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1.  Improvement in endothelial cell adhesion and retention under physiological shear stress using a laminin–apatite composite layer on titanium 
Apatite (Ap), laminin–apatite composite (L5Ap, L10Ap, L20Ap and L40Ap) and albumin–apatite (AlbAp) composite layers were prepared on titanium (Ti) using a supersaturated calcium phosphate solution supplemented with laminin (0, 5, 10, 20 and 40 μg ml−1) or albumin (800 μg ml−1). With an increase in the concentrations of laminin in the supersaturated calcium phosphate solutions, the amounts of laminin immobilized on the Ti increased. The number of human umbilical vein endothelial cells (HUVECs) adhered to the laminin–apatite composite layers were remarkably higher than those to the untreated Ti, Ap layer and AlbAp composite layer. The number of cells adhered to the L40Ap was 4.3 times the untreated Ti. Moreover, cells adhered to the laminin–apatite composite layers showed significantly higher cell retention under the physiological shear stress for 1 h and 2 h than those to the untreated Ti, Ap layer and AlbAp composite layer. The number of cells remaining on the L40Ap under the physiological shear stress for 2 h was 9.5 times that of the untreated Ti. The laminin–apatite composite layer is a promising interfacial layer for endothelialization of blood-contacting materials.
doi:10.1098/rsif.2013.0014
PMCID: PMC3627121  PMID: 23407573
titanium; apatite; laminin; endothelialization; cell adhesion; cell retention
2.  A fluid–structure interaction model to characterize bone cell stimulation in parallel-plate flow chamber systems 
Bone continuously adapts its internal structure to accommodate the functional demands of its mechanical environment and strain-induced flow of interstitial fluid is believed to be the primary mediator of mechanical stimuli to bone cells in vivo. In vitro investigations have shown that bone cells produce important biochemical signals in response to fluid flow applied using parallel-plate flow chamber (PPFC) systems. However, the exact mechanical stimulus experienced by the cells within these systems remains unclear. To fully understand this behaviour represents a most challenging multi-physics problem involving the interaction between deformable cellular structures and adjacent fluid flows. In this study, we use a fluid–structure interaction computational approach to investigate the nature of the mechanical stimulus being applied to a single osteoblast cell under fluid flow within a PPFC system. The analysis decouples the contribution of pressure and shear stress on cellular deformation and for the first time highlights that cell strain under flow is dominated by the pressure in the PPFC system rather than the applied shear stress. Furthermore, it was found that strains imparted on the cell membrane were relatively low whereas significant strain amplification occurred at the cell–substrate interface. These results suggest that strain transfer through focal attachments at the base of the cell are the primary mediators of mechanical signals to the cell under flow in a PPFC system. Such information is vital in order to correctly interpret biological responses of bone cells under in vitro stimulation and elucidate the mechanisms associated with mechanotransduction in vivo.
doi:10.1098/rsif.2012.0900
PMCID: PMC3627095  PMID: 23365189
parallel-plate flow chamber; fluid–structure interaction; bone cell mechanotransduction; fluid shear stress stimulation
3.  Using network theory to identify the causes of disease outbreaks of unknown origin 
The identification of undiagnosed disease outbreaks is critical for mobilizing efforts to prevent widespread transmission of novel virulent pathogens. Recent developments in online surveillance systems allow for the rapid communication of the earliest reports of emerging infectious diseases and tracking of their spread. The efficacy of these programs, however, is inhibited by the anecdotal nature of informal reporting and uncertainty of pathogen identity in the early stages of emergence. We developed theory to connect disease outbreaks of known aetiology in a network using an array of properties including symptoms, seasonality and case-fatality ratio. We tested the method with 125 reports of outbreaks of 10 known infectious diseases causing encephalitis in South Asia, and showed that different diseases frequently form distinct clusters within the networks. The approach correctly identified unknown disease outbreaks with an average sensitivity of 76 per cent and specificity of 88 per cent. Outbreaks of some diseases, such as Nipah virus encephalitis, were well identified (sensitivity = 100%, positive predictive values = 80%), whereas others (e.g. Chandipura encephalitis) were more difficult to distinguish. These results suggest that unknown outbreaks in resource-poor settings could be evaluated in real time, potentially leading to more rapid responses and reducing the risk of an outbreak becoming a pandemic.
doi:10.1098/rsif.2012.0904
PMCID: PMC3627096  PMID: 23389893
emerging infectious disease; encephalitis; complex networks; South Asia; cluster analysis; early warning systems
4.  A stability-based mechanism for hysteresis in the walk–trot transition in quadruped locomotion 
Quadrupeds vary their gaits in accordance with their locomotion speed. Such gait transitions exhibit hysteresis. However, the underlying mechanism for this hysteresis remains largely unclear. It has been suggested that gaits correspond to attractors in their dynamics and that gait transitions are non-equilibrium phase transitions that are accompanied by a loss in stability. In the present study, we used a robotic platform to investigate the dynamic stability of gaits and to clarify the hysteresis mechanism in the walk–trot transition of quadrupeds. Specifically, we used a quadruped robot as the body mechanical model and an oscillator network for the nervous system model to emulate dynamic locomotion of a quadruped. Experiments using this robot revealed that dynamic interactions among the robot mechanical system, the oscillator network, and the environment generate walk and trot gaits depending on the locomotion speed. In addition, a walk–trot transition that exhibited hysteresis was observed when the locomotion speed was changed. We evaluated the gait changes of the robot by measuring the locomotion of dogs. Furthermore, we investigated the stability structure during the gait transition of the robot by constructing a potential function from the return map of the relative phase of the legs and clarified the physical characteristics inherent to the gait transition in terms of the dynamics.
doi:10.1098/rsif.2012.0908
PMCID: PMC3627097  PMID: 23389894
quadruped; walk–trot transition; hysteresis; legged robot; central pattern generator; potential function
5.  Mechanics of plant fruit hooks 
Hook-like surface structures, observed in some plant species, play an important role in the process of plant growth and seed dispersal. In this study, we developed an elastic model and further used it to investigate the mechanical behaviour of fruit hooks in four plant species, previously measured in an experimental study. Based on Euler–Bernoulli beam theory, the force–displacement relationship is derived, and its Young's modulus is obtained. The result agrees well with the experimental data. The model aids in understanding the mechanics of hooks, and could be used in the development of new bioinspired Velcro-like materials.
doi:10.1098/rsif.2012.0913
PMCID: PMC3627098  PMID: 23365190
plant hooks; force–displacement curves; Young's modulus; Velcro
6.  New crosslinkers for electrospun chitosan fibre mats. Part II: mechanical properties 
Few studies exist on the mechanical performance of crosslinked electrospun chitosan (CS) fibre mats. In this study, we show that the mat structure and mechanical performance depend on the different crosslinking agents genipin, epichlorohydrin (ECH), and hexamethylene-1,6-diaminocarboxysulphonate (HDACS), as well as the post-electrospinning heat and base activation treatments. The mat structure was imaged by field emission scanning electron microscopy and the mechanical performance was tested in tension. The elastic modulus, tensile strength, strain at failure and work to failure were found to range from 52 to 592 MPa, 2 to 30 MPa, 2 to 31 per cent and 0.041 to 3.26 MJ m−3, respectively. In general, neat CS mats were found to be the stiffest and the strongest, though least ductile, while CS–ECH mats were the least stiff, weakest, but the most ductile, and CS–HDACS fibre mats exhibited intermediary mechanical properties. The mechanical performance of the mats is shown to reflect differences in the fibre diameter, number of fibre–fibre contacts formed within the mat, as well as varying intermolecular bonding and moisture content. The findings reported here complement the chemical properties of the mats, described in part I of this study.
doi:10.1098/rsif.2012.0946
PMCID: PMC3627100  PMID: 23349435
biopolymer; structure–property correlations; fibre diameter; genipin; diisocyanate; epichlorohydrin
7.  Orientation and size-dependent mechanical modulation within individual secondary osteons in cortical bone tissue 
Anisotropy is one of the most peculiar aspects of cortical bone mechanics; however, its anisotropic mechanical behaviour should be treated only with strict relationship to the length scale of investigation. In this study, we focus on quantifying the orientation and size dependence of the spatial mechanical modulation in individual secondary osteons of bovine cortical bone using nanoindentation. Tests were performed on the same osteonal structure in the axial (along the long bone axis) and transverse (normal to the long bone axis) directions along arrays going radially out from the Haversian canal at four different maximum depths on three secondary osteons. Results clearly show a periodic pattern of stiffness with spatial distance across the osteon. The effect of length scale on lamellar bone anisotropy and the critical length at which homogenization of the mechanical properties occurs were determined. Further, a laminate-composite-based analytical model was applied to the stiffness trends obtained at the highest spatial resolution to evaluate the elastic constants for a sub-layer of mineralized collagen fibrils within an osteonal lamella on the basis of the spatial arrangement of the fibrils. The hierarchical arrangement of lamellar bone is found to be a major determinant for modulation of mechanical properties and anisotropic mechanical behaviour of the tissue.
doi:10.1098/rsif.2012.0953
PMCID: PMC3627101  PMID: 23389895
hierarchical structure; anisotropy; length-scale effect; nanoindentation; secondary osteons
8.  Infectious disease transmission as a forensic problem: who infected whom? 
Observations on infectious diseases often consist of a sample of cases, distinguished by symptoms, and other characteristics, such as onset dates, spatial locations, genetic sequence of the pathogen and/or physiological and clinical data. Cases are often clustered, in space and time, suggesting that they are connected. By defining kernel functions for pairwise analysis of cases, a matrix of transmission probabilities can be estimated. We set up a Bayesian framework to integrate various sources of information to estimate the transmission network. The method is illustrated by analysing data from a multi-year study (2002–2007) of nosocomial outbreaks of norovirus in a large university hospital in the Netherlands. The study included 264 cases, the norovirus genotype was known in approximately 60 per cent of the patients. Combining all the available data allowed likely identification of individual transmission links between most of the cases (72%). This illustrates that the proposed method can be used to accurately reconstruct transmission networks, enhancing our understanding of outbreak dynamics and possibly leading to new insights into how to prevent outbreaks.
doi:10.1098/rsif.2012.0955
PMCID: PMC3627102  PMID: 23389896
infectious disease; transmission; networks; biostatistics
9.  Comparison of in vitro human endothelial cell response to self-expanding stent deployment in a straight and curved peripheral artery simulator 
Haemodynamic forces have a synergistic effect on endothelial cell (EC) morphology, proliferation, differentiation and biochemical expression profiles. Alterations to haemodynamic force levels have been observed at curved regions and bifurcations of arteries but also around struts of stented arteries, and are also known to be associated with various vascular pathologies. Therefore, curvature in combination with stenting might create a pro-atherosclerotic environment compared with stenting in a straight vessel, but this has never been investigated. The goal of this study was to compare EC morphology, proliferation and differentiation within in vitro models of curved stented peripheral vessel models with those of straight and unstented vessels. These models were generated using both static conditions and also subjected to 24 h of stimulation in a peripheral artery bioreactor. Medical-grade silicone tubes were seeded with human umbilical vein endothelial cells to produce pseudovessels that were then stented and subjected to 24 h of physiological levels of pulsatile pressure, radial distention and shear stress. Changes in cell number, orientation and nitric oxide (NO) production were assessed in straight, curved, non-stented and stented pseudovessels. We report that curved pseudovessels lead to higher EC numbers with random orientation and lower NO production per cell compared with straight pseudovessels after 24 h of biomechanical stimulation. Both stented curved and stented straight pseudovessels had lower NO production per cell than corresponding unstented pseudovessels. However, in contrast to straight stented pseudovessels, curved stented pseudovessels had fewer viable cells. The results of this study show, for the first time, that the response of the vascular endothelium is dependent on both curvature and stenting combined, and highlight the necessity for future investigations of the effects of curvature in combination with stenting to fully understand effects on the endothelial layer.
doi:10.1098/rsif.2012.0965
PMCID: PMC3627103  PMID: 23365191
peripheral artery; stent; endothelial cell; in vitro; bioreactor; haemodynamic force
10.  Tracking the long-distance dispersal of marine organisms: sensitivity to ocean model resolution 
Ocean circulation models are widely used to simulate organism transport in the open sea, where challenges of directly tracking organisms across vast spatial and temporal scales are daunting. Many recent studies tout the use of ‘high-resolution’ models, which are forced with atmospheric data on the scale of several hours and integrated with a time step of several minutes or seconds. However, in many cases, the model's outputs that are used to simulate organism movement have been averaged to considerably coarser resolutions (e.g. monthly mean velocity fields). To examine the sensitivity of tracking results to ocean circulation model output resolution, we took the native model output of one of the most sophisticated ocean circulation models available, the Global Hybrid Coordinate Ocean Model, and averaged it to commonly implemented spatial and temporal resolutions in studies of basin-scale dispersal. Comparisons between simulated particle trajectories and in situ near-surface drifter trajectories indicated that ‘over averaging’ model output yields predictions inconsistent with observations. Further analyses focused on the dispersal of juvenile sea turtles indicate that very different inferences regarding the pelagic ecology of these animals are obtained depending on the resolution of model output. We conclude that physical processes occurring at the scale of days and tens of kilometres should be preserved in ocean circulation model output to realistically depict the movement marine organisms and the resulting ecological and evolutionary processes.
doi:10.1098/rsif.2012.0979
PMCID: PMC3627105  PMID: 23349437
ocean circulation model; particle tracking; dispersal; pleuston; sea turtle; North Atlantic
11.  Walking, running, and resting under time, distance, and average speed constraints: optimality of walk–run–rest mixtures 
On a treadmill, humans switch from walking to running beyond a characteristic transition speed. Here, we study human choice between walking and running in a more ecological (non-treadmill) setting. We asked subjects to travel a given distance overground in a given allowed time duration. During this task, the subjects carried, and could look at, a stopwatch that counted down to zero. As expected, if the total time available were large, humans walk the whole distance. If the time available were small, humans mostly run. For an intermediate total time, humans often use a mixture of walking at a slow speed and running at a higher speed. With analytical and computational optimization, we show that using a walk–run mixture at intermediate speeds and a walk–rest mixture at the lowest average speeds is predicted by metabolic energy minimization, even with costs for transients—a consequence of non-convex energy curves. Thus, sometimes, steady locomotion may not be energy optimal, and not preferred, even in the absence of fatigue. Assuming similar non-convex energy curves, we conjecture that similar walk–run mixtures may be energetically beneficial to children following a parent and animals on long leashes. Humans and other animals might also benefit energetically from alternating between moving forward and standing still on a slow and sufficiently long treadmill.
doi:10.1098/rsif.2012.0980
PMCID: PMC3627106  PMID: 23365192
legged locomotion; walking and running; optimization; energy minimization; gait transition
12.  The impact of biases in mobile phone ownership on estimates of human mobility 
Mobile phone data are increasingly being used to quantify the movements of human populations for a wide range of social, scientific and public health research. However, making population-level inferences using these data is complicated by differential ownership of phones among different demographic groups that may exhibit variable mobility. Here, we quantify the effects of ownership bias on mobility estimates by coupling two data sources from the same country during the same time frame. We analyse mobility patterns from one of the largest mobile phone datasets studied, representing the daily movements of nearly 15 million individuals in Kenya over the course of a year. We couple this analysis with the results from a survey of socioeconomic status, mobile phone ownership and usage patterns across the country, providing regional estimates of population distributions of income, reported airtime expenditure and actual airtime expenditure across the country. We match the two data sources and show that mobility estimates are surprisingly robust to the substantial biases in phone ownership across different geographical and socioeconomic groups.
doi:10.1098/rsif.2012.0986
PMCID: PMC3627108  PMID: 23389897
mobile phone; human mobility; socio-economic status
13.  Response kinetics in the complex chemotaxis signalling pathway of Rhodobacter sphaeroides 
Chemotaxis is one of the best-characterized signalling systems in biology. It is the mechanism by which bacteria move towards optimal environments and is implicated in biofilm formation, pathogenesis and symbiosis. The properties of the bacterial chemosensory response have been described in detail for the single chemosensory pathway of Escherichia coli. We have characterized the properties of the chemosensory response of Rhodobacter sphaeroides, an α-proteobacterium with multiple chemotaxis pathways, under two growth conditions allowing the effects of protein expression levels and cell architecture to be investigated. Using tethered cell assays, we measured the responses of the system to step changes in concentration of the attractant propionate and show that, independently of the growth conditions, R. sphaeroides is chemotactic over at least five orders of magnitude and has a sensing profile following Weber's Law. Mathematical modelling also shows that, as E. coli, R. sphaeroides is capable of showing fold-change detection (FCD). Our results indicate that general features of bacterial chemotaxis such as the range and sensitivity of detection, adaptation times, adherence to Weber's Law and the presence of FCD may be integral features of chemotaxis systems in general, regardless of network complexity, protein expression levels and cellular architecture across different species.
doi:10.1098/rsif.2012.1001
PMCID: PMC3627110  PMID: 23365194
chemotaxis; Weber's Law; fold-change detection; response kinetics; Rhodobacter sphaeroides
14.  An exploration of the microrheological environment around the distal ileal villi and proximal colonic mucosa of the possum (Trichosurus vulpecula) 
Multiple particle-tracking techniques were used to quantify the thermally driven motion of ensembles of naked polystyrene (0.5 µm diameter) microbeads in order to determine the microrheological characteristics around the gut mucosa. The microbeads were introduced into living ex vivo preparations of the wall of the terminal ileum and proximal colon of the brushtail possum (Trichosurus vulpecula). The fluid environment surrounding both the ileal villi and colonic mucosa was heterogeneous; probably comprising discrete viscoelastic regions suspended in a continuous Newtonian fluid of viscosity close to water. Neither the viscosity of the continuous phase, the elastic modulus (G’) nor the sizes of viscoelastic regions varied significantly between areas within 20 µm and areas more than 20 µm from the villous mucosa nor from the tip to the sides of the villous mucosa. The viscosity of the continuous phase at distances further than 20 µm from the colonic mucosa was greater than that at the same distance from the ileal villous mucosa. Furthermore, the estimated sizes of viscoelastic regions were significantly greater in the colon than in the ileum. These findings validate the sensitivity of the method and call into question previous hypotheses that a contiguous layer of mucus envelops all intestinal mucosa and restricts diffusive mass transfer. Our findings suggest that, in the terminal ileum and colon at least, mixing and mass transfer are governed by more complex dynamics than were previously assumed, perhaps with gel filtration by viscoelastic regions that are suspended in a Newtonian fluid.
doi:10.1098/rsif.2012.1008
PMCID: PMC3627112  PMID: 23389898
microrheology; mucosa; ileum; colon
15.  Negative feedback in ants: crowding results in less trail pheromone deposition 
Crowding in human transport networks reduces efficiency. Efficiency can be increased by appropriate control mechanisms, which are often imposed externally. Ant colonies also have distribution networks to feeding sites outside the nest and can experience crowding. However, ants do not have external controllers or leaders. Here, we report a self-organized negative feedback mechanism, based on local information, which downregulates the production of recruitment signals in crowded parts of a network by Lasius niger ants. We controlled crowding by manipulating trail width and the number of ants on a trail, and observed a 5.6-fold reduction in the number of ants depositing trail pheromone from least to most crowded conditions. We also simulated crowding by placing glass beads covered in nest-mate cuticular hydrocarbons on the trail. After 10 bead encounters over 20 cm, forager ants were 45 per cent less likely to deposit pheromone. The mechanism of negative feedback reported here is unusual in that it acts by downregulating the production of a positive feedback signal, rather than by direct inhibition or the production of an inhibitory signal.
doi:10.1098/rsif.2012.1009
PMCID: PMC3627113  PMID: 23365196
crowding; pheromone trails; recruitment; negative feedback; foraging; traffic
16.  Computed tomography-based diagnosis of diffuse compensatory enlargement of coronary arteries using scaling power laws 
Glagov's positive remodelling in the early stages of coronary atherosclerosis often results in plaque rupture and acute events. Because positive remodelling is generally diffused along the epicardial coronary arterial tree, it is difficult to diagnose non-invasively. Hence, the objective of the study is to assess the use of scaling power law for the diagnosis of positive remodelling of coronary arteries based on computed tomography (CT) images. Epicardial coronary arterial trees were reconstructed from CT scans of six Ossabaw pigs fed on a high-fat, high-cholesterol, atherogenic diet for eight months as well as the same number of body-weight-matched farm pigs fed on a lean chow (101.9±16.1 versus 91.5±13.1 kg). The high-fat diet Ossabaw pig model showed diffuse positive remodelling of epicardial coronary arteries. Good fit of measured coronary data to the length–volume scaling power law ( where Lc and Vc are crown length and volume) were found for both the high-fat and control groups (R2 = 0.95±0.04 and 0.99±0.01, respectively). The coefficient, KLV, decreased significantly in the high-fat diet group when compared with the control (14.6±2.6 versus 40.9±5.6). The flow–length scaling power law, however, was nearly unaffected by the positive remodelling. The length–volume and flow–length scaling power laws were preserved in epicardial coronary arterial trees after positive remodelling. KLV < 18 in the length–volume scaling relation is a good index of positive remodelling of coronary arteries. These findings provide a clinical rationale for simple, accurate and non-invasive diagnosis of positive remodelling of coronary arteries, using conventional CT scans.
doi:10.1098/rsif.2012.1015
PMCID: PMC3627114  PMID: 23365197
coronary compensatory enlargement; scaling power law; computed tomography
17.  Predictability of spatio-temporal patterns in a lattice of coupled FitzHugh–Nagumo oscillators 
In many biological systems, variability of the components can be expected to outrank statistical fluctuations in the shaping of self-organized patterns. In pioneering work in the late 1990s, it was hypothesized that a drift of cellular parameters (along a ‘developmental path’), together with differences in cell properties (‘desynchronization’ of cells on the developmental path) can establish self-organized spatio-temporal patterns (in their example, spiral waves of cAMP in a colony of Dictyostelium discoideum cells) starting from a homogeneous state. Here, we embed a generic model of an excitable medium, a lattice of diffusively coupled FitzHugh–Nagumo oscillators, into a developmental-path framework. In this minimal model of spiral wave generation, we can now study the predictability of spatio-temporal patterns from cell properties as a function of desynchronization (or ‘spread’) of cells along the developmental path and the drift speed of cell properties on the path. As a function of drift speed and desynchronization, we observe systematically different routes towards fully established patterns, as well as strikingly different correlations between cell properties and pattern features. We show that the predictability of spatio-temporal patterns from cell properties contains important information on the pattern formation process as well as on the underlying dynamical system.
doi:10.1098/rsif.2012.1016
PMCID: PMC3627115  PMID: 23349439
FitzHugh–Nagumo; developmental path; spatio-temporal pattern formation; variability; spiral waves; Dictyostelium discoideum
18.  Enhanced entrainability of genetic oscillators by period mismatch 
Biological oscillators coordinate individual cellular components so that they function coherently and collectively. They are typically composed of multiple feedback loops, and period mismatch is unavoidable in biological implementations. We investigated the advantageous effect of this period mismatch in terms of a synchronization response to external stimuli. Specifically, we considered two fundamental models of genetic circuits: smooth and relaxation oscillators. Using phase reduction and Floquet multipliers, we numerically analysed their entrainability under different coupling strengths and period ratios. We found that a period mismatch induces better entrainment in both types of oscillator; the enhancement occurs in the vicinity of the bifurcation on their limit cycles. In the smooth oscillator, the optimal period ratio for the enhancement coincides with the experimentally observed ratio, which suggests biological exploitation of the period mismatch. Although the origin of multiple feedback loops is often explained as a passive mechanism to ensure robustness against perturbation, we study the active benefits of the period mismatch, which include increasing the efficiency of the genetic oscillators. Our findings show a qualitatively different perspective for both the inherent advantages of multiple loops and their essentiality.
doi:10.1098/rsif.2012.1020
PMCID: PMC3627117  PMID: 23389900
genetic oscillator; dynamical systems; entrainment
19.  Dispersion of swimming algae in laminar and turbulent channel flows: consequences for photobioreactors 
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 Péclet 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 Péclet number. The cell effective axial diffusivity increases and decreases with Péclet 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.
doi:10.1098/rsif.2012.1041
PMCID: PMC3627118  PMID: 23407572
algae; swimming micro-organisms; Taylor dispersion; direct numerical simulation; turbulent transport; photobioreactors
20.  A strong magnetic pulse affects the precision of departure direction of naturally migrating adult but not juvenile birds 
The mechanisms by which migratory birds achieve their often spectacular navigational performance are still largely unclear, but perception of cues from the Earth's magnetic field is thought to play a role. Birds that possess migratory experience can use map-based navigation, which may involve a receptor that uses ferrimagnetic material for detecting gradients in the magnetic field. Such a mechanism can be experimentally disrupted by applying a strong magnetic pulse that re-magnetizes ferrimagnetic materials. In captivity, this treatment indeed affected bearings of adult but not of naive juvenile birds. However, field studies, which expose birds to various navigational cues, yielded mixed results. Supportive studies were difficult to interpret because they were conducted in spring when all age groups navigate back to breeding areas. The present study, therefore, applied a magnetic pulse treatment in autumn to naturally migrating, radio-tagged European robins. We found that, although overall bearings were seasonally correct, orientation of adult but not juvenile robins was compromised by a pulse. Pulsed adults that departed within 10 days of treatment failed to show significant orientation and deviated more from mean migration direction than adult controls and juveniles. Thus, our data give field-based support for a possible ferrimagnetic map-sense during bird migration.
doi:10.1098/rsif.2012.1047
PMCID: PMC3627120  PMID: 23389901
navigation; ferrimagnetic; map; migration; robin
21.  Spreading dynamics on spatially constrained complex brain networks 
The study of dynamical systems defined on complex networks provides a natural framework with which to investigate myriad features of neural dynamics and has been widely undertaken. Typically, however, networks employed in theoretical studies bear little relation to the spatial embedding or connectivity of the neural networks that they attempt to replicate. Here, we employ detailed neuroimaging data to define a network whose spatial embedding represents accurately the folded structure of the cortical surface of a rat brain and investigate the propagation of activity over this network under simple spreading and connectivity rules. By comparison with standard network models with the same coarse statistics, we show that the cortical geometry influences profoundly the speed of propagation of activation through the network. Our conclusions are of high relevance to the theoretical modelling of epileptic seizure events and indicate that such studies which omit physiological network structure risk simplifying the dynamics in a potentially significant way.
doi:10.1098/rsif.2013.0016
PMCID: PMC3627122  PMID: 23407574
spreading dynamics; network science; neuroscience; epilepsy; connectome
22.  Cell lineage tracing in the developing enteric nervous system: superstars revealed by experiment and simulation 
Cell lineage tracing is a powerful tool for understanding how proliferation and differentiation of individual cells contribute to population behaviour. In the developing enteric nervous system (ENS), enteric neural crest (ENC) cells move and undergo massive population expansion by cell division within self-growing mesenchymal tissue. We show that single ENC cells labelled to follow clonality in the intestine reveal extraordinary and unpredictable variation in number and position of descendant cells, even though ENS development is highly predictable at the population level. We use an agent-based model to simulate ENC colonization and obtain agent lineage tracing data, which we analyse using econometric data analysis tools. In all realizations, a small proportion of identical initial agents accounts for a substantial proportion of the total final agent population. We term these individuals superstars. Their existence is consistent across individual realizations and is robust to changes in model parameters. This inequality of outcome is amplified at elevated proliferation rate. The experiments and model suggest that stochastic competition for resources is an important concept when understanding biological processes which feature high levels of cell proliferation. The results have implications for cell-fate processes in the ENS.
doi:10.1098/rsif.2013.0815
PMCID: PMC3928926  PMID: 24501272
cell lineage; invasion wave; enteric nervous system; cell-fate decisions
23.  Novel biological strategies for treatment of wear particle-induced periprosthetic osteolysis of orthopaedic implants for joint replacement 
Wear particles and by-products from joint replacements and other orthopaedic implants may result in a local chronic inflammatory and foreign body reaction. This may lead to persistent synovitis resulting in joint pain and swelling, periprosthetic osteolysis, implant loosening and pathologic fracture. Strategies to modulate the adverse effects of wear debris may improve the function and longevity of joint replacements and other orthopaedic implants, potentially delaying or avoiding complex revision surgical procedures. Three novel biological strategies to mitigate the chronic inflammatory reaction to orthopaedic wear particles are reported. These include (i) interference with systemic macrophage trafficking to the local implant site, (ii) modulation of macrophages from an M1 (pro-inflammatory) to an M2 (anti-inflammatory, pro-tissue healing) phenotype in the periprosthetic tissues, and (iii) local inhibition of the transcription factor nuclear factor kappa B (NF-κB) by delivery of an NF-κB decoy oligodeoxynucleotide, thereby interfering with the production of pro-inflammatory mediators. These three approaches have been shown to be viable strategies for mitigating the undesirable effects of wear particles in preclinical studies. Targeted local delivery of specific biologics may potentially extend the lifetime of orthopaedic implants.
doi:10.1098/rsif.2013.0962
PMCID: PMC3928932  PMID: 24478281
wear particles; orthopaedic implants; inflammation; cell trafficking; macrophage polarization; NF-κB
24.  Spatio-temporal skin strain distributions evoke low variability spike responses in cuneate neurons 
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.
doi:10.1098/rsif.2013.1015
PMCID: PMC3928934  PMID: 24451390
contact mechanics; spatio-temporal skin stimulation; cuneate nucleus
25.  Re-epithelialization: advancing epithelium frontier during wound healing 
The first function of the skin is to serve as a protective barrier against the environment. Its loss of integrity as a result of injury or illness may lead to a major disability and the first goal of healing is wound closure involving many biological processes for repair and tissue regeneration. In vivo wound healing has four phases, one of them being the migration of the healthy epithelium surrounding the wound in the direction of the injury in order to cover it. Here, we present a theoretical model of the re-epithelialization phase driven by chemotaxis for a circular wound. This model takes into account the diffusion of chemoattractants both in the wound and the neighbouring tissue, the uptake of these molecules by the surface receptors of epithelial cells, the migration of the neighbour epithelium, the tension and proliferation at the wound border. Using a simple Darcy's law for cell migration transforms our biological model into a free-boundary problem, which is analysed in the simplified circular geometry leading to explicit solutions for the closure and making stability analysis possible. It turns out that for realistic wound sizes of the order of centimetres and from experimental data, the re-epithelialization is always an unstable process and the perfect circle cannot be observed, a result confirmed by fully nonlinear simulations and in agreement with experimental observations.
doi:10.1098/rsif.2013.1038
PMCID: PMC3928935  PMID: 24451391
chemotaxis; re-epithelialization; wound healing; free-boundary problem; level-set methods

Results 1-25 (1412)