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Probing the complexity of wood with computer vision: from pixels to properties J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-04-17 Mirko Lukovic, Laure Ciernik, Gauthier Müller, Dan Kluser, Tuan Pham, Ingo Burgert, Mark Schubert
We use data produced by industrial wood grading machines to train a machine learning model for predicting strength-related properties of wood lamellae from colour images of their surfaces. The focus was on samples of Norway spruce (Picea abies) wood, which display visible fibre pattern formations on their surfaces. We used a pre-trained machine learning model based on the residual network ResNet50
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Uncertainty quantification of the impact of peripheral arterial disease on abdominal aortic aneurysms in blood flow simulations J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-04-10 Sharp C. Y. Lo, Jon W. S. McCullough, Xiao Xue, Peter V. Coveney
Peripheral arterial disease (PAD) and abdominal aortic aneurysms (AAAs) often coexist and pose significant risks of mortality, yet their mutual interactions remain largely unexplored. Here, we introduce a fluid mechanics model designed to simulate the haemodynamic impact of PAD on AAA-associated risk factors. Our focus lies on quantifying the uncertainty inherent in controlling the flow rates within
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Characterization of the layer, direction and time-dependent mechanical behaviour of the human oesophagus and the effects of formalin preservation J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-04-10 Ciara Durcan, Mokarram Hossain, Grégory Chagnon, Djordje Perić, Edouard Girard
The mechanical characterization of the oesophagus is essential for applications such as medical device design, surgical simulations and tissue engineering, as well as for investigating the organ’s pathophysiology. However, the material response of the oesophagus has not been established ex vivo in regard to the more complex aspects of its mechanical behaviour using fresh, human tissue: as of yet, in
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Optimization of periodic treatment strategies for bacterial biofilms using an agent-based in silico approach J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-04-10 Johanna A. Blee, Thomas E. Gorochowski, Sabine Hauert
Biofilms are responsible for most chronic infections and are highly resistant to antibiotic treatments. Previous studies have demonstrated that periodic dosing of antibiotics can help sensitize persistent subpopulations and reduce the overall dosage required for treatment. Because the dynamics and mechanisms of biofilm growth and the formation of persister cells are diverse and are affected by environmental
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The angiogenic growth of cities J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-04-03 Isabella Capel-Timms, David Levinson, Bahman Lahoorpoor, Sara Bonetti, Gabriele Manoli
Describing the space–time evolution of urban population is a fundamental challenge in the science of cities, yet a complete theoretical treatment of the underlying dynamics is still missing. Here, we first reconstruct the evolution of London (UK) over 180 years and show that urban growth consists of an initial phase of diffusion-limited growth, followed by the development of the railway transport network
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Gaps in the wall of a perivascular space act as valves to produce a directed flow of cerebrospinal fluid: a hoop-stress model J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-04-03 Yiming Gan, John H. Thomas, Douglas H. Kelley
The flow of cerebrospinal fluid (CSF) along perivascular spaces (PVSs) is an important part of the brain’s system for clearing metabolic waste. Astrocyte endfeet bound the PVSs of penetrating arteries, separating them from brain extracellular space. Gaps between astrocyte endfeet might provide a low-resistance pathway for fluid transport across the wall. Recent studies suggest that the astrocyte endfeet
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Analysis of collision avoidance in honeybee flight J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-27 Shreyansh Singh, Matthew Garratt, Mandyam Srinivasan, Sridhar Ravi
Insects are excellent at flying in dense vegetation and navigating through other complex spatial environments. This study investigates the strategies used by honeybees (Apis mellifera) to avoid collisions with an obstacle encountered frontally during flight. Bees were trained to fly through a tunnel that contained a solitary vertically oriented cylindrical obstacle placed along the midline. Flight
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Robot motor learning shows emergence of frequency-modulated, robust swimming with an invariant Strouhal number J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-27 Hankun Deng, Donghao Li, Colin Nitroy, Andrew Wertz, Shashank Priya, Bo Cheng
Fish locomotion emerges from diverse interactions among deformable structures, surrounding fluids and neuromuscular activations, i.e. fluid–structure interactions (FSI) controlled by fish's motor systems. Previous studies suggested that such motor-controlled FSI may possess embodied traits. However, their implications in motor learning, neuromuscular control, gait generation, and swimming performance
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A model free method of predicting transient dynamics in anaerobic digestion J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-27 Christopher M. Heggerud, Alan Hastings
Transient dynamics pose unique challenges when dealing with predictions and management of ecological systems yet little headway has been made on understanding when an ecological system might be in a transient state. As a start we consider a specific model, here focusing on a canonical model for anaerobic digestion. Through a series of simplifications, we analyse the potential of the model for transient
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Multipad agarose plate: a rapid and high-throughput approach for antibiotic susceptibility testing J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-27 Morten Kals, Leonardo Mancini, Jurij Kotar, Allen Donald, Pietro Cicuta
We describe a phenotypic antibiotic susceptibility testing (AST) method that can provide an eightfold speed-up in turnaround time compared with the current clinical standard by leveraging advances in microscopy and single-cell imaging. A newly developed growth plate containing 96 agarose pads, termed the multipad agarose plate (MAP), can be assembled at low cost. Pads can be prepared with dilution
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Turbulence causes kinematic and behavioural adjustments in a flapping flier J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-20 Emmanouil Lempidakis, Andrew N. Ross, Michael Quetting, Krishnamoorthy Krishnan, Baptiste Garde, Martin Wikelski, Emily L. C. Shepard
Turbulence is a widespread phenomenon in the natural world, but its influence on flapping fliers remains little studied. We assessed how freestream turbulence affected the kinematics, flight effort and track properties of homing pigeons (Columba livia), using the fine-scale variations in flight height as a proxy for turbulence levels. Birds showed a small increase in their wingbeat amplitude with increasing
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A Matlab-based application for quantification of yeast cell growth on solid media J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-20 Ehtisham Wahid, Ohiemi Benjamin Ocheja, Nicoletta Guaragnella, Cataldo Guaragnella
Quantitative assessment of growth and survival is a suitable technique in studying biochemical, genetic and physiological processes in the cells. The budding yeast Saccharomyces cerevisiae is one of the most widely used eukaryotic model organisms for studying cellular mechanisms and processes in evolutionarily distant species, including humans. Yeast growth can be evaluated on both liquid and solid
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Oscillatory differentiation dynamics fundamentally restricts the resolution of pseudotime reconstruction algorithms J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-20 Huy K. Vo, Jonathan H. P. Dawes, Robert N. Kelsh
The challenge to understand differentiation and cell lineages in development has resulted in many bioinformatics software tools, notably those working with gene expression data obtained via single-cell RNA sequencing obtained at snapshots in time. Reconstruction methods for trajectories often proceed by dimension reduction, data clustering and then computation of a tree graph in which edges indicate
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Latent evolutionary signatures: a general framework for analysing music and cultural evolution J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-20 Jonathan Warrell, Leonidas Salichos, Michael Gancz, Mark B. Gerstein
Cultural processes of change bear many resemblances to biological evolution. The underlying units of non-biological evolution have, however, remained elusive, especially in the domain of music. Here, we introduce a general framework to jointly identify underlying units and their associated evolutionary processes. We model musical styles and principles of organization in dimensions such as harmony and
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A hybrid neural ordinary differential equation model of the cardiovascular system J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-20 Gevik Grigorian, Sandip V. George, Sam Lishak, Rebecca J. Shipley, Simon Arridge
In the human cardiovascular system (CVS), the interaction between the left and right ventricles of the heart is influenced by the septum and the pericardium. Computational models of the CVS can capture this interaction, but this often involves approximating solutions to complex nonlinear equations numerically. As a result, numerous models have been proposed, where these nonlinear equations are either
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Language-based game theory in the age of artificial intelligence J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-13 Valerio Capraro, Roberto Di Paolo, Matjaž Perc, Veronica Pizziol
Understanding human behaviour in decision problems and strategic interactions has wide-ranging applications in economics, psychology and artificial intelligence. Game theory offers a robust foundation for this understanding, based on the idea that individuals aim to maximize a utility function. However, the exact factors influencing strategy choices remain elusive. While traditional models try to explain
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Can institutions foster cooperation by wealth redistribution? J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-13 Hiroaki Chiba-Okabe, Joshua B. Plotkin
Theoretical models prescribe how institutions can promote cooperation in a population by imposing appropriate punishments or rewards on individuals. However, many real-world institutions are not sophisticated or responsive enough to ensure cooperation by calibrating their policies. Or, worse yet, an institution might selfishly exploit the population it governs for its own benefit. Here, we study the
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Prosocial punishment bots breed social punishment in human players J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-13 Chen Shen, Zhixue He, Lei Shi, Zhen Wang, Jun Tanimoto
Prosocial punishment, an important factor to stabilize cooperation in social dilemma games, often faces challenges like second-order free-riders—who cooperate but avoid punishing to save costs—and antisocial punishers, who defect and retaliate against cooperators. Addressing these challenges, our study introduces prosocial punishment bots that consistently cooperate and punish free-riders. Our findings
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Composite material in the sea urchin Cidaris rugosa: ordered and disordered micrometre-scale bicontinuous geometries J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-13 Anna-Lee Jessop, Allan J. Millsteed, Jacob J. K. Kirkensgaard, Jeremy Shaw, Peta L. Clode, Gerd E. Schröder-Turk
The sponge-like biomineralized calcite materials found in echinoderm skeletons are of interest in terms of both structure formation and biological function. Despite their crystalline atomic structure, they exhibit curved interfaces that have been related to known triply periodic minimal surfaces. Here, we investigate the endoskeleton of the sea urchin Cidaris rugosa that has long been known to form
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Incorporating recirculation effects into metrics of feeding performance for current-feeding zooplankton J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-13 Kiarash Samsami, Ludivine Sanchez Arias, Haven Redd, Rob Stoll, Rachel E. Pepper, Henry Chien Fu
The feeding performance of zooplankton influences their evolution and can explain their behaviour. A commonly used metric for feeding performance is the volume of fluid that flows through a filtering surface and is scanned for food. Here, we show that such a metric may give incorrect results for organisms that produce recirculatory flows, so that fluid flowing through the filter may have been already
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Cooperation among unequal players with aspiration-driven learning J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-13 Fang Chen, Lei Zhou, Long Wang
Direct reciprocity promotes the evolution of cooperation when players are sufficiently equal, such that they have similar influence on each other. In the light of ubiquitous inequality, this raises the question of how reciprocity evolves among unequal players. Existing studies on inequality mainly focus on payoff-driven learning rules, which rely on the knowledge of others’ strategies. However, inferring
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Backspin in Ruellia ciliatiflora does not maximize seed dispersal range, but provides moderate dispersal range that is robust to launch conditions J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-13 Joseph L. Hesse-Withbroe, Dwight L. Whitaker
Ruellia ciliatiflora is a perennial herb whose fruits explosively dehisce, launching their thin disc-like seeds over 6 m with a backspin up to 1660 Hz. While it has been previously shown that the backspin launch orientation minimizes the aerodynamic drag experienced by the seeds, it is not immediately obvious whether backspin is also the range-maximizing launch orientation. Here the three-dimensional
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Understanding the impact of numerical solvers on inference for differential equation models J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-06 Richard Creswell, Katherine M. Shepherd, Ben Lambert, Gary R. Mirams, Chon Lok Lei, Simon Tavener, Martin Robinson, David J. Gavaghan
Most ordinary differential equation (ODE) models used to describe biological or physical systems must be solved approximately using numerical methods. Perniciously, even those solvers that seem sufficiently accurate for the forward problem, i.e. for obtaining an accurate simulation, might not be sufficiently accurate for the inverse problem, i.e. for inferring the model parameters from data. We show
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A Bayesian approach to identifying the role of hospital structure and staff interactions in nosocomial transmission of SARS-CoV-2 J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-06 Jessica R. E. Bridgen, Joseph M. Lewis, Stacy Todd, Miriam Taegtmeyer, Jonathan M. Read, Chris P. Jewell
Nosocomial infections threaten patient safety, and were widely reported during the COVID-19 pandemic. Effective hospital infection control requires a detailed understanding of the role of different transmission pathways, yet these are poorly quantified. Using patient and staff data from a large UK hospital, we demonstrate a method to infer unobserved epidemiological event times efficiently and disentangle
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Parameter identifiability and model selection for partial differential equation models of cell invasion J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-06 Yue Liu, Kevin Suh, Philip K. Maini, Daniel J. Cohen, Ruth E. Baker
When employing mechanistic models to study biological phenomena, practical parameter identifiability is important for making accurate predictions across wide ranges of unseen scenarios, as well as for understanding the underlying mechanisms. In this work, we use a profile-likelihood approach to investigate parameter identifiability for four extensions of the Fisher–Kolmogorov–Petrovsky–Piskunov (Fisher–KPP)
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Role of seasonal importation and genetic drift on selection for drug-resistant genotypes of Plasmodium falciparum in high-transmission settings J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-06 Robert J. Zupko, Joseph L. Servadio, Tran Dang Nguyen, Thu Nguyen-Anh Tran, Kien Trung Tran, Anyirékun Fabrice Somé, Maciej F. Boni
Historically Plasmodium falciparum has followed a pattern of drug resistance first appearing in low-transmission settings before spreading to high-transmission settings. Several features of low-transmission regions are hypothesized as explanations: higher chance of symptoms and treatment seeking, better treatment access, less within-host competition among clones and lower rates of recombination. Here
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Optimal control of ribosome population for gene expression under periodic nutrient intake J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-06 Clément Soubrier, Eric Foxall, Luca Ciandrini, Khanh Dao Duc
Translation of proteins is a fundamental part of gene expression that is mediated by ribosomes. As ribosomes significantly contribute to both cellular mass and energy consumption, achieving efficient management of the ribosome population is also crucial to metabolism and growth. Inspired by biological evidence for nutrient-dependent mechanisms that control both ribosome-active degradation and genesis
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Reconciling the efficacy and effectiveness of masking on epidemic outcomes J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-06 Wan Yang, Jeffrey Shaman
During the COVID-19 pandemic, mask wearing in public settings has been a key control measure. However, the reported effectiveness of masking has been much lower than laboratory measures of efficacy, leading to doubts on the utility of masking. Here, we develop an agent-based model that comprehensively accounts for individual masking behaviours and infectious disease dynamics, and test the impact of
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Human leucocytes processed by fast-rate inertial microfluidics retain conventional functional characteristics J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-06 Tom Carvell, Paul Burgoyne, Laura Milne, John D. M. Campbell, Alasdair R. Fraser, Helen Bridle
The manufacturing of clinical cellular therapies is a complex process frequently requiring manipulation of cells, exchange of buffers and volume reduction. Current manufacturing processes rely on either low throughput open centrifugation-based devices, or expensive closed-process alternatives. Inertial focusing (IF) microfluidic devices offer the potential for high-throughput, inexpensive equipment
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Predicting the long-term collective behaviour of fish pairs with deep learning J. Royal Soc. Interface (IF 3.9) Pub Date : 2024-03-06 Vaios Papaspyros, Ramón Escobedo, Alexandre Alahi, Guy Theraulaz, Clément Sire, Francesco Mondada
Modern computing has enhanced our understanding of how social interactions shape collective behaviour in animal societies. Although analytical models dominate in studying collective behaviour, this study introduces a deep learning model to assess social interactions in the fish species Hemigrammus rhodostomus. We compare the results of our deep learning approach with experiments and with the results
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Evolutionary dynamics of mutants that modify population structure. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-11-29 Josef Tkadlec,Kamran Kaveh,Krishnendu Chatterjee,Martin A Nowak
Natural selection is usually studied between mutants that differ in reproductive rate, but are subject to the same population structure. Here we explore how natural selection acts on mutants that have the same reproductive rate, but different population structures. In our framework, population structure is given by a graph that specifies where offspring can disperse. The invading mutant disperses offspring
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A geometric process of evolutionary game dynamics. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-11-29 Philip LaPorte,Martin A Nowak
Many evolutionary processes occur in phenotype spaces which are continuous. It is therefore of interest to explore how selection operates in continuous spaces. One approach is adaptive dynamics, which assumes that mutants are local. Here we study a different process which also allows non-local mutants. We assume that a resident population is challenged by an invader who uses a strategy chosen from
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A general model for the motion of multivalent cargo interacting with substrates. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-11-29 L S Mosby,A Straube,M Polin
Multivalent interactions are common in biology at many different length scales, and can result in the directional motion of multivalent cargo along substrates. Here, a general analytical model has been developed that can describe the directional motion of multivalent cargo as a response to position dependence in the binding and unbinding rates exhibited by their interaction sites. Cargo exhibit both
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Assessing the impacts of genetic defects on starch metabolism in Arabidopsis plants using the carbon homeostasis model. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-11-29 Shuichi N Kudo,Carolina C M Bello,Anthony Artins,Camila Caldana,Akiko Satake
Starch serves as an important carbon storage mechanism for many plant species, facilitating their adaptation to the cyclic variations in the light environment, including day-night cycles as well as seasonal changes in photoperiod. By dynamically adjusting starch accumulation and degradation rates, plants maintain carbon homeostasis, enabling continuous growth under fluctuating environmental conditions
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Strong attachment as an adaptation of flightless weevils on windy oceanic islands. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-11-22 Lu-Yi Wang,Chung-Ping Lin,Stanislav N Gorb,Hamed Rajabi
Enhanced attachment ability is common in plants on islands to avoid potential fatal passive dispersal. However, whether island insects also have increased attachment ability remains unclear. Here we measured the attachment of a flightless weevil, Pachyrhynchus sarcitis kotoensis, from tropical islands, and compared it with documented arthropods from the mainland. We examined the morphology and material
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Honeybee cluster-not insulation but stressful heat sink. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-11-22 Derek Mitchell
Since the early twentieth century, the outer layer (mantle) of honeybees (Apis mellifera) in the winter cluster has been said to insulate the cluster core. This has encouraged enforced clustering, by the beekeepers' dominant use of inadequately insulated hives and, in North America, refrigeration. This is often seen as a benign or even a necessary process, with beekeeping and academic research considering
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The hydrodynamics and kinematics of the appendicularian tail underpin peristaltic pumping. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-11-15 Terra C Hiebert,Brad J Gemmell,George von Dassow,Keats R Conley,Kelly R Sutherland
Planktonic organisms feed while suspended in water using various hydrodynamic pumping strategies. Appendicularians are a unique group of plankton that use their tail to pump water over mucous mesh filters to concentrate food particles. As ubiquitous and often abundant members of planktonic ecosystems, they play a major role in oceanic food webs. Yet, we lack a complete understanding of the fluid flow
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An upright life, the postural stability of birds: a tensegrity system. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-11-15 Anick Abourachid,Christine Chevallereau,Idriss Pelletan,Philippe Wenger
Birds are so stable that they can rest and even sleep standing up. We propose that stable static balance is achieved by tensegrity. The rigid bones can be held together by tension in the tendons, allowing the system to stabilize under the action of gravity. We used the proportions of the bird's osteomuscular system to create a mathematical model. First, the extensor muscles and tendons of the leg are
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A geometric framework for reaction enumeration in computational nucleic acid devices. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-11-15 Sarika Kumar,Matthew R Lakin
Cascades of DNA strand displacement reactions enable the design of potentially large circuits with complex behaviour. Computational modelling of such systems is desirable to enable rapid design and analysis. In previous work, the expressive power of graph theory was used to enumerate reactions implementing strand displacement across a wide range of complex structures. However, coping with the rich
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Evolutionary rescue on genotypic fitness landscapes. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-11-15 L M Wahl,Paulo R A Campos
Populations facing adverse environments, novel pathogens or invasive competitors may be destined to extinction if they are unable to adapt rapidly. Quantitative predictions of the probability of survival through adaptation, evolutionary rescue, have been previously developed for one of the most natural and well-studied mappings from an organism's traits to its fitness, Fisher's geometric model (FGM)
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Red edge excitation shift spectroscopy is highly sensitive to tryptophan composition. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-11-08 Annmaree K Warrender,Jolyn Pan,Chris Pudney,Vickery L Arcus,William Kelton
Red edge excitation shift (REES) spectroscopy relies on the unique emission profiles of fluorophore-solvent interactions to profile protein molecular dynamics. Recently, we reported the use of REES to compare the stability of 32 polymorphic IgG antibodies natively containing tryptophan reporter fluorophores. Here, we expand on this work to investigate the sensitivity of REES to variations in tryptophan
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A two-scale numerical study on the mechanobiology of abdominal aortic aneurysms. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-11-01 Misael Dalbosco,Michele Terzano,Thiago A Carniel,Eduardo A Fancello,Gerhard A Holzapfel
Abdominal aortic aneurysms (AAAs) are a serious condition whose pathophysiology is related to phenomena occurring at different length scales. To gain a better understanding of the disease, this work presents a multi-scale computational study that correlates AAA progression with microstructural and mechanical alterations in the tissue. Macro-scale geometries of a healthy aorta and idealized aneurysms
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The ecology-evolution continuum and the origin of life. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-11-01 David A Baum,Zhen Peng,Emily Dolson,Eric Smith,Alex M Plum,Praful Gagrani
Prior research on evolutionary mechanisms during the origin of life has mainly assumed the existence of populations of discrete entities with information encoded in genetic polymers. Recent theoretical advances in autocatalytic chemical ecology establish a broader evolutionary framework that allows for adaptive complexification prior to the emergence of bounded individuals or genetic encoding. This
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Characterizing network circuity among heterogeneous urban amenities. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-11-01 Bibandhan Poudyal,Gourab Ghoshal,Alec Kirkley
The spatial configuration of urban amenities and the streets connecting them collectively provide the structural backbone of a city, influencing its accessibility, vitality and ultimately the well-being of its residents. Most accessibility measures focus on the proximity of amenities in space or along transportation networks, resulting in metrics largely determined by urban density alone. These measures
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Immobilization protects enzymes from plasma-mediated inactivation. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-10-25 Tim Dirks,Abdulkadir Yayci,Sabrina Klopsch,Marco Krewing,Wuyuan Zhang,Frank Hollmann,Julia E Bandow
Non-thermal plasmas are used in various applications to inactivate biological agents or biomolecules. A complex cocktail of reactive species, (vacuum) UV radiation and in some cases exposure to an electric field together cause the detrimental effects. In contrast to this disruptive property of technical plasmas, we have shown previously that it is possible to use non-thermal plasma-generated species
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The role of hydrodynamics in collective motions of fish schools and bioinspired underwater robots. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-10-25 Hungtang Ko,George Lauder,Radhika Nagpal
Collective behaviour defines the lives of many animal species on the Earth. Underwater swarms span several orders of magnitude in size, from coral larvae and krill to tunas and dolphins. Agent-based algorithms have modelled collective movements of animal groups by use of social forces, which approximate the behaviour of individual animals. But details of how swarming individuals interact with the fluid
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The cold atmospheric pressure plasma-generated species superoxide, singlet oxygen and atomic oxygen activate the molecular chaperone Hsp33. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-10-25 Tim Dirks,Marco Krewing,Katharina Vogel,Julia E Bandow
Cold atmospheric pressure plasmas are used for surface decontamination or disinfection, e.g. in clinical settings. Protein aggregation has been shown to significantly contribute to the antibacterial mechanisms of plasma. To investigate the potential role of the redox-activated zinc-binding chaperone Hsp33 in preventing protein aggregation and thus mediating plasma resistance, we compared the plasma
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Modelling the impacts of male alternative reproductive tactics on population dynamics. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-10-25 Jennifer A M Young,Sigal Balshine,David J D Earn
Observations of male alternative reproductive tactics (ARTs) in a variety of species have stimulated the development of mathematical models that can account for the evolution and stable coexistence of multiple male phenotypes. However, little attention has been given to the population dynamic consequences of ARTs. We present a population model that takes account of the existence of two male ARTs (guarders
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How honeybees respond to heat stress from the individual to colony level. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-10-18 Jitesh Jhawar,Jacob D Davidson,Anja Weidenmüller,Benjamin Wild,David M Dormagen,Tim Landgraf,Iain D Couzin,Michael L Smith
A honey bee colony functions as an integrated collective, with individuals coordinating their behaviour to adapt and respond to unexpected disturbances. Nest homeostasis is critical for colony function; when ambient temperatures increase, individuals switch to thermoregulatory roles to cool the nest, such as fanning and water collection. While prior work has focused on bees engaged in specific behaviours
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A variable heart rate multi-compartmental coupled model of the cardiovascular and respiratory systems. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-10-18 Sam Lishak,Gevik Grigorian,Sandip V George,Nicholas C Ovenden,Rebecca J Shipley,Simon Arridge
Current mathematical models of the cardiovascular system that are based on systems of ordinary differential equations are limited in their ability to mimic important features of measured patient data, such as variable heart rates (HR). Such limitations present a significant obstacle in the use of such models for clinical decision-making, as it is the variations in vital signs such as HR and systolic
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A tumour-spheroid manufacturing and cryopreservation process that yields a highly reproducible product ready for direct use in drug screening assays. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-10-11 Md Shafiullah Shajib,Kathryn Futrega,Anthony M Davies,Rose Ann G Franco,Eamonn McKenna,Bianca Guillesser,Travis J Klein,Ross W Crawford,Michael R Doran
If it were possible to purchase tumour-spheroids as a standardised product, ready for direct use in assays, this may contribute to greater research reproducibility, potentially reducing costs and accelerating outcomes. Herein, we describe a workflow where uniformly sized cancer tumour-spheroids are mass-produced using microwell culture, cryopreserved with high viability, and then cultured in neutral
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Correction to: 'Bayesian inference on a microstructural, hyperelastic model of tendon deformation' (2022) by Forsyth et al. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-10-11 Jessica E Forsyth,James Casey,Simon L Cotter,William J Parnell,Tom Shearer
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Information theory-based direct causality measure to assess cardiac fibrillation dynamics. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-10-11 Xili Shi,Arunashis Sau,Xinyang Li,Kiran Patel,Nikesh Bajaj,Marta Varela,Huiyi Wu,Balvinder Handa,Ahran Arnold,Matthew Shun-Shin,Daniel Keene,James Howard,Zachary Whinnett,Nicholas Peters,Kim Christensen,Henrik Jeldtoft Jensen,Fu Siong Ng
Understanding the mechanism sustaining cardiac fibrillation can facilitate the personalization of treatment. Granger causality analysis can be used to determine the existence of a hierarchical fibrillation mechanism that is more amenable to ablation treatment in cardiac time-series data. Conventional Granger causality based on linear predictability may fail if the assumption is not met or given sparsely
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A primer on correlation-based dimension reduction methods for multi-omics analysis. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-10-11 Tim Downing,Nicos Angelopoulos
The continuing advances of omic technologies mean that it is now more tangible to measure the numerous features collectively reflecting the molecular properties of a sample. When multiple omic methods are used, statistical and computational approaches can exploit these large, connected profiles. Multi-omics is the integration of different omic data sources from the same biological sample. In this review
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Rapid, non-invasive, in vivo measurement of tissue mechanical properties using gravitational loading and a nonlinear virtual fields method. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-10-11 S L Evans,B E Keenan,J Hill,S Zappala,N Bennion,S Avril
Measuring the mechanical properties of soft tissues in vivo is important in biomechanics and for diagnosis and staging of diseases, but challenging because it is difficult to control the boundary conditions. We present a novel, non-invasive method for measuring tissue properties using gravitational loading. MRI images of an organ in different positions are registered to measure tissue displacements
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Rapid and reversible humidity-dependent colour change by water film formation in a scaled springtail. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-10-04 Bram Vanthournout,Frans Janssens,Gerben Debruyn,Johan Mertens,Karen De Clerck,Liliana D'Alba,Matthew Shawkey
Colour is often not a static trait but can change over time either through biotic or abiotic factors. Humidity-dependent colour change can occur through either morphological change (e.g. to feather barbules in birds) or by the replacement of air by water causing a shift in refractive index, as seen in arthropod multi-layer cuticles or scales. The scaled springtail Lepidocyrtus cyaneus has scales that
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A simple model of wake capture aerodynamics. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-09-27 Mostafa R A Nabawy
Flapping wings may encounter or 'capture' the wake from previous half-stroke, leading to local changes in the instantaneous aerodynamic force on the wing at the start of each half-stroke. In this paper, I developed a simple approach to integrating prediction of these wake capture effects into existing analytical quasi-steady models for hovering insect flapping flight. The local wake flow field is modelled
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Micromagnetic calculation of the magnetite magnetosomal morphology control of magnetism in magnetotactic bacteria. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-09-27 Zhaowen Pei,Liao Chang,Fan Bai,Richard J Harrison
Magnetotactic bacteria (MTB), which precisely bio-synthesize magnetosomes of magnetite or greigite nanoparticles, have attracted broad interdisciplinary interests in microbiology, magnetic materials, biotechnology and geobiology. Previous experimental and numerical investigations demonstrate a close link among MTB species, magnetosome crystal habits, and magnetic characteristics, but quantitative constraints
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The effect of fibre cell remodelling on the power and optical quality of the lens. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-09-20 J Rodriguez,Q Tan,H Šikić,L A Taber,S Bassnett
Vertebrate eye lenses are uniquely adapted to form a refractive index gradient (GRIN) for improved acuity, and to grow slowly in size despite constant cell proliferation. The mechanisms behind these adaptations remain poorly understood. We hypothesize that cell compaction contributes to both. To test this notion, we examined the relationship between lens size and shape, refractive characteristics and
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Counterintuitive prey strategies against predators with finite budgets: protection heterogeneity among sites matters more than their number. J. Royal Soc. Interface (IF 3.9) Pub Date : 2023-09-20 Paul Clémençon,Steve Alpern,Shmuel Gal,Jérôme Casas
Combining the search and pursuit aspects of predator-prey interactions into a single game, where the payoff to the Searcher (predator) is the probability of finding and capturing the Hider (prey) within a fixed number of searches was proposed by Gal and Casas (J. R. Soc. Interface 11, 20140062 (doi:10.1098/rsif.2014.0062)). Subsequent models allowed the predator to continue its search (in another 'round')