Pub Date : 2025-03-19 DOI: 10.1016/j.plrev.2025.03.013
Chiara De Livio , Anna M. Borghi , Charles Fernyhough
{"title":"Inner speech is not a simulation of language but an act of speaking: Comment on “The Sound of Thought: Form Matters – The Prosody of Inner Speech” by Hamutal Kreiner, Zohar Eviatar","authors":"Chiara De Livio ,&nbsp;Anna M. Borghi ,&nbsp;Charles Fernyhough","doi":"10.1016/j.plrev.2025.03.013","DOIUrl":"10.1016/j.plrev.2025.03.013","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"53 ","pages":"Pages 218-220"},"PeriodicalIF":13.7,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143679136","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}
引用次数: 0
Goals for kinematic coding: Insights from the posture-based motion planning perspective
IF 13.7 1区 生物学
Physics of Life Reviews Pub Date : 2025-03-19 DOI: 10.1016/j.plrev.2025.03.017
Aviad Ozana , Frouke Hermens , David A. Rosenbaum
{"title":"Goals for kinematic coding: Insights from the posture-based motion planning perspective","authors":"Aviad Ozana ,&nbsp;Frouke Hermens ,&nbsp;David A. Rosenbaum","doi":"10.1016/j.plrev.2025.03.017","DOIUrl":"10.1016/j.plrev.2025.03.017","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"53 ","pages":"Pages 277-278"},"PeriodicalIF":13.7,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143747945","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}
引用次数: 0
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