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Sökning: L773:1742 5689 OR L773:1742 5662

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1.
  • Bagheri, Zahra M, et al. (författare)
  • Properties of neuronal facilitation that improve target tracking in natural pursuit simulations.
  • 2015
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5662 .- 1742-5689. ; 12:108
  • Tidskriftsartikel (refereegranskat)abstract
    • Although flying insects have limited visual acuity (approx. 1°) and relatively small brains, many species pursue tiny targets against cluttered backgrounds with high success. Our previous computational model, inspired by electrophysiological recordings from insect 'small target motion detector' (STMD) neurons, did not account for several key properties described from the biological system. These include the recent observations of response 'facilitation' (a slow build-up of response to targets that move on long, continuous trajectories) and 'selective attention', a competitive mechanism that selects one target from alternatives. Here, we present an elaborated STMD-inspired model, implemented in a closed loop target-tracking system that uses an active saccadic gaze fixation strategy inspired by insect pursuit. We test this system against heavily cluttered natural scenes. Inclusion of facilitation not only substantially improves success for even short-duration pursuits, but it also enhances the ability to 'attend' to one target in the presence of distracters. Our model predicts optimal facilitation parameters that are static in space and dynamic in time, changing with respect to the amount of background clutter and the intended purpose of the pursuit. Our results provide insights into insect neurophysiology and show the potential of this algorithm for implementation in artificial visual systems and robotic applications.
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2.
  • Ballo, Ahmed, 1978, et al. (författare)
  • Bone tissue reactions to biomimetic ion-substituted apatite surfaces on titanium implants
  • 2012
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 9:72, s. 1615-1624
  • Tidskriftsartikel (refereegranskat)abstract
    • The aim of this study was to evaluate the bone tissue response to strontium-and silicon-substituted apatite (Sr-HA and Si-HA) modified titanium (Ti) implants. Sr-HA, Si-HA and HA were grown on thermally oxidized Ti implants by a biomimetic process. Oxidized implants were used as controls. Surface properties, i.e. chemical composition, surface thickness, morphology/pore characteristics, crystal structure and roughness, were characterized with various analytical techniques. The implants were inserted in rat tibiae and block biopsies were prepared for histology, histomorphometry and scanning electron microscopy analysis. Histologically, new bone formed on all implant surfaces. The bone was deposited directly onto the Sr-HA and Si-HA implants without any intervening soft tissue. The statistical analysis showed significant higher amount of bone-implant contact (BIC) for the Si-doped HA modification (P = 0.030), whereas significant higher bone area (BA) for the Sr-doped HA modification (P = 0.034), when compared with the non-doped HA modification. The differences were most pronounced at the early time point. The healing time had a significant impact for both BA and BIC (P < 0.001). The present results show that biomimetically prepared Si-HA and Sr-HA on Ti implants provided bioactivity and promoted early bone formation.
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3.
  • Bar-Dolev, Maya, et al. (författare)
  • New insights into ice growth and melting modifications by antifreeze proteins
  • 2012
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 9:77, s. 3249-3259
  • Tidskriftsartikel (refereegranskat)abstract
    • Antifreeze proteins (AFPs) evolved in many organisms, allowing them to survive in cold climates by controlling ice crystal growth. The specific interactions of AFPs with ice determine their potential applications in agriculture, food preservation and medicine. AFPs control the shapes of ice crystals in a manner characteristic of the particular AFP type. Moderately active AFPs cause the formation of elongated bipyramidal crystals, often with seemingly defined facets, while hyperactive AFPs produce more varied crystal shapes. These different morphologies are generally considered to be growth shapes. In a series of bright light and fluorescent microscopy observations of ice crystals in solutions containing different AFPs, we show that crystal shaping also occurs during melting. In particular, the characteristic ice shapes observed in solutions of most hyperactive AFPs are formed during melting. We relate these findings to the affinities of the hyperactive AFPs for the basal plane of ice. Our results demonstrate the relation between basal plane affinity and hyperactivity and show a clear difference in the ice-shaping mechanisms of most moderate and hyperactive AFPs. This study provides key aspects associated with the identification of hyperactive AFPs.
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4.
  • Berntsen, Peter, 1974, et al. (författare)
  • Biomechanical effects of environmental and engineered particles on human airway smooth muscle cells
  • 2010
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 7:Suppl 3
  • Tidskriftsartikel (refereegranskat)abstract
    • The past decade has seen significant increases in combustion-generated ambient particles, which contain a nanosized fraction (less than 100 nm), and even greater increases have occurred in engineered nanoparticles (NPs) propelled by the booming nanotechnology industry. Although inhalation of these particulates has become a public health concern, human health effects and mechanisms of action for NPs are not well understood. Focusing on the human airway smooth muscle cell, here we show that the cellular mechanical function is altered by particulate exposure in a manner that is dependent upon particle material, size and dose. We used Alamar Blue assay to measure cell viability and optical magnetic twisting cytometry to measure cell stiffness and agonist-induced contractility. The eight particle species fell into four categories, based on their respective effect on cell viability and on mechanical function. Cell viability was impaired and cell contractility was decreased by (i) zinc oxide (40-100 nm and less than 44 mu m) and copper(II) oxide (less than 50 nm); cell contractility was decreased by (ii) fluorescent polystyrene spheres (40 nm), increased by (iii) welding fumes and unchanged by (iv) diesel exhaust particles, titanium dioxide (25 nm) and copper(II) oxide (less than 5 mu m), although in none of these cases was cell viability impaired. Treatment with hydrogen peroxide up to 500 mu M did not alter viability or cell mechanics, suggesting that the particle effects are unlikely to be mediated by particle-generated reactive oxygen species. Our results highlight the susceptibility of cellular mechanical function to particulate exposures and suggest that direct exposure of the airway smooth muscle cells to particulates may initiate or aggravate respiratory diseases.
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5.
  • Bianco, Giuseppe, et al. (författare)
  • Analysis of self-overlap reveals trade-offs in plankton swimming trajectories.
  • 2014
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5662 .- 1742-5689. ; 11:96
  • Tidskriftsartikel (refereegranskat)abstract
    • Movement is a fundamental behaviour of organisms that not only brings about beneficial encounters with resources and mates, but also at the same time exposes the organism to dangerous encounters with predators. The movement patterns adopted by organisms should reflect a balance between these contrasting processes. This trade-off can be hypothesized as being evident in the behaviour of plankton, which inhabit a dilute three-dimensional environment with few refuges or orienting landmarks. We present an analysis of the swimming path geometries based on a volumetric Monte Carlo sampling approach, which is particularly adept at revealing such trade-offs by measuring the self-overlap of the trajectories. Application of this method to experimentally measured trajectories reveals that swimming patterns in copepods are shaped to efficiently explore volumes at small scales, while achieving a large overlap at larger scales. Regularities in the observed trajectories make the transition between these two regimes always sharper than in randomized trajectories or as predicted by random walk theory. Thus, real trajectories present a stronger separation between exploration for food and exposure to predators. The specific scale and features of this transition depend on species, gender and local environmental conditions, pointing at adaptation to state and stage-dependent evolutionary trade-offs.
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6.
  • Biasetti, Jacopo, et al. (författare)
  • Blood flow and coherent vortices in the normal and aneurysmatic aortas : a fluid dynamical approach to intraluminal thrombus formation
  • 2011
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 8:63, s. 1449-1461
  • Tidskriftsartikel (refereegranskat)abstract
    • Abdominal aortic aneurysms (AAAs) are frequently characterized by the development of an intra-luminal thrombus (ILT), which is known to have multiple biochemical and biomechanical implications. Development of the ILT is not well understood, and shear-stress-triggered activation of platelets could be the first step in its evolution. Vortical structures (VSs) in the flow affect platelet dynamics, which motivated the present study of a possible correlation between VS and ILT formation in AAAs. VSs educed by the lambda(2)-method using computational fluid dynamics simulations of the backward-facing step problem, normal aorta, fusiform AAA and saccular AAA were investigated. Patient-specific luminal geometries were reconstructed from computed tomography scans, and Newtonian and Carreau-Yasuda models were used to capture salient rheological features of blood flow. Particularly in complex flow domains, results depended on the constitutive model. VSs developed all along the normal aorta, showing that a clear correlation between VSs and high wall shear stress (WSS) existed, and that VSs started to break up during late systole. In contrast, in the fusiform AAA, large VSs developed at sites of tortuous geometry and high WSS, occupying the entire lumen, and lasting over the entire cardiac cycle. Downward motion of VSs in the AAA was in the range of a few centimetres per cardiac cycle, and with a VS burst at that location, the release (from VSs) of shear-stress-activated platelets and their deposition to the wall was within the lower part of the diseased artery, i.e. where the thickest ILT layer is typically observed. In the saccular AAA, only one VS was found near the healthy portion of the aorta, while in the aneurysmatic bulge, no VSs occurred. We present a fluid-dynamics-motivated mechanism for platelet activation, convection and deposition in AAAs that has the potential of improving our current understanding of the pathophysiology of fluid-driven ILT growth.
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7.
  • Biasetti, Jacopo, et al. (författare)
  • Synergy between shear-induced migration and secondary flows on red blood cells transport in arteries : considerations on oxygen transport
  • 2014
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 11:97, s. 20140403-
  • Tidskriftsartikel (refereegranskat)abstract
    • Shear-induced migration of red blood cells (RBCs) is a well-known phenomenon characterizing blood flow in the small vessels (micrometre to millimetre size) of the cardiovascular system. In large vessels, like the abdominal aorta and the carotid artery (millimetre to centimetre size), the extent of this migration and its interaction with secondary flows has not been fully elucidated. RBC migration exerts its influence primarily on platelet concentration, oxygen transport and oxygen availability at the luminal surface, which could influence vessel wall disease processes in and adjacent to the intima. Phillips' shear-induced particle migration model, coupled to the Quemada viscosity model, was employed to simulate the macroscopic behaviour of RBCs in four patient-specific geometries: a normal abdominal aorta, an abdominal aortic aneurysm (AAA), a normal carotid bifurcation and a stenotic carotid bifurcation. Simulations show a migration of RBCs from the near-wall region with a lowering of wall haematocrit (volume fraction of RBCs) on the posterior side of the normal aorta and on the lateral-external side of the iliac arteries. A marked migration is observed on the outer wall of the carotid sinus, along the common carotid artery and in the carotid stenosis. No significant migration is observed in the AAA. The spatial and temporal patterns of wall haematocrit are correlated with the near-wall shear layer and with the secondary flows induced by the vessel curvature. In particular, secondary flows accentuate the initial lowering in RBC near-wall concentration by convecting RBCs from the inner curvature side to the outer curvature side. The results reinforce data in literature showing a decrease in oxygen partial pressure on the inner curvature wall of the carotid sinus induced by the presence of secondary flows. The lowering of wall haematocrit is postulated to induce a decrease in oxygen availability at the luminal surface through a diminished concentration of oxyhaemoglobin, hence contributing, with the reported lowered oxygen partial pressure, to local hypoxia.
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8.
  • Bonsall, Michael B., et al. (författare)
  • Bipolar disorder dynamics : affective instabilities, relaxation oscillations and noise
  • 2015
  • Ingår i: Journal of the Royal Society Interface. - : ROYAL SOC. - 1742-5689 .- 1742-5662. ; 12:112
  • Tidskriftsartikel (refereegranskat)abstract
    • Bipolar disorder is a chronic, recurrent mental illness characterized by extreme episodes of depressed and manic mood, interspersed with less severe but highly variable mood fluctuations. Here, we develop a novel mathematical approach for exploring the dynamics of bipolar disorder. We investigate how the dynamics of subjective experience of mood in bipolar disorder can be understood using a relaxation oscillator (RO) framework and test the model against mood time-series fluctuations from a set of individuals with bipolar disorder. We show that variable mood fluctuations in individuals diagnosed with bipolar disorder can be driven by the coupled effects of deterministic dynamics (captured by ROs) and noise. Using a statistical likelihood-based approach, we show that, in general, mood dynamics are described by two independent ROs with differing levels of endogenous variability among individuals. We suggest that this sort of nonlinear approach to bipolar disorder has neurobiological, cognitive and clinical implications for understanding this mental illness through a mechacognitive framework.
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9.
  • Bonsall, Michael B., et al. (författare)
  • Temporal dynamics of trauma memory persistence
  • 2023
  • Ingår i: Journal of the Royal Society Interface. - : Royal Society. - 1742-5689 .- 1742-5662. ; 20:203
  • Tidskriftsartikel (refereegranskat)abstract
    • Traumatic events lead to distressing memories, but such memories are made all the worse when they intrude to mind unbidden and recurrently. Intrusive memories and flashbacks after trauma are prominent in several mental disorders, including post-traumatic stress disorder and can persist for years. Critically, the reduction of intrusive memories provides a treatment target. While cognitive and descriptive models for psychological trauma exist, these lack formal quantitative structure and robust empirical validation. Here, using techniques from stochastic process theory, we develop a mechanistically driven, quantitative framework to extend understanding of the temporal dynamic processes of trauma memory. Our approach is to develop a probabilistic description of memory mechanisms to link to the broader goals of trauma treatment. We show how the marginal gains of treatments for intrusive memories can be enhanced as key properties (intervention strength and reminder strength) of the intervention and memory consolidation (probability memories are labile) vary. Parametrizing the framework with empirical data highlights that while emerging interventions to reduce occurrence of intrusive memories can be effective, counterintuitively, weakening multiple reactivation cues may help reduce intrusive memories more than would stronger cues. More broadly, the approach provides a quantitative framework for associating neural mechanisms of memory with broader cognitive processes.
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10.
  • Bosco, C, et al. (författare)
  • Exploring the high-resolution mapping of gender-disaggregated development indicators
  • 2017
  • Ingår i: Journal of the Royal Society, Interface. - : The Royal Society. - 1742-5662 .- 1742-5689. ; 14:129
  • Tidskriftsartikel (refereegranskat)abstract
    • Improved understanding of geographical variation and inequity in health status, wealth and access to resources within countries is increasingly being recognized as central to meeting development goals. Development and health indicators assessed at national or subnational scale can often conceal important inequities, with the rural poor often least well represented. The ability to target limited resources is fundamental, especially in an international context where funding for health and development comes under pressure. This has recently prompted the exploration of the potential of spatial interpolation methods based on geolocated clusters from national household survey data for the high-resolution mapping of features such as population age structures, vaccination coverage and access to sanitation. It remains unclear, however, how predictable these different factors are across different settings, variables and between demographic groups. Here we test the accuracy of spatial interpolation methods in producing gender-disaggregated high-resolution maps of the rates of literacy, stunting and the use of modern contraceptive methods from a combination of geolocated demographic and health surveys cluster data and geospatial covariates. Bayesian geostatistical and machine learning modelling methods were tested across four low-income countries and varying gridded environmental and socio-economic covariate datasets to build 1×1 km spatial resolution maps with uncertainty estimates. Results show the potential of the approach in producing high-resolution maps of key gender-disaggregated socio-economic indicators, with explained variance through cross-validation being as high as 74–75% for female literacy in Nigeria and Kenya, and in the 50–70% range for many other variables. However, substantial variations by both country and variable were seen, with many variables showing poor mapping accuracies in the range of 2–30% explained variance using both geostatistical and machine learning approaches. The analyses offer a robust basis for the construction of timely maps with levels of detail that support geographically stratified decision-making and the monitoring of progress towards development goals. However, the great variability in results between countries and variables highlights the challenges in applying these interpolation methods universally across multiple countries, and the importance of validation and quantifying uncertainty if this is undertaken.
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11.
  • Bottinelli, Arianna, et al. (författare)
  • Efficiency and shrinking in evolving networks
  • 2019
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 16:154
  • Tidskriftsartikel (refereegranskat)abstract
    • Characterizing the spatio-temporal evolution of networks is a central topic in many disciplines. While network expansion has been studied thoroughly, less is known about how empirical networks behave when shrinking. For transportation networks, this is especially relevant on account of their connection with the socio-economical substrate, and we focus here on the evolution of the French railway network from its birth in 1840 to 2000, in relation to the country's demographic dynamics. The network evolved in parallel with technology (e.g. faster trains) and under strong constraints, such as preserving a good population coverage and balancing cost and efficiency. We show that the shrinking phase that started in 1930 decreased the total length of the network while preserving efficiency and population coverage: efficiency and robustness remained remarkably constant while the total length of the network shrank by 50% between 1930 and 2000, and the total travel time and time-diameter decreased by more than 75% during the same period. Moreover, shrinking the network did not affect the overall accessibility with an average travel time that decreases steadily since its formation. This evolution leads naturally to an increase in transportation multimodality (such as a massive use of cars) and shows the importance of considering together transportation modes acting at different spatial scales. More generally, our results suggest that shrinking is not necessarily associated with a decay in performance and functions but can be beneficial in terms of design goals and can be part of the natural evolution of an adaptive network.
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12.
  • Bottinelli, Arianna, et al. (författare)
  • Local cost minimization in ant transport networks : from small-scale data to large-scale trade-offs
  • 2015
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 12:112
  • Tidskriftsartikel (refereegranskat)abstract
    • Transport networks distribute resources and information in many human and biological systems. Their construction requires optimization and balance of conflicting criteria such as robustness against disruptions, transport efficiency and building cost. The colonies of the polydomous Australian meat ant Iridomyrmex purpureus are a striking example of such a decentralized network, consisting of trails that connect spatially separated nests. Here we study the rules that underlie network construction in these ants. We find that a simple model of network growth, which we call the minimum linking model (MLM), is sufficient to explain the growth of real ant colonies. For larger networks, the MLM shows a qualitative similarity with a Euclidean minimum spanning tree, prioritizing cost and efficiency over robustness. We introduce a variant of our model to show that a balance between cost, efficiency and robustness can be also reproduced at larger scales than ant colonies. Remarkably, such a balance is influenced by a parameter reflecting the specific features of the modelled transport system. The extended MLM could thus be a suitable source of inspiration for the construction of cheap and efficient transport networks with non-zero robustness, suggesting possible applications in the design of human-made networks.
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13.
  • Briant, L. J. B., et al. (författare)
  • Functional identification of islet cell types by electrophysiological fingerprinting
  • 2017
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 14:128
  • Tidskriftsartikel (refereegranskat)abstract
    • The alpha-, beta- and delta-cells of the pancreatic islet exhibit different electrophysiological features. We used a large dataset of whole- cell patch- clamp recordings from cells in intactmouse islets (N = 288 recordings) to investigatewhether it is possible to reliably identify cell type (alpha,beta or gamma) based on their electrophysiological characteristics. We quantified 15 electrophysiological variables in each recorded cell. Individually, none of the variables could reliably distinguish the cell types. We therefore constructed a logistic regressionmodel that included all quantified variables, to determine whether they could together identify cell type. The model identified cell typewith 94% accuracy. Thismodelwas applied to a dataset of cells recorded from hyperglycaemic bV59M mice; it correctly identified cell type in all cells and was able to distinguish cells that co-expressed insulin and glucagon. Based on this revised functional identification, we were able to improve conductance-based models of the electrical activity in alpha-cells and generate a model of gamma-cell electrical activity. These new models could faithfully emulate alpha- and gamma-cell electrical activity recorded experimentally.
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14.
  • Britton, Tom, et al. (författare)
  • Estimation in emerging epidemics : biases and remedies
  • 2019
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 16:150
  • Tidskriftsartikel (refereegranskat)abstract
    • When analysing new emerging infectious disease outbreaks, one typically has observational data over a limited period of time and several parameters to estimate, such as growth rate, the basic reproduction number R-0, the case fatality rate and distributions of serial intervals, generation times, latency and incubation times and times between onset of symptoms, notification, death and recovery/discharge. These parameters form the basis for predicting a future outbreak, planning preventive measures and monitoring the progress of the disease outbreak. We study inference problems during the emerging phase of an outbreak, and point out potential sources of bias, with emphasis on: contact tracing backwards in time, replacing generation times by serial intervals, multiple potential infectors and censoring effects amplified by exponential growth. These biases directly affect the estimation of, for example, the generation time distribution and the case fatality rate, but can then propagate to other estimates such as R-0 and growth rate. We propose methods to remove or at least reduce bias using statistical modelling. We illustrate the theory by numerical examples and simulations.
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15.
  • Chai, Wen L., et al. (författare)
  • The biological seal of the implant-soft tissue interface evaluated in a tissue-engineered oral mucosal model
  • 2012
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 9:77, s. 3528-3538
  • Tidskriftsartikel (refereegranskat)abstract
    • For dental implants, it is vital that an initial soft tissue seal is achieved as this helps to stabilize and preserve the peri-implant tissues during the restorative stages following placement. The study of the implant-soft tissue interface is usually undertaken in animal models. We have developed an in vitro three-dimensional tissue-engineered oral mucosal model (3D OMM), which lends itself to the study of the implant-soft tissue interface as it has been shown that cells from the three-dimensional OMM attach onto titanium (Ti) surfaces forming a biological seal (BS). This study compares the quality of the BS achieved using the three-dimensional OMM for four types of Ti surfaces: polished, machined, sandblasted and anodized (TiUnite). The BS was evaluated quantitatively by permeability and cell attachment tests. Tritiated water (HTO) was used as the tracing agent for the permeability test. At the end of the permeability test, the Ti discs were removed from the three-dimensional OMM and an Alamar Blue assay was used for the measurement of residual cells attached to the Ti discs. The penetration of the HTO through the BS for the four types of Ti surfaces was not significantly different, and there was no significant difference in the viability of residual cells that attached to the Ti surfaces. The BS of the tissue-engineered oral mucosa around the four types of Ti surface topographies was not significantly different.
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16.
  • Chen, Xiaojie, et al. (författare)
  • First carrot, then stick : how the adaptive hybridization of incentives promotes cooperation
  • 2015
  • Ingår i: Journal of the Royal Society Interface. - : ROYAL SOC. - 1742-5689 .- 1742-5662. ; 12:102
  • Tidskriftsartikel (refereegranskat)abstract
    • Social institutions often use rewards and penalties to promote cooperation. Providing incentives tends to be costly, so it is important to find effective and efficient policies for the combined use of rewards and penalties. Most studies of cooperation, however, have addressed rewarding and punishing in isolation and have focused on peer-to-peer sanctioning as opposed to institutional sanctioning. Here, we demonstrate that an institutional sanctioning policy we call 'first carrot, then stick' is unexpectedly successful in promoting cooperation. The policy switches the incentive from rewarding to punishing when the frequency of cooperators exceeds a threshold. We find that this policy establishes and recovers full cooperation at lower cost and under a wider range of conditions than either rewards or penalties alone, in both well-mixed and spatial populations. In particular, the spatial dynamics of cooperation make it evident how punishment acts as a 'booster stage' that capitalizes on and amplifies the pro-social effects of rewarding. Together, our results show that the adaptive hybridization of incentives offers the 'best of both worlds' by combining the effectiveness of rewarding in establishing cooperation with the effectiveness of punishing in recovering it, thereby providing a surprisingly inexpensive and widely applicable method of promoting cooperation.
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17.
  • Christoffer Johansson, L., et al. (författare)
  • Mechanical power curve measured in the wake of pied flycatchers indicates modulation of parasite power across flight speeds
  • 2018
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 15:138
  • Tidskriftsartikel (refereegranskat)abstract
    • How aerodynamic power required for animal flight varies with flight speed determines optimal speeds during foraging and migratory flight. Despite its relevance, aerodynamic power provides an elusive quantity to measure directly in animal flight. Here, we determine the aerodynamic power from wake velocity fields, measured using tomographical particle image velocimetry, of pied flycatchers flying freely in a wind tunnel. We find a shallow U-shaped power curve, which is flatter than expected by theory. Based on how the birds vary body angle with speed, we speculate that the shallow curve results from increased body drag coefficient and body frontal area at lower flight speeds. Including modulation of body drag in the model results in a more reasonable fit with data than the traditional model. From the wake structure, we also find a single starting vortex generated from the two wings during the downstroke across flight speeds (1–9 m s21). This is accomplished by the arm wings interacting at the beginning of the downstroke, generating a unified starting vortex above the body of the bird. We interpret this as a mechanism resulting in a rather uniform downwash and low induced power, which can help explain the higher aerodynamic performance in birds compared with bats.
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18.
  • Comellas, E., et al. (författare)
  • A homeostatic-driven turnover remodelling constitutive model for healing in soft tissues
  • 2016
  • Ingår i: Journal of the Royal Society Interface. - : Royal Society of London. - 1742-5689 .- 1742-5662. ; 13:116
  • Tidskriftsartikel (refereegranskat)abstract
    • Remodelling of soft biological tissue is characterized by interacting biochemical and biomechanical events, which change the tissue's microstructure, and, consequently, its macroscopic mechanical properties. Remodelling is a well-defined stage of the healing process, and aims at recovering or repairing the injured extracellular matrix. Like other physiological processes, remodelling is thought to be driven by homeostasis, i.e. it tends to re-establish the properties of the uninjured tissue. However, homeostasis may never be reached, such that remodelling may also appear as a continuous pathological transformation of diseased tissues during aneurysm expansion, for example. A simple constitutive model for soft biological tissues that regards remodelling as homeostatic-driven turnover is developed. Specifically, the recoverable effective tissue damage, whose rate is the sum of a mechanical damage rate and a healing rate, serves as a scalar internal thermodynamic variable. In order to integrate the biochemical and biomechanical aspects of remodelling, the healing rate is, on the one hand, driven by mechanical stimuli, but, on the other hand, subjected to simple metabolic constraints. The proposed model is formulated in accordance with continuum damage mechanics within an open-system thermodynamics framework. The numerical implementation in an in-house finite-element code is described, particularized for Ogden hyperelasticity. Numerical examples illustrate the basic constitutive characteristics of the model and demonstrate its potential in representing aspects of remodelling of soft tissues. Simulation results are verified for their plausibility, but also validated against reported experimental data.
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19.
  • Coy, R., et al. (författare)
  • Combining in silico and in vitro models to inform cell seeding strategies in tissue engineering
  • 2020
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society Publishing. - 1742-5689 .- 1742-5662. ; 17:164
  • Tidskriftsartikel (refereegranskat)abstract
    • The seeding density of therapeutic cells in engineered tissue impacts both cell survival and vascularization. Excessively high seeded cell densities can result in increased death and thus waste of valuable cells, whereas lower seeded cell densities may not provide sufficient support for the tissue in vivo, reducing efficacy. Additionally, the production of growth factors by therapeutic cells in low oxygen environments offers a way of generating growth factor gradients, which are important for vascularization, but hypoxia can also induce unwanted levels of cell death. This is a complex problem that lends itself to a combination of computational modelling and experimentation. Here, we present a spatio-temporal mathematical model parametrized using in vitro data capable of simulating the interactions between a therapeutic cell population, oxygen concentrations and vascular endothelial growth factor (VEGF) concentrations in engineered tissues. Simulations of collagen nerve repair constructs suggest that specific seeded cell densities and non-uniform spatial distributions of seeded cells could enhance cell survival and the generation of VEGF gradients. These predictions can now be tested using targeted experiments.
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20.
  • Croze, Ottavio A., et al. (författare)
  • Dispersion of swimming algae in laminar and turbulent channel flows : consequences for photobioreactors
  • 2013
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 10:81, s. 20121041-
  • Tidskriftsartikel (refereegranskat)abstract
    • Shear flow significantly affects the transport of swimming algae in suspension. For example, viscous and gravitational torques bias bottom-heavy cells to swim towards regions of downwelling fluid (gyrotaxis). It is necessary to understand how such biases affect algal dispersion in natural and industrial flows, especially in view of growing interest in algal photobioreactors. Motivated by this, we here study the dispersion of gyrotactic algae in laminar and turbulent channel flows using direct numerical simulation (DNS) and a previously published analytical swimming dispersion theory. Time-resolved dispersion measures are evaluated as functions of the Peclet and Reynolds numbers in upwelling and downwelling flows. For laminar flows, DNS results are compared with theory using competing descriptions of biased swimming cells in shear flow. Excellent agreement is found for predictions that employ generalized Taylor dispersion. The results highlight peculiarities of gyrotactic swimmer dispersion relative to passive tracers. In laminar downwelling flow the cell distribution drifts in excess of the mean flow, increasing in magnitude with Peclet number. The cell effective axial diffusivity increases and decreases with Peclet number (for tracers it merely increases). In turbulent flows, gyrotactic effects are weaker, but discernable and manifested as non-zero drift. These results should have a significant impact on photobioreactor design.
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21.
  • Crutchfield, J. P., et al. (författare)
  • Objects that make objects: the population dynamics of structural complexity
  • 2006
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 3:7, s. 345-349
  • Tidskriftsartikel (refereegranskat)abstract
    • To analyse the evolutionary emergence of structural complexity in physical processes, we introduce a general, but tractable, model of objects that interact to produce new objects. Since the objects-epsilon-machines-have well-defined structural properties, we demonstrate that complexity in the resulting population dynamical system emerges on several distinct organizational scales during evolution-from individuals to nested levels of mutually self-sustaining interaction. The evolution to increased organization is dominated by the spontaneous creation of structural hierarchies and this, in turn, is facilitated by the innovation and maintenance of relatively low-complexity, but general individuals.
  •  
22.
  • Davenport, F., et al. (författare)
  • Neurodegenerative disease of the brain: a survey of interdisciplinary approaches
  • 2023
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 20:198
  • Forskningsöversikt (refereegranskat)abstract
    • Neurodegenerative diseases of the brain pose a major and increasing global health challenge, with only limited progress made in developing effective therapies over the last decade. Interdisciplinary research is improving understanding of these diseases and this article reviews such approaches, with particular emphasis on tools and techniques drawn from physics, chemistry, artificial intelligence and psychology.
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23.
  • Delhaye, Benoit, et al. (författare)
  • Surface strain measurements of fingertip skin under shearing
  • 2016
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society Publishing. - 1742-5689 .- 1742-5662. ; 13:115
  • Tidskriftsartikel (refereegranskat)abstract
    • The temporal evolution of surface strain, resulting from a combination of normal and tangential loading forces on the fingerpad, was calculated from high-resolution images. A customized robotic device loaded the fingertip with varying normal force, tangential direction and tangential speed. We observed strain waves that propagated from the periphery to the centre of the contact area. Consequently, different regions of the contact area were subject to varying degrees of compression, stretch and shear. The spatial distribution of both the strains and the strain energy densities depended on the stimulus direction. Additionally, the strains varied with the normal force level and were substantial, e.g. peak strains of 50% with a normal force of 5 N, i.e. at force levels well within the range of common dexterous manipulation tasks. While these observations were consistent with some theoretical predictions from contact mechanics, we also observed substantial deviations as expected given the complex geometry and mechanics of fingertips. Specifically, from in-depth analyses, we conclude that some of these deviations depend on local fingerprint patterns. Our data provide useful information for models of tactile afferent responses and background for the design of novel haptic interfaces.
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24.
  • El Khalifi, Mohamed, et al. (författare)
  • Extending susceptible-infectious-recovered-susceptible epidemics to allow for gradual waning of immunity
  • 2023
  • Ingår i: Journal of the Royal Society Interface. - 1742-5689 .- 1742-5662. ; 20:206
  • Tidskriftsartikel (refereegranskat)abstract
    • Susceptible-infectious-recovered-susceptible (SIRS) epidemic models assume that individual immunity wanes in one leap, from complete immunity to complete susceptibility. For many diseases immunity on the contrary wanes gradually, something that has become even more evident during COVID-19 pandemic where also recently infected have a reinfection risk, and booster vaccines are given to increase immunity. Here, a novel mathematical model is presented allowing for the gradual decay of immunity following linear or exponential waning functions. The two new models and the SIRS model are compared assuming all three models have the same cumulative immunity. When no intervention is put in place, we find that the long-term prevalence is higher for the models with gradual waning. If aiming for herd immunity by continuous vaccination, it is shown that larger vaccine quantities are required when immunity wanes gradually compared with results obtained from the SIRS model, and this difference is the biggest for the most realistic assumption of exponentially waning of immunity. For parameter choices fitting to COVID-19, the critical amount of vaccine supply is about 50% higher if immunity wanes linearly, and more than 150% higher when immunity wanes exponentially, when compared with the classic SIRS epidemic model.
  •  
25.
  • Favero, Martina, et al. (författare)
  • Modelling preventive measures and their effect on generation times in emerging epidemics
  • 2022
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 19:191
  • Tidskriftsartikel (refereegranskat)abstract
    • We present a stochastic epidemic model to study the effect of various preventive measures, such as uniform reduction of contacts and transmission, vaccination, isolation, screening and contact tracing, on a disease outbreak in a homogeneously mixing community. The model is based on an infectivity process, which we define through stochastic contact and infectiousness processes, so that each individual has an independent infectivity profile. In particular, we monitor variations of the reproduction number and of the distribution of generation times. We show that some interventions, i.e. uniform reduction and vaccination, affect the former while leaving the latter unchanged, whereas other interventions, i.e. isolation, screening and contact tracing, affect both quantities. We provide a theoretical analysis of the variation of these quantities, and we show that, in practice, the variation of the generation time distribution can be significant and that it can cause biases in the estimation of reproduction numbers. The framework, because of its general nature, captures the properties of many infectious diseases, but particular emphasis is on COVID-19, for which numerical results are provided.
  •  
26.
  • Federico, Salvatore, et al. (författare)
  • Nonlinear elasticity of biological tissues with statistical fibre orientation
  • 2010
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 7:47, s. 955-966
  • Tidskriftsartikel (refereegranskat)abstract
    • The elastic strain energy potential for nonlinear fibre-reinforced materials is customarily obtained by superposition of the potentials of the matrix and of each family of fibres. Composites with statistically oriented fibres, such as biological tissues, can be seen as being reinforced by a continuous infinity of fibre families, the orientation of which can be represented by means of a probability density function defined on the unit sphere (i.e. the solid angle). In this case, the superposition procedure gives rise to an integral form of the elastic potential such that the deformation features in the integral, which therefore cannot be calculated a priori. As a consequence, an analytical use of this potential is impossible. In this paper, we implemented this integral form of the elastic potential into a numerical procedure that evaluates the potential, the stress and the elasticity tensor at each deformation step. The numerical integration over the unit sphere is performed by means of the method of spherical designs, in which the result of the integral is approximated by a suitable sum over a discrete subset of the unit sphere. As an example of application, we modelled the collagen fibre distribution in articular cartilage, and used it in simulating displacement-controlled tests: the unconfined compression of a cylindrical sample and the contact problem in the hip joint.
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27.
  • Ferraz, Natalia, et al. (författare)
  • Haemocompatibility and ion exchange capability of nanocellulose polypyrrole membranes intended for blood purification
  • 2012
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 9:73, s. 1943-1955
  • Tidskriftsartikel (refereegranskat)abstract
    • Composites of nanocellulose and the conductive polymer polypyrrole (PPy) are presented as candidates for a new generation of haemodialysis membranes. The composites may combine active ion exchange with passive ultrafiltration, and the large surface area (about 80 m2 g−1) could potentially provide compact dialysers. Herein, the haemocompatibility of the novel membranes and the feasibility of effectively removing small uraemic toxins by potential-controlled ion exchange were studied. The thrombogenic properties of the composites were improved by applying a stable heparin coating. In terms of platelet adhesion and thrombin generation, the composites were comparable with haemocompatible polymer polysulphone, and regarding complement activation, the composites were more biocompatible than commercially available membranes. It was possible to extract phosphate and oxalate ions from solutions with physiological pH and the same tonicity as that of the blood. The exchange capacity of the materials was found to be 600 ± 26 and 706 ± 31 μmol g−1 in a 0.1 M solution (pH 7.4) and in an isotonic solution of phosphate, respectively. The corresponding values with oxalate were 523 ± 5 in a 0.1 M solution (pH 7.4) and 610 ± 1 μmol g−1 in an isotonic solution. The heparinized PPy–cellulose composite is consequently a promising haemodialysis material, with respect to both potential-controlled extraction of small uraemic toxins and haemocompatibility.
  •  
28.
  • Fitzer, Susan C., et al. (författare)
  • Ocean acidification alters the material properties of Mytilus edulis shells
  • 2015
  • Ingår i: Journal of the Royal Society Interface. - : Royal Society Publishing. - 1742-5689 .- 1742-5662. ; 12:103
  • Tidskriftsartikel (refereegranskat)abstract
    • Ocean acidification (OA) and the resultant changing carbonate saturation states is threatening the formation of calcium carbonate shells and exoskeletons of marine organisms. The production of biominerals in such organisms relies on the availability of carbonate and the ability of the organism to biomineralize in changing environments. To understand how biomineralizers will respond to OA the common blue mussel, Mytilus edulis, was cultured at projected levels of pCO(2) (380, 550, 750, 1000 mu atm) and increased temperatures (ambient, ambient plus 2 degrees C). Nanoindentation (a single mussel shell) and microhardness testing were used to assess the material properties of the shells. Young's modulus (E), hardness (H) and toughness (K-IC) were measured in mussel shells grown in multiple stressor conditions. OA caused mussels to produce shell calcite that is stiffer (higher modulus of elasticity) and harder than shells grown in control conditions. The outer shell (calcite) is more brittle in OA conditions while the inner shell (aragonite) is softer and less stiff in shells grown under OA conditions. Combining increasing ocean pCO(2) and temperatures as projected for future global ocean appears to reduce the impact of increasing pCO(2) on the material properties of the mussel shell. OA may cause changes in shell material properties that could prove problematic under predation scenarios for the mussels; however, this may be partially mitigated by increasing temperature.
  •  
29.
  • Fragkopoulos, Alexandros A., et al. (författare)
  • Self-generated oxygen gradients control collective aggregation of photosynthetic microbes
  • 2021
  • Ingår i: Journal of the Royal Society Interface. - : ROYAL SOC. - 1742-5689 .- 1742-5662. ; 18:185
  • Tidskriftsartikel (refereegranskat)abstract
    • For billions of years, photosynthetic microbes have evolved under the variable exposure to sunlight in diverse ecosystems and microhabitats all over our planet. Their abilities to dynamically respond to alterations of the luminous intensity, including phototaxis, surface association and diurnal cell cycles, are pivotal for their survival. If these strategies fail in the absence of light, the microbes can still sustain essential metabolic functionalities and motility by switching their energy production from photosynthesis to oxygen respiration. For suspensions of motile C. reinhardtii cells above a critical density, we demonstrate that this switch reversibly controls collective microbial aggregation. Aerobic respiration dominates over photosynthesis in conditions of low light, which causes the microbial motility to sensitively depend on the local availability of oxygen. For dense microbial populations in self-generated oxygen gradients, microfluidic experiments and continuum theory based on a reaction-diffusion mechanism show that oxygen-regulated motility enables the collective emergence of highly localized regions of high and low cell densities.
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30.
  • Gasser, T. Christian, et al. (författare)
  • Hyperelastic modelling of arterial layers with distributed collagen fibre orientations
  • 2006
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 3:6, s. 15-35
  • Forskningsöversikt (refereegranskat)abstract
    • Constitutive relations are fundamental to the solution of problems in continuum mechanics, and are required in the study of, for example, mechanically dominated clinical interventions involving soft biological tissues. Structural continuum constitutive models of arterial layers integrate information about the tissue morphology and therefore allow investigation of the interrelation between structure and function in response to mechanical loading. Collagen fibres are key ingredients in the structure of arteries. In the media (the middle layer of the artery wall) they are arranged in two helically distributed families with a small pitch and very little dispersion in their orientation (i.e. they are aligned quite close to the circumferential direction). By contrast, in the adventitial and intimal layers, the orientation of the collagen fibres is dispersed, as shown by polarized light microscopy of stained arterial tissue. As a result, continuum models that do not account for the dispersion are not able to capture accurately the stress-strain response of these layers. The purpose of this paper, therefore, is to develop a structural continuum framework that is able to represent the dispersion of the collagen fibre orientation. This then allows the development of a new hyperelastic free-energy function that is particularly suited for representing the anisotropic elastic properties of adventitial and intimal layers of arterial walls, and is a generalization of the fibre-reinforced structural model introduced by Holzapfel & Gasser (Holzapfel & Gasser 2001 Comput. Meth. Appl. Mech. Eng. 190, 4379-4403) and Holzapfel et al. (Holzapfel et al. 2000 J. Elast. 61, 1-48). The model incorporates an additional scalar structure parameter that characterizes the dispersed collagen orientation. An efficient finite element implementation of the model is then presented and numerical examples show that the dispersion of the orientation of collagen fibres in the adventitia of human iliac arteries has a significant effect on their mechanical response.
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31.
  • Gerlee, Philip, 1980, et al. (författare)
  • Extinction rates in tumour public goods games
  • 2017
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 14:134
  • Tidskriftsartikel (refereegranskat)abstract
    • Cancer evolution and progression are shaped by cellular interactions and Darwinian selection. Evolutionary game theory incorporates both of these principles, and has been proposed as a framework to understand tumour cell population dynamics. A cornerstone of evolutionary dynamics is the replicator equation, which describes changes in the relative abundance of different cell types, and is able to predict evolutionary equilibria. Typically, the replicator equation focuses on differences in relative fitness. We here showthat this framework might not be sufficient under all circumstances, as it neglects important aspects of population growth. Standard replicator dynamics might miss critical differences in the time it takes to reach an equilibrium, as this time also depends on cellular turnover in growing but bounded populations. As the system reaches a stable manifold, the time to reach equilibrium depends on cellular death and birth rates. These rates shape the time scales, in particular, in coevolutionary dynamics of growth factor producers and free-riders. Replicator dynamics might be an appropriate framework only when birth and death rates are of similar magnitude. Otherwise, population growth effects cannot be neglected when predicting the time to reach an equilibrium, and cell-type-specific rates have to be accounted for explicitly.
  •  
32.
  • Gerlee, Philip, 1980, et al. (författare)
  • Gene divergence and pathway duplication in the metabolic network of yeast and digital organisms
  • 2009
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 6, s. 1233-1245
  • Tidskriftsartikel (refereegranskat)abstract
    • We have studied the metabolic gene–function network in yeast and digital organisms evolved in the artificial life platform Avida. The gene–function network is a bipartite network in which a link exists between a gene and a function (pathway) if that function depends on that gene, and can also be viewed as a decomposition of the more traditional functional gene networks, where two genes are linked if they share any function. We show that the gene–function network exhibits two distinct degree distributions: the gene degree distribution is scale-free while the pathway distribution is exponential. This is true for both yeast and digital organisms, which suggests that this is a general property of evolving systems, and we propose that the scale-free gene degree distribution is due to pathway duplication, i.e. the development of a new pathway where the original function is still retained. Pathway duplication would serve as preferential attachment for the genes, and the experiments with Avida revealed precisely this; genes involved in many pathways are more likely to increase their connectivity. Measuring the overlap between different pathways, in terms of the genes that constitute them, showed that pathway duplication also is a likely mechanism in yeast evolution. This analysis sheds new light on the evolution of genes and functionality, and suggests that function duplication could be an important mechanism in evolution.
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33.
  • Giordano, Chiara, et al. (författare)
  • Connecting Fractional Anisotropy from Medical Images with Mechanical Anisotropy of a Hyperviscoelastic Fibre-reinforced Constitutive Model for Brain Tissue
  • 2014
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 11:91, s. 20130914-
  • Tidskriftsartikel (refereegranskat)abstract
    • Brain tissue modelling has been an active area of research for years. Brain matter does not follow the constitutive relations for common materials and loads applied to the brain turn into stresses and strains depending on tissue local morphology. In this work, a hyperviscoelastic fibre-reinforced anisotropic law is used for computational brain injury prediction. Thanks to a fibrere-inforcement dispersion parameter, this formulation accounts for anisotropic features and heterogeneities of the tissue owing to different axon alignment. The novelty of the work is the correlation of the material mechanical anisotropy with fractional anisotropy (FA) from diffusion tensor images. Finite-element (FE) models are used to investigate the influence of the fibre distribution for different loading conditions. In the case of tensile-compressive loads, the comparison between experiments and simulations highlights the validity of the proposed FA-k correlation. Axon alignment affects the deformation predicted by FE models and, when the strain in the axonal direction is large with respect to the maximum principal strain, decreased maximum deformations are detected. It is concluded that the introduction of fibre dispersion information into the constitutive law of brain tissue affects the biofidelity of the simulations.
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34.
  • Goodman, Rosa (författare)
  • An architectural understanding of natural sway frequencies in trees
  • 2019
  • Ingår i: Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 16
  • Tidskriftsartikel (refereegranskat)abstract
    • The relationship between form and function in trees is the subject of a long-standing debate in forest ecology and provides the basis for theories concerning forest ecosystem structure and metabolism. Trees interact with the wind in a dynamic manner and exhibit natural sway frequencies and damping processes that are important in understanding wind damage. Tree-wind dynamics are related to tree architecture, but this relationship is not well understood. We present a comprehensive view of natural sway frequencies in trees by compiling a dataset of field measurement spanning conifers and broadleaves, tropical and temperate forests. The field data show that a cantilever beam approximation adequately predicts the fundamental frequency of conifers, but not that of broadleaf trees. We also use structurally detailed tree dynamics simulations to test fundamental assumptions underpinning models of natural frequencies in trees. We model the dynamic properties of greater than 1000 trees using a finite-element approach based on accurate three-dimensional model trees derived from terrestrial laser scanning data. We show that (1) residual variation, the variation not explained by the cantilever beam approximation, in fundamental frequencies of broadleaf trees is driven by their architecture; (2) slender trees behave like a simple pendulum, with a single natural frequency dominating their motion, which makes them vulnerable to wind damage and (3) the presence of leaves decreases both the fundamental frequency and the damping ratio. These findings demonstrate the value of new three-dimensional measurements for understanding wind impacts on trees and suggest new directions for improving our understanding of tree dynamics from conifer plantations to natural forests.
  •  
35.
  • Grandfield, Kathryn, et al. (författare)
  • Visualizing biointerfaces in three dimensions : electron tomography of the bone-hydroxyapatite interface
  • 2010
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 7:51, s. 1497-501
  • Tidskriftsartikel (refereegranskat)abstract
    • A positive interaction between human bone tissue and synthetics is crucial for the success of bone-regenerative materials. A greater understanding of the mechanisms governing bone-bonding is often gained via visualization of the bone-implant interface. Interfaces to bone have long been imaged with light, X-rays and electrons. Most of these techniques, however, only provide low-resolution or two-dimensional information. With the advances in modern day transmission electron microscopy, including new hardware and increased software computational speeds, the high-resolution visualization and analysis of three-dimensional structures is possible via electron tomography. We report, for the first time, a three-dimensional reconstruction of the interface between human bone and a hydroxyapatite implant using Z-contrast electron tomography. Viewing this structure in three dimensions enabled us to observe the nanometre differences in the orientation of hydroxyapatite crystals precipitated on the implant surface in vivo versus those in the collagen matrix of bone. Insight into the morphology of biointerfaces is considerably enhanced with three-dimensional techniques. In this regard, electron tomography may revolutionize the approach to high-resolution biointerface characterization.
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36.
  • Guidolin, Andrea, et al. (författare)
  • Geometry of spiking patterns in early visual cortex : a topological data analytic approach
  • 2022
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 19:196
  • Tidskriftsartikel (refereegranskat)abstract
    • In the brain, spiking patterns live in a high-dimensional space of neurons and time. Thus, determining the intrinsic structure of this space presents a theoretical and experimental challenge. To address this challenge, we introduce a new framework for applying topological data analysis (TDA) to spike train data and use it to determine the geometry of spiking patterns in the visual cortex. Key to our approach is a parametrized family of distances based on the timing of spikes that quantifies the dissimilarity between neuronal responses. We applied TDA to visually driven single-unit and multiple single-unit spiking activity in macaque V1 and V2. TDA across timescales reveals a common geometry for spiking patterns in V1 and V2 which, among simple models, is most similar to that of a low-dimensional space endowed with Euclidean or hyperbolic geometry with modest curvature. Remarkably, the inferred geometry depends on timescale and is clearest for the timescales that are important for encoding contrast, orientation and spatial correlations.
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37.
  • Gyllingberg, Linnéa, et al. (författare)
  • Using neuronal models to capture burst-and-glide motion and leadership in fish
  • 2023
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 20:204
  • Tidskriftsartikel (refereegranskat)abstract
    • While mathematical models, in particular self-propelled particle models, capture many properties of large fish schools, they do not always capture the interactions of smaller shoals. Nor do these models tend to account for the use of intermittent locomotion, often referred to as burst-and-glide, by many species. In this paper, we propose a model of social burst-and-glide motion by combining a well-studied model of neuronal dynamics, the FitzHugh-Nagumo model, with a model of fish motion. We first show that our model can capture the motion of a single fish swimming down a channel. Extending to a two-fish model, where visual stimulus of a neighbour affects the internal burst or glide state of the fish, we observe a rich set of dynamics found in many species. These include: leader-follower behaviour; periodic changes in leadership; apparently random (i.e. chaotic) leadership change; and tit-for-tat turn taking. Moreover, unlike previous studies where a randomness is required for leadership switching to occur, we show that this can instead be the result of deterministic interactions. We give several empirically testable predictions for how bursting fish interact and discuss our results in light of recently established correlations between fish locomotion and brain activity.
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38.
  • Hakansson, Jonas, et al. (författare)
  • Body lift, drag and power are relatively higher in large-eared than in small-eared bat species
  • 2017
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 14:135
  • Tidskriftsartikel (refereegranskat)abstract
    • Bats navigate the dark using echolocation. Echolocation is enhanced by external ears, but external ears increase the projected frontal area and reduce the streamlining of the animal. External ears are thus expected to compromise flight efficiency, but research suggests that very large ears may mitigate the cost by producing aerodynamic lift. Here we compare quantitative aerodynamic measures of flight efficiency of two bat species, one large-eared (Plecotus auritus) and one small-eared (Glossophaga soricina), flying freely in a wind tunnel. We find that the body drag of both species is higher than previously assumed and that the large-eared species has a higher body drag coefficient, but also produces relatively more ear/body lift than the small-eared species, in line with prior studies on model bats. The measured aerodynamic power of P. auritus was higher than predicted from the aerodynamic model, while the small-eared species aligned with predictions. The relatively higher power of the large-eared species results in lower optimal flight speeds and our findings support the notion of a trade-off between the acoustic benefits of large external ears and aerodynamic performance. The result of this trade-off would be the ecomorphological correlation in bat flight, with large-eared bats generally adopting slow-flight feeding strategies.
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39.
  • Hayward, Vincent, et al. (författare)
  • Spatio-temporal skin strain distributions evoke low variability spike responses in cuneate neurons
  • 2014
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5662 .- 1742-5689. ; 11:93
  • Tidskriftsartikel (refereegranskat)abstract
    • A common method to explore the somatosensory function of the brain is to relate skin stimuli to neurophysiological recordings. However, interaction with the skin involves complex mechanical effects. Variability in mechanically induced spike responses is likely to be due in part to mechanical variability of the transformation of stimuli into spiking patterns in the primary sensors located in the skin. This source of variability greatly hampers detailed investigations of the response of the brain to different types of mechanical stimuli. A novel stimulation technique designed to minimize the uncertainty in the strain distributions induced in the skin was applied to evoke responses in single neurons in the cat. We show that exposure to specific spatio-temporal stimuli induced highly reproducible spike responses in the cells of the cuneate nucleus, which represents the first stage of integration of peripheral inputs to the brain. Using precisely controlled spatio-temporal stimuli, we also show that cuneate neurons, as a whole, were selectively sensitive to the spatial and to the temporal aspects of the stimuli. We conclude that the present skin stimulation technique based on localized differential tractions greatly reduces response variability that is exogenous to the information processing of the brain and hence paves the way for substantially more detailed investigations of the brain's somatosensory system.
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40.
  • Hedenström, Anders, et al. (författare)
  • Beyond robins: aerodynamic analyses of animal flight.
  • 2008
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5662 .- 1742-5689. ; 5:23, s. 595-601
  • Tidskriftsartikel (refereegranskat)abstract
    • Recent progress in studies of animal flight mechanics is reviewed. A range of birds, and now bats, has been studied in wind tunnel facilities, revealing an array of wake patterns caused by the beating wings and also by the drag on the body. Nevertheless, the quantitative analysis of these complex wake structures shows a degree of similarity among all the different wake patterns and a close agreement with standard quasi-steady aerodynamic models and predictions. At the same time, new data on the flow over a bat wing in mid-downstroke show that, at least in this case, such simplifications cannot be useful in describing in detail either the wing properties or control prospects. The reasons for these apparently divergent results are discussed and prospects for future advances are considered.
  •  
41.
  • Hedenström, Anders, et al. (författare)
  • Vortex wakes generated by robins Erithacus rubecula during free flight in a wind tunnel
  • 2006
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5662 .- 1742-5689. ; 3:7, s. 263-276
  • Tidskriftsartikel (refereegranskat)abstract
    • The wakes of two individual robins were measured in digital particle image velocimetry (DPIV) experiments conducted in the Lund wind tunnel. Wake measurements were compared with each other, and with previous studies in the same facility. There was no significant individual variation in any of the measured quantities. Qualitatively, the wake structure and its gradual variation with flight speed were exactly as previously measured for the thrush nightingale. A procedure that accounts for the disparate sources of circulation spread over the complex wake structure nevertheless can account for the vertical momentum flux required to support the weight, and an example calculation is given for estimating drag from the components of horizontal momentum flux (whose net value is zero). The measured circulations of the largest structures in the wake can be predicted quite well by simple models, and expressions are given to predict these and other measurable quantities in future bird flight experiments.
  •  
42.
  • Henningsson, Per, et al. (författare)
  • Aerodynamics of manoeuvring flight in brown long-eared bats (Plecotus auritus)
  • 2018
  • Ingår i: Journal of the Royal Society, Interface. - : The Royal Society. - 1742-5662 .- 1742-5689. ; 15:148
  • Tidskriftsartikel (refereegranskat)abstract
    • In this study, we explicitly examine the aerodynamics of manoeuvring flight in animals. We studied brown long-eared bats flying in a wind tunnel while performing basic sideways manoeuvres. We used particle image velocimetry in combination with high-speed filming to link aerodynamics and kinematics to understand the mechanistic basis of manoeuvres. We predicted that the bats would primarily use the downstroke to generate the asymmetries for the manoeuvre since it has been shown previously that the majority of forces are generated during this phase of the wingbeat. We found instead that the bats more often used the upstroke than they used the downstroke for this. We also found that the bats used both drag/thrust-based and lift-based asymmetries to perform the manoeuvre and that they even frequently switch between these within the course of a manoeuvre. We conclude that the bats used three main modes: lift asymmetries during downstroke, thrust/drag asymmetries during downstroke and thrust/drag asymmetries during upstroke. For future studies, we hypothesize that lift asymmetries are used for fast turns and thrust/drag for slow turns and that the choice between up- and downstroke depends on the timing of when the bat needs to generate asymmetries.
  •  
43.
  • Henningsson, Per, et al. (författare)
  • The complex aerodynamic footprint of desert locusts revealed by large-volume tomographic particle image velocimetry.
  • 2015
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5662 .- 1742-5689. ; 12:108
  • Tidskriftsartikel (refereegranskat)abstract
    • Particle image velocimetry has been the preferred experimental technique with which to study the aerodynamics of animal flight for over a decade. In that time, hardware has become more accessible and the software has progressed from the acquisition of planes through the flow field to the reconstruction of small volumetric measurements. Until now, it has not been possible to capture large volumes that incorporate the full wavelength of the aerodynamic track left behind during a complete wingbeat cycle. Here, we use a unique apparatus to acquire the first instantaneous wake volume of a flying animal's entire wingbeat. We confirm the presence of wake deformation behind desert locusts and quantify the effect of that deformation on estimates of aerodynamic force and the efficiency of lift generation. We present previously undescribed vortex wake phenomena, including entrainment around the wing-tip vortices of a set of secondary vortices borne of Kelvin-Helmholtz instability in the shear layer behind the flapping wings.
  •  
44.
  • Henningsson, Per, et al. (författare)
  • Time-resolved vortex wake of a common swift flying over a range of flight speeds.
  • 2011
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5662 .- 1742-5689. ; 8, s. 807-816
  • Tidskriftsartikel (refereegranskat)abstract
    • The wake of a freely flying common swift (Apus apus L.) is examined in a wind tunnel at three different flight speeds, 5.7, 7.7 and 9.9 m s(-1). The wake of the bird is visualized using high-speed stereo digital particle image velocimetry (DPIV). Wake images are recorded in the transverse plane, perpendicular to the airflow. The wake of a swift has been studied previously using DPIV and recording wake images in the longitudinal plane, parallel to the airflow. The high-speed DPIV system allows for time-resolved wake sampling and the result shows features that were not discovered in the previous study, but there was approximately a 40 per cent vertical force deficit. As the earlier study also revealed, a pair of wingtip vortices are trailing behind the wingtips, but in addition, a pair of tail vortices and a pair of 'wing root vortices' are found that appear to originate from the wing/body junction. The existence of wing root vortices suggests that the two wings are not acting as a single wing, but are to some extent aerodynamically detached from each other. It is proposed that this is due to the body disrupting the lift distribution over the wing by generating less lift than the wings.
  •  
45.
  • Henze, Miriam J., et al. (författare)
  • Pterin-pigmented nanospheres create the colours of the polymorphic damselfly Ischnura elegans
  • 2019
  • Ingår i: Journal of the Royal Society, Interface. - : The Royal Society. - 1742-5662 .- 1742-5689. ; 16:153
  • Tidskriftsartikel (refereegranskat)abstract
    • Animal colours commonly act as signals for mates or predators. In many damselfly species, both sexes go through a developmental colour change as adults, and females often show colour polymorphism, which may have a function in mate choice, avoidance of mating harassment and camouflage. In the blue-tailed damselfly, Ischnura elegans, young males are bright green and turn blue as they reach maturity. Females are red ( rufescens) or violet ( violacea) as immatures and, when mature, either mimic the blue colour of the males ( androchrome), or acquire an inconspicuous olive-green ( infuscans) or olive-brown ( obsoleta). The genetic basis of these differences is still unknown. Here, we quantify the colour development of all morphs of I. elegans and investigate colour formation by combining anatomical data and reflectance spectra with optical finite-difference time-domain simulations. While the coloration primarily arises from a disordered assembly of nanospheres in the epidermis, morph-dependent changes result from adjustments in the composition of pterin pigments within the nanospheres, and from associated shifts in optical density. Other pigments fine-tune hue and brilliance by absorbing stray light. These mechanisms produce an impressive palette of colours and offer guidance for genetic studies on the evolution of colour polymorphism and visual communication.
  •  
46.
  • Hoffecker, IT, et al. (författare)
  • Tuning intercellular adhesion with membrane-anchored oligonucleotides
  • 2019
  • Ingår i: Journal of the Royal Society, Interface. - : The Royal Society. - 1742-5662 .- 1742-5689. ; 16:159, s. 20190299-
  • Tidskriftsartikel (refereegranskat)abstract
    • Adhesive interactions between cells play an integral role in development, differentiation and regeneration. Existing methods for controlling cell–cell cohesion and adhesion by manipulating protein expression are constrained by biological interdependencies, e.g. coupling of cadherins to actomyosin force-feedback mechanisms. We use oligonucleotides conjugated to PEGylated lipid anchors (ssDNAPEGDPPE) to introduce artificial cell–cell adhesion that is largely decoupled from the internal cytoskeleton. We describe cell–cell doublets with a mechanical model based on isotropic, elastic deformation of spheres to estimate the adhesion at the cell–cell interface. Physical manipulation of adhesion by modulating the PEG-lipid to ssDNAPEGDPPE ratio, and conversely treating with actin-depolymerizing cytochalasin D, resulted in decreases and increases in doublet contact area, respectively. Our data are relevant to the ongoing discussion over mechanisms of tissue surface tension and in agreement with models based on opposing cortical and cohesive forces. PEG-lipid modulation of doublet geometries resulted in a well-defined curve indicating continuity, enabling prescriptive calibration for controlling doublet geometry. Our study demonstrates tuning of basic doublet adhesion, laying the foundation for more complex multicellular adhesion control independent of protein expression.
  •  
47.
  • Holme, Petter (författare)
  • Model validation of simple-graph representations of metabolism
  • 2009
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 6:40, s. 1027-1034
  • Tidskriftsartikel (refereegranskat)abstract
    • The large-scale properties of chemical reaction systems, such as metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information, lists of chemical reactions, available in databases. Even for the simplest type of graph representation, this reduction can be done in several ways. We investigate different simple network representations by testing how well they encode information about one biologically important network structure-network modularity (the propensity for edges to be clustered into dense groups that are sparsely connected between each other). To achieve this goal, we design a model of reaction systems where network modularity can be controlled and measure how well the reduction to simple graphs captures the modular structure of the model reaction system. We find that the network types that best capture the modular structure of the reaction system are substrate-product networks (where substrates are linked to products of a reaction) and substance networks (with edges between all substances participating in a reaction). Furthermore, we argue that the proposed model for reaction systems with tunable clustering is a general framework for studies of how reaction systems are affected by modularity. To this end, we investigate statistical properties of the model and find, among other things, that it recreates correlations between degree and mass of the molecules.
  •  
48.
  • Holme, Petter, et al. (författare)
  • Role-similarity based functional prediction in networked systems : application to the yeast proteome
  • 2005
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 2:4, s. 327-333
  • Tidskriftsartikel (refereegranskat)abstract
    • We propose a general method to predict functions of vertices where (i) the wiring of the network is somehow related to the vertex functionality and (ii) a fraction of the vertices are functionally classified. The method is influenced by role-similarity measures of social network analysis. The two versions of our prediction scheme axe tested on model networks where the functions of the vertices are designed to match their network surroundings. We also apply these methods to the proteome of the yeast Saccharomyces cerevisiae and find the results compatible with more specialized methods.
  •  
49.
  • Holzapfel, Gerhard A., et al. (författare)
  • Modelling the layer-specific three-dimensional residual stresses in arteries, with an application to the human aorta
  • 2010
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 7:46, s. 787-799
  • Tidskriftsartikel (refereegranskat)abstract
    • This paper provides the first analysis of the three-dimensional state of residual stress and stretch in an artery wall consisting of three layers (intima, media and adventitia), modelled as a circular cylindrical tube. The analysis is based on experimental results on human aortas with non-atherosclerotic intimal thickening documented in a recent paper by Holzapfel et al. (Holzapfel et al. 2007 Ann. Biomed. Eng. 35, 530-545 (doi:10.1007/s10439-006-9252-z)). The intima is included in the analysis because it has significant thickness and load-bearing capacity, unlike in a young, healthy human aorta. The mathematical model takes account of bending and stretching in both the circumferential and axial directions in each layer of the wall. Previous analysis of residual stress was essentially based on a simple application of the opening-angle method, which cannot accommodate the three-dimensional residual stretch and stress states observed in experiments. The geometry and nonlinear kinematics of the intima, media and adventitia are derived and the associated stress components determined explicitly using the nonlinear theory of elasticity. The theoretical results are then combined with the mean numerical values of the geometrical parameters and material constants from the experiments to illustrate the three-dimensional distributions of the stretches and stresses throughout the wall. The results highlight the compressive nature of the circumferential stress in the intima, which may be associated with buckling of the intima and its delamination from the media, and show that the qualitative features of the stretch and stress distributions in the media and adventitia are unaffected by the presence or absence of the intima. The circumferential residual stress in the intima increases significantly as the associated residual deformation in the intima increases while the corresponding stress in the media (which is compressive at its inner boundary and tensile at its outer boundary) is only slightly affected. The theoretical framework developed herein enables the state of residual stress to be calculated directly, serves to improve insight into the mechanical response of an unloaded artery wall and can be extended to accommodate more general geometries, kinematics and states of residual stress as well as more general constitutive models.
  •  
50.
  • Håkansson, Jonas, et al. (författare)
  • The wake of hovering flight in bats.
  • 2015
  • Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5662 .- 1742-5689. ; 12:109
  • Tidskriftsartikel (refereegranskat)abstract
    • Hovering means stationary flight at zero net forward speed, which can be achieved by animals through muscle powered flapping flight. Small bats capable of hovering typically do so with a downstroke in an inclined stroke plane, and with an aerodynamically active outer wing during the upstroke. The magnitude and time history of aerodynamic forces should be reflected by vorticity shed into the wake. We thus expect hovering bats to generate a characteristic wake, but this has until now never been studied. Here we trained nectar-feeding bats, Leptonycteris yerbabuenae, to hover at a feeder and using time-resolved stereoscopic particle image velocimetry in conjunction with high-speed kinematic analysis we show that hovering nectar-feeding bats produce a series of bilateral stacked vortex loops. Vortex visualizations suggest that the downstroke produces the majority of the weight support, but that the upstroke contributes positively to the lift production. However, the relative contributions from downstroke and upstroke could not be determined on the basis of the wake, because wake elements from down- and upstroke mix and interact. We also use a modified actuator disc model to estimate lift force, power and flap efficiency. Based on our quantitative wake-induced velocities, the model accounts for weight support well (108%). Estimates of aerodynamic efficiency suggest hovering flight is less efficient than forward flapping flight, while the overall energy conversion efficiency (mechanical power output/metabolic power) was estimated at 13%.
  •  
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