{"title":"Dynamic network entropy for pinpointing the pre-outbreak stage of infectious disease.","authors":"Qibin Song, Haoming Zhang, Yanping Jiang, Hua Chai, Zhengrong Liu, Jiayuan Zhong","doi":"10.1098/rsif.2025.0047","DOIUrl":"10.1098/rsif.2025.0047","url":null,"abstract":"<p><p>Infectious disease outbreaks have the potential to result in substantial human casualties and financial losses. Issuing timely warnings and taking appropriate measures before infectious disease outbreaks can effectively hinder or even prevent the spread of epidemics. However, the spread of infectious diseases is a complex and dynamic process that involves both biological and social systems. Consequently, issuing accurate early warnings for infectious disease outbreaks in real time remains a significant challenge. In this study, we have developed a novel computational approach called dynamic network entropy (DNE) by constructing city networks and leveraging extensive hospital visit record data to pinpoint early warning signals for infectious disease outbreaks. Specifically, the proposed method can accurately identify pre-outbreak of infectious diseases including influenza and hand, foot and mouth disease (HFMD). The predicted early warning signals preceded the outbreaks or initial peaks by at least six weeks for influenza and five weeks for HFMD. Additionally, compared to other existing methods, our proposed approach exhibits good performance in pinpointing critical warning signals. Therefore, by harnessing detailed dynamic and high-dimensional information, our DNE method presents an innovative strategy for identifying the critical point or pre-outbreak stage prior to the catastrophic transition into a pandemic outbreak, which holds significant potential for application in the field of public health surveillance.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 229","pages":"20250047"},"PeriodicalIF":3.5,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12364572/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144883113","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}
Harshavardhan Bv, Hanuma Sai Billakurthi, Sarah Adigwe, Kishore Hari, Herbert Levine, Tomas Gedeon, Mohit Kumar Jolly
{"title":"Emergent dynamics of cellular decision making in multi-node mutually repressive regulatory networks.","authors":"Harshavardhan Bv, Hanuma Sai Billakurthi, Sarah Adigwe, Kishore Hari, Herbert Levine, Tomas Gedeon, Mohit Kumar Jolly","doi":"10.1098/rsif.2025.0190","DOIUrl":"10.1098/rsif.2025.0190","url":null,"abstract":"<p><p>Stem cell differentiation during development is governed by the dynamics of the underlying gene regulatory networks (GRNs). Mutually inhibiting nodes/collection of nodes encompass the GRNs that govern differentiation to two distinct fates. However, the properties of GRNs that can allow differentiation into n-terminal phenotypes are poorly understood. In this study, we examine toggle-n networks, encompassing mutual inhibitions among multiple transcription factors (TFs), to derive generalized insights regarding the dynamics underlying differentiation into n-terminal phenotypes. We show through numerical and analytical methods that steady-state distributions of these networks involve co-expression of multiple cell state-specific TFs, indicating the presence of multi-potent hybrid phenotypes during multi-lineage differentiation. Furthermore, incorporating a case study of T-helper cell differentiation, we show that cytokine signalling and specific asymmetry of regulatory links can drive further directed differentiation of these hybrid phenotypes into particular cell states within our mathematical framework.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 229","pages":"20250190"},"PeriodicalIF":3.5,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12364581/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144883114","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}
Claire M Miller, Domenic P J Germano, Alicia M Chenoweth, Sarah Holdsworth-Carson
{"title":"Mathematical modelling of macrophage and natural killer cell immune response during early stages of peritoneal endometriosis lesion onset.","authors":"Claire M Miller, Domenic P J Germano, Alicia M Chenoweth, Sarah Holdsworth-Carson","doi":"10.1098/rsif.2025.0076","DOIUrl":"10.1098/rsif.2025.0076","url":null,"abstract":"<p><p>The immune system is hypothesized to contribute to the onset of endometriosis lesions. However, the precise mechanisms underlying its role are not yet known. We introduce a novel compartmental model that describes the interactions between innate immune cells, specifically macrophages and natural killer cells, and endometrial cells, occurring within the peritoneal fluid during the early stages of (superficial peritoneal) endometriosis lesion onset. Our study focuses on retrograde influx, immune detection and immune clearance. Results show an increased influx of endometrial cells into peritoneal fluid correlates with heightened pro-inflammatory macrophage activation, but does not lead to an increase in disease. We compare the system's response to changes in immune cytotoxicity and ability to detect ectopic endometrial cells. We predict that reduced cytotoxicity is a key driver of disease. These findings align with the increased immune activation observed clinically. Finally, we predict that an individual can transition to a diseased state following a reduction in immune system cytotoxicity and/or reduced ability to detect ectopic cells. Due to hysteresis, a significant improvement is then required to restore an individual to the disease-free state. This work provides a valuable framework to explore hypotheses of endometriosis lesion onset and assist in understanding of the disease.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 229","pages":"20250076"},"PeriodicalIF":3.5,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12343144/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144835421","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}
Louisa Traser, Mario Fleischer, Daniel Priegnitz, Fiona Stritt, Marie Köberlein, Jonas Kirsch, Johannes Fischer, Hanspeter Herzel, Dirk Mürbe, Bernhard Richter, Matthias Echternach
{"title":"<i>In vivo</i> insights into irregular voice production as a complex nonlinear system-a case study.","authors":"Louisa Traser, Mario Fleischer, Daniel Priegnitz, Fiona Stritt, Marie Köberlein, Jonas Kirsch, Johannes Fischer, Hanspeter Herzel, Dirk Mürbe, Bernhard Richter, Matthias Echternach","doi":"10.1098/rsif.2025.0086","DOIUrl":"10.1098/rsif.2025.0086","url":null,"abstract":"<p><p>The human voice exhibits diverse expressions, primarily generated by the regular oscillatory movement of both vocal folds. However, further vocal tract structures can also oscillate, as observed in different singing styles, supraglottic voice substitutes and functional voice disorders. To describe the spectrum of irregular phonation types from a nonlinear systems perspective, we conducted <i>in vivo</i> investigations with a professional metal singer using transnasal high-speed digital imaging combined with electroglottography and acoustic data. Here, we analysed 10 distinct voice qualities. Some of these show oscillatory mechanisms characterized by nearly periodic patterns that differ in three key aspects: the ratio of glottal to supraglottic oscillations, their behaviour during the glissando and the oscillating structures primarily involved. Both reduced glottal adduction and increased glottal and supraglottic compression contribute to a greater degree of irregularity. The supraglottic oscillations can coexist with various glottal oscillation mechanisms. Based on the <i>in vivo</i> data, we identified various nonlinear phenomena of different categories that include synchronized oscillations with defined frequency ratios, bifurcations, biphonations and chaotic oscillations.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 229","pages":"20250086"},"PeriodicalIF":3.5,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12344453/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144835417","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}
{"title":"Interplay of asexual and sexual reproduction in bifunctional insects.","authors":"Oran Ayalon, Harikrishnan Rajendran","doi":"10.1098/rsif.2025.0202","DOIUrl":"10.1098/rsif.2025.0202","url":null,"abstract":"<p><p>Reproduction is a fundamental biological process, with organisms reproducing sexually, asexually, and, in some cases, utilizing both modes of reproduction within the same population. Does the ability to reproduce through a combination of asexual and sexual modes offer an evolutionary advantage over relying on either mode alone? Here, we introduce an empirically driven theoretical model to examine the dynamics and interplay between sexual and asexual reproduction in stick insect populations. We analyse it using a novel phase transition approach and corroborate it using published experimental data. We find that the presence of males can either increase or decrease the overall population size. However, maintaining an optimal ratio of parthenogenetic to sexual reproduction is crucial for male resilience, effectively delaying male extinction. Conversely, extreme levels of parthenogenetic reproduction-whether too high or too low-can lead to male extinction, emphasizing the need for a balanced number of virgin females to ensure the persistence of males. Our model also explains male absence in <i>Carausius morosus</i> and persistence in <i>Extatosoma tiaratum</i>. Our findings provide valuable insights into the interplay of reproductive strategies and contribute to broader discussions on the transitions between sexual and asexual reproduction.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 229","pages":"20250202"},"PeriodicalIF":3.5,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12344454/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144835420","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}
Andreas Kuhn, Timothy Krüger, Magdalena Schüttler, Markus Engstler, Sabine Christine Fischer
{"title":"Correction: 'Quantification of <i>Trypanosoma brucei</i> social motility indicates different colony growth phases' (2024), by Kuhn <i>et al</i>.","authors":"Andreas Kuhn, Timothy Krüger, Magdalena Schüttler, Markus Engstler, Sabine Christine Fischer","doi":"10.1098/rsif.2025.0568","DOIUrl":"10.1098/rsif.2025.0568","url":null,"abstract":"","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 229","pages":"20250568"},"PeriodicalIF":3.5,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12364560/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144883110","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}
{"title":"Cumulative dose responses for adapting biological systems.","authors":"Ankit Gupta, Eduardo Sontag","doi":"10.1098/rsif.2024.0877","DOIUrl":"10.1098/rsif.2024.0877","url":null,"abstract":"<p><p>Physiological adaptation is a fundamental property of biological systems across all levels of organization, ensuring survival and proper function. Adaptation is typically formulated as an asymptotic property of the <i>dose response (DR</i>), defined as the level of a response variable with respect to an input parameter. In pharmacology, the input could be a drug concentration; in immunology, it might correspond to an antigen level. In contrast to the DR, this paper develops the concept of a transient, finite-time, cumulative dose response (cDR)<i>,</i> which is obtained by integrating the response variable over a fixed time interval and viewing that integral-area under the curve-as a function of the input parameter. This study is motivated by experimental observations of cytokine accumulation under T-cell stimulation, which exhibit a non-monotonic cDR. It is known from the systems biology literature that only two types of network motifs, incoherent feedforward loops and negative integral feedback (IFB) mechanisms, can generate adaptation. Three paradigmatic such motifs-two types of incoherent loops and one integral feedback-have been the focus of much study. Surprisingly, it is shown here that these two incoherent feedforward loop motifs-despite their capacity for non-monotonic DR-always yield a monotonic cDR, and are therefore inconsistent with these experimental data. On the other hand, this work reveals that the IFB motif is indeed capable of producing a non-monotonic cDR, and is thus consistent with these data.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 229","pages":"20240877"},"PeriodicalIF":3.5,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12343139/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144835418","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}
Andreas Fischer, Regine Gries, Camila A Roman-Torres, Anand Devireddy, Gerhard Gries
{"title":"Glandular quinoline-derivates protect crustacean woodlice from spider predation.","authors":"Andreas Fischer, Regine Gries, Camila A Roman-Torres, Anand Devireddy, Gerhard Gries","doi":"10.1098/rsif.2025.0260","DOIUrl":"10.1098/rsif.2025.0260","url":null,"abstract":"<p><p>In evolutionary time, aquatic crustaceans colonized land and faced new terrestrial predators such as spiders and ants. We tested the hypothesis that the crustacean terrestrial woodlouse <i>Porcellio scaber</i> produces defensive metabolites that provide protection against terrestrial predators. When attacked by a predator, <i>P. scaber</i> expels proteinaceous secretions from its tegumental glands. Analyses of gland secretion extracts by gas chromatography-mass spectrometry and by liquid chromatography-mass spectrometry revealed four metabolites: methyl 8-hydroxy-quinoline-2-carboxylate, methyl 8-hydroxy-4-methoxy-quinoline-2-carboxylate, methyl 8-(sulfooxy)quinoline-2-carboxylate and methyl 4-methoxy-8-(sulfooxy)quinoline-2-carboxylate, the latter three being natural products not previously known. In behavioural experiments, <i>Steatoda grossa</i> spiders readily preyed on <i>Tenebrio molitor</i> beetles but avoided chemically well-defended <i>P. scaber</i>. When beetles were rendered chemically well-defended by topical applications of either <i>P. scaber</i> gland secretion extract or synthetic metabolites identified in these extracts, spiders rejected the beetles as prey. Our data support the hypothesis that <i>P. scaber</i> produces defensive metabolites against terrestrial predators. We show that the crustacean <i>P. scaber</i>, like many insects, is chemically defended against predators.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 229","pages":"20250260"},"PeriodicalIF":3.5,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12324876/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144789480","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}
Chenyan Wang, Yuanwan Lou, Yabo Ye, Shuiyang Shen, Fangjun Bao, Junjie Wang, Ahmed Elsheikh
{"title":"Evaluating corneal cross-linking using Stress-Strain Index maps: a finite element study.","authors":"Chenyan Wang, Yuanwan Lou, Yabo Ye, Shuiyang Shen, Fangjun Bao, Junjie Wang, Ahmed Elsheikh","doi":"10.1098/rsif.2025.0234","DOIUrl":"https://doi.org/10.1098/rsif.2025.0234","url":null,"abstract":"<p><p>Keratoconus (KC) is a progressive corneal ectasia leading to visual impairment if untreated. Corneal collagen cross-linking (CXL) is an effective treatment to halt KC progression by strengthening corneal biomechanics. However, current CXL treatments lack customization based on regional corneal stiffness, which is crucial for optimal outcomes. This study introduces a novel approach using Stress-Strain Index (SSI) maps to evaluate localized CXL effects on corneal biomechanics. Numerical modelling based on the finite element method was used to carry out inverse analysis of the human eye to simulate KC and CXL treatments, incorporating regional stiffness variations based on collagen fibril density. SSI maps were generated pre- and post-CXL to assess stiffness changes in treated regions. Results demonstrated that CXL increased corneal stiffness within the treated area, but the extent of stiffness recovery varied with CXL diameter and alignment with the KC cone. Smaller CXL diameters led to higher localized stiffness increases, while misalignment between CXL and KC areas resulted in suboptimal biomechanical restoration. The study highlights the potential of SSI mapping for personalized CXL treatments, enabling precise targeting of biomechanically weakened regions to restore corneal health. This approach contributes to the development of biomechanics-based customization of CXL therapies.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 229","pages":"20250234"},"PeriodicalIF":3.5,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12380491/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144959218","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}
Mohammad Tanver Hossain, Dakota Piorkowski, Andrew Lowe, Wonsik Eom, Abhishek Shetty, Sameh H Tawfick, Douglas S Fudge, Randy H Ewoldt
{"title":"Physics of unravelling and micromechanics of hagfish threads.","authors":"Mohammad Tanver Hossain, Dakota Piorkowski, Andrew Lowe, Wonsik Eom, Abhishek Shetty, Sameh H Tawfick, Douglas S Fudge, Randy H Ewoldt","doi":"10.1098/rsif.2025.0503","DOIUrl":"https://doi.org/10.1098/rsif.2025.0503","url":null,"abstract":"<p><p>Hagfish slime is a unique biological material composed of mucus and protein threads that rapidly deploy into a cohesive network when deployed in seawater. The forces involved in thread deployment and interactions among mucus and threads are key to understanding how hagfish slime rapidly assembles into a cohesive, functional network. Despite extensive interest in its biophysical properties, the mechanical forces governing thread deployment and interaction remain poorly quantified. Here, we present the first direct <i>in situ</i> measurements of the micromechanical forces involved in hagfish slime formation, including mucus mechanical properties, skein peeling force, thread-mucus adhesion and thread-thread cohesion. Using a custom glass-rod force sensing system, we show that thread deployment initiates when peeling forces exceed a threshold of approximately 6.8 nN. To understand the flow strength required for unravelling, we used a rheo-optic setup to impose controlled shear flow, enabling us to directly observe unravelling dynamics and determine the critical shear rate for unravelling of the skeins, which we then interpreted using an updated peeling-based force balance model. Our results reveal that thread-mucus adhesion dominates over thread-thread cohesion and that deployed threads contribute minimally to bulk shear rheology at constant flow rate. These findings clarify the physics underlying the rapid, flow-triggered assembly of hagfish slime and inform future designs of synthetic deployable fibre-gel systems.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 229","pages":"20250503"},"PeriodicalIF":3.5,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12380483/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144959230","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}