Journal of The Royal Society Interface最新文献

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Viscoelastic differences between isolated and live MCF7 cancer cell nuclei resolved with AFM microrheology. 用AFM微流变学分析分离和活MCF7癌细胞细胞核的粘弹性差异。
IF 3.5 2区 综合性期刊
Journal of The Royal Society Interface Pub Date : 2025-06-01 Epub Date: 2025-06-18 DOI: 10.1098/rsif.2024.0885
Ellen Juel Pørtner, Anna Mularski, Tobias William Jarrett, Stine Lauritzen Sønder, Jesper Nylandsted, Adam Cohen Simonsen
{"title":"Viscoelastic differences between isolated and live MCF7 cancer cell nuclei resolved with AFM microrheology.","authors":"Ellen Juel Pørtner, Anna Mularski, Tobias William Jarrett, Stine Lauritzen Sønder, Jesper Nylandsted, Adam Cohen Simonsen","doi":"10.1098/rsif.2024.0885","DOIUrl":"10.1098/rsif.2024.0885","url":null,"abstract":"<p><p>Cell nuclei are commonly isolated for mechanobiology studies although isolated nuclei may display viscoelastic properties differing from those of live cells. Nuclear mechanics is generally dependent on the time scale of the applied load and cannot accurately be assessed by a simple elasticity parameter. Active microrheology with an atomic force microscope (AFMMR) is a versatile tool for probing nuclear mechanics and we employ the technique for exploring isolated and live-cell nuclei in MCF7 cells, including the significance of actin depolymerization. We successfully validate the method using polyacrylamide hydrogels with correction for cantilever drag in the fluid. The AFMMR results reveal that isolated and live-cell nuclei are equivalent to within a scaling factor, in their frequency-dependent modulus, with isolated nuclei being softer. The loss tangent reveals a transition from solid- to liquid-like behaviour occurring at higher frequency in isolated than in live-cell nuclei. Viscoelastic modelling using the Jeffreys model describes the frequency-dependent modulus of all measured nuclei. Model parameters display sensitivity to nuclei isolation and to actin depolymerization in live cells. Sections of the Jeffreys circuit can potentially be assigned to internal and external nucleus structures, respectively, thereby establishing a minimal mechanistic framework for interpreting microrheology data on cell nuclei.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 227","pages":"20240885"},"PeriodicalIF":3.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12173521/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144317252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Golden eagles regularly use gravity waves to soar: new insights from high-resolution weather data. 金雕经常利用重力波翱翔:来自高分辨率天气数据的新见解。
IF 3.7 2区 综合性期刊
Journal of The Royal Society Interface Pub Date : 2025-06-01 Epub Date: 2025-06-04 DOI: 10.1098/rsif.2024.0891
Tom Carrard, Elham Nourani, Lukas Jansing, Tim Zimmermann, Petra Sumasgutner, Matthias Tschumi, David Jenny, Martin Wikelski, Kamran Safi, Michael Sprenger, Martina Scacco
{"title":"Golden eagles regularly use gravity waves to soar: new insights from high-resolution weather data.","authors":"Tom Carrard, Elham Nourani, Lukas Jansing, Tim Zimmermann, Petra Sumasgutner, Matthias Tschumi, David Jenny, Martin Wikelski, Kamran Safi, Michael Sprenger, Martina Scacco","doi":"10.1098/rsif.2024.0891","DOIUrl":"10.1098/rsif.2024.0891","url":null,"abstract":"<p><p>Soaring flight allows birds to reduce the metabolic cost of flight by harnessing energy from the atmosphere. The study of soaring behaviour has been significantly constrained by the low resolution of available atmospheric data, limiting our ability to accurately describe the conditions enabling soaring and its adaptability to different updraught types. For instance, while the use of thermals and orographic lifting updraughts are well described in the literature, the role of gravity waves has remained largely unexplored. Advancements in high-resolution atmospheric modelling, with hourly output available at the kilometre-scale grid spacing, offer new opportunities to investigate the flexibility of soaring flight in response to complex atmospheric dynamics, including gravity waves. In this study, we used a combination of a high-resolution atmospheric analysis and high-resolution global positioning system tracking data to characterize the updraught sources used by golden eagles, <i>Aquila chrysaetos</i>, in the European Alps. Our findings reveal that golden eagles repeatedly used gravity waves, with at least 19% of the inspected soaring segments involving this updraught source. Thermals remained the primary energy source for soaring, but during winter, when thermals were more scarce, the quasi-totality of soaring events were powered by gravity waves or orographic lifting. Our results provide a new perspective on the environmental energy available to soaring birds and on landscape connectivity in topographically complex regions.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 227","pages":"20240891"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12134756/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Run-and-tumble dynamics of Escherichia coli is governed by its mechanical properties. 大肠杆菌的奔跑和翻滚动力学是由其机械特性决定的。
IF 3.7 2区 综合性期刊
Journal of The Royal Society Interface Pub Date : 2025-06-01 Epub Date: 2025-06-18 DOI: 10.1098/rsif.2025.0035
Bohan Wu-Zhang, Peixin Zhang, Renaud Baillou, Anke Lindner, Eric Clement, Gerhard Gompper, Dmitry A Fedosov
{"title":"Run-and-tumble dynamics of <i>Escherichia coli</i> is governed by its mechanical properties.","authors":"Bohan Wu-Zhang, Peixin Zhang, Renaud Baillou, Anke Lindner, Eric Clement, Gerhard Gompper, Dmitry A Fedosov","doi":"10.1098/rsif.2025.0035","DOIUrl":"10.1098/rsif.2025.0035","url":null,"abstract":"<p><p>The huge variety of microorganisms motivates fundamental studies of their behaviour with the possibility to construct artificial mimics. A prominent example is the <i>Escherichia coli</i> bacterium, which employs several helical flagella to exhibit a motility pattern that alternates between run (directional swimming) and tumble (change in swimming direction) phases. We establish a detailed <i>E. coli</i> model, coupled to fluid flow described by the dissipative particle dynamics method, and investigate its run-and-tumble behaviour. Different <i>E. coli</i> characteristics, including body geometry, flagella bending rigidity, the number of flagella and their arrangement at the body, are considered. Experiments are also performed to directly compare with the model. Interestingly, in both simulations and experiments, the swimming velocity is nearly independent of the number of flagella. The rigidity of a hook (the short part of a flagellum that connects it directly to the motor), polymorphic transformation (spontaneous change in flagella helicity) of flagella and their arrangement at the body surface strongly influence the run-and-tumble behaviour. Mesoscale hydrodynamics simulations with the developed model help us better understand physical mechanisms that govern <i>E. coli</i> dynamics, yielding the run-and-tumble behaviour that compares well with experimental observations. This model can further be used to explore the behaviour of <i>E. coli</i> and other peritrichous bacteria in more complex realistic environments.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 227","pages":"20250035"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12173490/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144317251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Correlated evolution of elaborate intromission mechanics during copulation between the sexes in leaf beetles. 叶甲虫两性交配过程中精细渗透机制的相关进化。
IF 3.7 2区 综合性期刊
Journal of The Royal Society Interface Pub Date : 2025-06-01 Epub Date: 2025-06-11 DOI: 10.1098/rsif.2025.0155
Yoko Matsumura, Shayan Ramezanpour, Thomas van de Kamp, Stanislav Gorb, Alexander Kovalev, Hamed Rajabi
{"title":"Correlated evolution of elaborate intromission mechanics during copulation between the sexes in leaf beetles.","authors":"Yoko Matsumura, Shayan Ramezanpour, Thomas van de Kamp, Stanislav Gorb, Alexander Kovalev, Hamed Rajabi","doi":"10.1098/rsif.2025.0155","DOIUrl":"10.1098/rsif.2025.0155","url":null,"abstract":"<p><p>Diverse female and male genitalia have evolved. Although the evolutionary mechanisms behind this phenomenon have been studied extensively, the mechanical interactions between female and male genitalia are much less understood. Here, we provide an in-depth biomechanical study on the intromission of elongated tube-like female and male genitalia, termed the spermathecal duct and flagellum, in tortoise leaf beetles. Our findings reveal that this seemingly straightforward penetration mechanism is underpinned by structural and material specializations of the genitalia. We employed synchrotron-based micro-computed tomography and confocal laser scanning microscopy (CLSM) to visualize the precise mechanical interactions between female and male genitalia. Mechanical tests revealed a stiffness gradient within the flagellum and correlated stiffness variations between the sexes. Combining CLSM and cryo-microtome techniques, we characterized a heterogeneous material distribution at the flagellum tip; this specialization was more remarkable in the species with a more sclerotized spermathecal duct. Finite element analyses incorporating the observed material properties demonstrated that the observed material distribution reduced the penetration force required tremendously and dispersed the stress at the flagellum tip. This study unveils that structural and material adaptations in female and male genitalia have probably coevolved and highlights the importance of biomechanics in genital studies.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 227","pages":"20250155"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12153159/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144266523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Generative design as a tool to analyse the uncertain loading regimes of intricate skeletal structures. 生成设计是一种分析复杂骨架结构不确定载荷的工具。
IF 3.7 2区 综合性期刊
Journal of The Royal Society Interface Pub Date : 2025-05-01 Epub Date: 2025-05-14 DOI: 10.1098/rsif.2025.0023
John Michael Racy, Bart Boom, Adam Summers
{"title":"Generative design as a tool to analyse the uncertain loading regimes of intricate skeletal structures.","authors":"John Michael Racy, Bart Boom, Adam Summers","doi":"10.1098/rsif.2025.0023","DOIUrl":"10.1098/rsif.2025.0023","url":null,"abstract":"<p><p>The morphology of a skeletal structure is driven in part by the forces it endures over evolutionary time. We demonstrate that generative design, an iterative engineering tool, can yield insight into the loading regimes of complex skeletal elements. With only a simple model of the spatial constraints and potential forces seen by a skeletal element, we generated analogous structures. We used this technique to provide insights into the specialization of the radial elements of batoid pectoral fins, a case that would be challenging to analyse by conventional means. Particular configurations of generative designs resulted in structures with a morphology remarkably similar to that of real radials. We suggest that these cases reveal the loading configurations that the real radials have evolved to withstand.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 226","pages":"20250023"},"PeriodicalIF":3.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12076017/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144023874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Advection and diffusion in perivascular and extracellular spaces in the brain. 脑内血管周围和细胞外空间的平流和扩散。
IF 3.7 2区 综合性期刊
Journal of The Royal Society Interface Pub Date : 2025-05-01 Epub Date: 2025-05-21 DOI: 10.1098/rsif.2025.0010
Yisen Guo, Keelin Quirk, Douglas H Kelley, John H Thomas
{"title":"Advection and diffusion in perivascular and extracellular spaces in the brain.","authors":"Yisen Guo, Keelin Quirk, Douglas H Kelley, John H Thomas","doi":"10.1098/rsif.2025.0010","DOIUrl":"10.1098/rsif.2025.0010","url":null,"abstract":"<p><p>Knowledge of the relative importance of advection and diffusion in clearing waste from the brain has been elusive, especially concerning the extracellular space (ECS). With local and global computational models of the mouse brain, we explore how the presence or absence of advection in the ECS affects solute transport. Without advection in the ECS, clearance would occur by diffusion into flowing cerebrospinal fluid in perivascular spaces (PVSs) or elsewhere, but we find this process to be severely limited by build-up of solute in the PVSs. We simulate flow in the ECS driven by a pressure drop between arteriole and venule PVSs, which enhances clearance considerably. To assess the relative importance of advection and diffusion, we introduce a <i>local</i> Péclet number [Formula: see text], a dimensionless scalar field. For our simulations, [Formula: see text] through much of the ECS but [Formula: see text] near PVSs near the brain surface. This local dominance of advection in the ECS establishes a clearance mechanism markedly different from that produced by diffusion alone. In network simulations that explore different parameter values and efflux routes, the pressures needed to drive the PVS flows measured <i>in vivo</i> are unrealistically large for most cases lacking ECS flow. Collectively, our models indicate that a flow in the ECS is necessary to explain experimental measurements and maintain homeostasis.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 226","pages":"20250010"},"PeriodicalIF":3.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12092104/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144110776","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Electrical wave generation and spatial organization in uterine tissue. 子宫组织中的电波产生与空间组织。
IF 3.7 2区 综合性期刊
Journal of The Royal Society Interface Pub Date : 2025-05-01 Epub Date: 2025-05-14 DOI: 10.1098/rsif.2024.0638
Shawn A Means, Jagir R Hussan, Amy S Garrett, Leo K Cheng, Alys Rachel Clark
{"title":"Electrical wave generation and spatial organization in uterine tissue.","authors":"Shawn A Means, Jagir R Hussan, Amy S Garrett, Leo K Cheng, Alys Rachel Clark","doi":"10.1098/rsif.2024.0638","DOIUrl":"10.1098/rsif.2024.0638","url":null,"abstract":"<p><p>Healthy uterine function requires coordinated and spatially organized contractions over the menstrual cycle (oestrus in animals) and at term in pregnancy. The underlying mechanisms triggering and coordinating uterine contractions, without a distinct pacemaking region, are poorly understood. Potentially, gap-junction coupling between excitable smooth muscle cells themselves or between electrically passive cells (telocytes or fibroblasts) and excitable cells may be key. Here, we present a lattice-tissue model of coupled excitable and passive cells to investigate a potential mechanism of coordinated tissue contraction. Bifurcation analysis of cell pairs quantifies parameter windows exhibiting oscillatory behaviour. Within these windows, we demonstrate conditions when the magnitude and spatial distribution of coupling strengths generate electrical waves. Energy-based analysis of excitable cells provides quantification of intercellular energy differences cells required for spontaneous wave generation. Our model suggests passive cells must rest at a membrane voltage sufficiently higher than smooth muscle cells to trigger activity and that coupling between excitable and passive cells in spatially concentrated regions could influence the direction of tissue-wide electrical waves. This suggests that both the total number of gap junctions and their spatial expression may play a role in coordinating uterine contractility.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 226","pages":"20240638"},"PeriodicalIF":3.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12076165/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144002167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Wing extension-flexion coupled aeroelastic effects improve avian gliding performance. 机翼伸屈耦合气动弹性效应提高了鸟类的滑翔性能。
IF 3.5 2区 综合性期刊
Journal of The Royal Society Interface Pub Date : 2025-05-01 Epub Date: 2025-05-07 DOI: 10.1098/rsif.2024.0753
Jasmin C M Wong, Vaibhav Joshi, Rajeev K Jaiman, Douglas L Altshuler
{"title":"Wing extension-flexion coupled aeroelastic effects improve avian gliding performance.","authors":"Jasmin C M Wong, Vaibhav Joshi, Rajeev K Jaiman, Douglas L Altshuler","doi":"10.1098/rsif.2024.0753","DOIUrl":"10.1098/rsif.2024.0753","url":null,"abstract":"<p><p>During flight, birds instigate remarkably large changes in wing shape, commonly termed 'wing morphing'. These changes in shape, particularly extension-flexion, have been well documented to influence the production of aerodynamic forces. However, it is unknown how wing stiffness changes as a result of the structural rearrangements needed for morphing. We address this gap in knowledge through mechanical testing of <i>in situ</i> flight feathers in anaesthetized pigeons and found that while the most distal portion of the feathered wing remained unaffected, proximal areas saw an increase in out-of-plane stiffness due to wing folding. Following this, we used computational fluid-structure interaction simulations to evaluate how this morphing-coupled change in stiffness might modulate local flow patterns to affect aerodynamic performance. We found that flexible wings perform better than entirely rigid wings as an increase in near-wall vorticity delayed flow separation. Furthermore, an increase in stiffness in a folded wing during high-speed flight prevented the reduction in lift seen in more flexible cases caused by aeroelastic flutter modes destructively interfering with shed leading-edge vortices. Collectively, these results reveal that mechanical changes coupled with wing morphing can provide a speed-dependent mechanism to enhance flight performance.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 226","pages":"20240753"},"PeriodicalIF":3.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12055289/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144029338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Human shape perception spontaneously discovers the biological origin of novel, but natural, stimuli. 人类的形状感知自发地发现了新奇但自然的刺激的生物起源。
IF 3.7 2区 综合性期刊
Journal of The Royal Society Interface Pub Date : 2025-05-01 Epub Date: 2025-05-21 DOI: 10.1098/rsif.2024.0931
Kira Isabel Dehn, Guido Maiello, Frieder Tom Hartmann, Yaniv Morgenstern, Sara Joy Hawkins, Thomas Offner, Joshua Walter, Thomas Hassenklöver, Ivan Manzini, Roland W Fleming
{"title":"Human shape perception spontaneously discovers the biological origin of novel, but natural, stimuli.","authors":"Kira Isabel Dehn, Guido Maiello, Frieder Tom Hartmann, Yaniv Morgenstern, Sara Joy Hawkins, Thomas Offner, Joshua Walter, Thomas Hassenklöver, Ivan Manzini, Roland W Fleming","doi":"10.1098/rsif.2024.0931","DOIUrl":"10.1098/rsif.2024.0931","url":null,"abstract":"<p><p>Humans excel at categorizing objects by shape. This facility involves identifying shape features that objects have in common with other members of their class and relies-at least in part-on semantic/cognitive constructs. For example, plants sprout branches, fish grow fins, shoes are moulded to our feet. Can humans parse shapes according to the processes that give shapes their key characteristics, even when such processes are hidden? To answer this, we investigated how humans perceive the shape of cells from the olfactory system of <i>Xenopus laevis</i> tadpoles. These objects are novel to most humans yet occur in nature and cluster into classes following their underlying biological function. We reconstructed three-dimensional (3D) cell models through 3D microscopy and photogrammetry, then conducted psychophysical experiments. Human participants performed two tasks: they arranged 3D-printed cell models by similarity and rated them along eight visual dimensions. Participants were highly consistent in their arrangements and ratings and spontaneously grouped stimuli to reflect the cell classes, unwittingly revealing the underlying processes shaping these forms. Our findings thus demonstrate that human perceptual organization mechanisms spontaneously parse the biological systematicities of never-before-seen, natural shapes. Integrating such human perceptual strategies into automated systems may enhance morphology-based analysis in biology and medicine.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 226","pages":"20240931"},"PeriodicalIF":3.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12092133/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144110906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bayesian networks for network inference in biology. 生物学中网络推理的贝叶斯网络。
IF 3.7 2区 综合性期刊
Journal of The Royal Society Interface Pub Date : 2025-05-01 Epub Date: 2025-05-07 DOI: 10.1098/rsif.2024.0893
James Hammond, V Anne Smith
{"title":"Bayesian networks for network inference in biology.","authors":"James Hammond, V Anne Smith","doi":"10.1098/rsif.2024.0893","DOIUrl":"https://doi.org/10.1098/rsif.2024.0893","url":null,"abstract":"<p><p>Bayesian networks (BNs) have been used for reconstructing interactions from biological data, in disciplines ranging from molecular biology to ecology and neuroscience. BNs learn conditional dependencies between variables, which best 'explain' the data, represented as a directed graph which approximates the relationships between variables. In the 2000s, BNs were a popular method that promised an approach capable of inferring biological networks from data. Here, we review the use of BNs applied to biological data over the past two decades and evaluate their efficacy. We find that BNs are successful in inferring biological networks, frequently identifying novel interactions or network components missed by previous analyses. We suggest that as false positive results are underreported, it is difficult to assess the accuracy of BNs in inferring biological networks. BN learning appears most successful for small numbers of variables with high-quality datasets that either discretize the data into few states or include perturbative data. We suggest that BNs have failed to live up to the promise of the 2000s but that this is most likely due to experimental constraints on datasets, and the success of BNs at inferring networks in a variety of biological contexts suggests they are a powerful tool for biologists.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 226","pages":"20240893"},"PeriodicalIF":3.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12055290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144017267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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